From 332f63e2e84a68cc8884c494edd6e9ca371e9dce Mon Sep 17 00:00:00 2001 From: Justin Bousquin Date: Tue, 23 Sep 2025 16:31:52 -0500 Subject: [PATCH 01/22] Develop (#78) * Create coverage.yaml Init commit * Update coverage.yaml Make sure the report name is specified * Update coverage.yaml Try to get report from ./cobertura.xml * Update coverage.yaml Not there... but try being specific * Update coverage.yaml In case . is somewhere else be specific about where to write * Update coverage.yaml Simplify * Update coverage.yaml Point action to correct coverage report file * Update coverage.yaml Attempt permissions route to post comment vs PAT --- .github/workflows/coverage.yaml | 75 +++++++++++++++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 .github/workflows/coverage.yaml diff --git a/.github/workflows/coverage.yaml b/.github/workflows/coverage.yaml new file mode 100644 index 0000000..23f3c55 --- /dev/null +++ b/.github/workflows/coverage.yaml @@ -0,0 +1,75 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [develop] + pull_request: + branches: [develop] + +name: test-coverage + +permissions: + contents: write + checks: write + pull-requests: write + +jobs: + test-coverage: + runs-on: ubuntu-latest + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::covr, any::xml2 + needs: coverage + + - name: Test coverage + run: | + cov <- covr::package_coverage( + quiet = FALSE, + clean = FALSE, + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") + ) + print(cov) + covr::to_cobertura(cov) + shell: Rscript {0} + + - name: Show testthat output + if: always() + run: | + ## -------------------------------------------------------------------- + find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload test results + if: failure() + uses: actions/upload-artifact@v4 + with: + name: coverage-test-failures + path: ${{ runner.temp }}/package + if-no-files-found: ignore # Suppress warnings if no files are found + + - name: Upload coverage report + uses: actions/upload-artifact@v4 + with: + name: coverage-report + path: ./cobertura.xml + + - name: Comment coverage + uses: 5monkeys/cobertura-action@master + with: + report_name: coverage-report + path: ./cobertura.xml + minimum_coverage: 10 + show_missing: true + link_missing_lines: true + + From ebbeab28eae4f2e7c599d907f3a51e7ac849e26f Mon Sep 17 00:00:00 2001 From: Weber Date: Tue, 23 Sep 2025 14:51:34 -0700 Subject: [PATCH 02/22] Trying Jeff's epar package to generate code cov badge --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 52d8f77..29b3299 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,7 @@ [![cran checks](https://badges.cranchecks.info/worst/StreamCatTools.svg)](https://cran.r-project.org/web/checks/check_results_StreamCatTools.html) [![R-CMD-check](https://github.com/USEPA/StreamCatTools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/USEPA/StreamCatTools/actions/workflows/R-CMD-check.yaml) [![Downloads](https://cranlogs.r-pkg.org/badges/StreamCatTools)](https://cran.r-project.org/package=StreamCatTools) +[![CodeCov](https://img.shields.io/badge/test%20coverage-87%25-388600.svg)](https://img.shields.io/badge/test%20coverage-87%25-388600.svg) ## StreamCatTools: Tools to work with the [StreamCat](https://www.epa.gov/national-aquatic-resource-surveys/streamcat-dataset) API within R and access the full suite of StreamCat and [LakeCat](https://www.epa.gov/national-aquatic-resource-surveys/lakecat-dataset) metrics. From f057869647405f2898f21e781a81bf965ded3f48 Mon Sep 17 00:00:00 2001 From: Weber Date: Wed, 24 Sep 2025 14:32:06 -0700 Subject: [PATCH 03/22] incrementing dev version --- DESCRIPTION | 2 +- NEWS.md | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 82e4a72..e6b4b11 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: StreamCatTools Type: Package Title: 'StreamCatTools' -Version: 0.7.0 +Version: 0.7.0.9000 Authors@R: c(person(given = "Marc", family = "Weber", role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 1eae8d8..aa2d7d6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# StreamCatTools (development version) + +- Added code coverage to the package + # StreamCatTools 0.7.0 - Updated both `sc_get_data` and `lc_get_data` to pass parameters in From b4cb12d811e96027a22fefed4364f3f142d52e7e Mon Sep 17 00:00:00 2001 From: Marc Weber Date: Fri, 3 Oct 2025 14:36:35 -0700 Subject: [PATCH 04/22] Metric categories (#79) * updated params metrics function and added dontrun for examples * test passing with updates to sc and lc params functions and new sc and lc get_metric_names functions --- NAMESPACE | 2 + NEWS.md | 5 +- R/lc_get_comid.R | 2 +- R/lc_get_data.R | 4 +- R/lc_get_params.R | 103 ++++++++++++++++++++++++- R/sc_get_comid.R | 2 +- R/sc_get_data.R | 4 +- R/sc_get_params.R | 113 ++++++++++++++++++++++++++-- README.md | 2 +- man/lc_get_comid.Rd | 2 +- man/lc_get_data.Rd | 2 +- man/lc_get_metric_names.Rd | 34 +++++++++ man/lc_get_params.Rd | 6 +- man/lc_nlcd.Rd | 2 +- man/sc_get_comid.Rd | 2 +- man/sc_get_data.Rd | 2 +- man/sc_get_metric_names.Rd | 38 ++++++++++ man/sc_get_params.Rd | 7 +- man/sc_nlcd.Rd | 2 +- tests/testthat/test-lc_get_params.R | 22 +++--- tests/testthat/test-sc_get_params.R | 33 +++++++- 21 files changed, 350 insertions(+), 39 deletions(-) create mode 100644 man/lc_get_metric_names.Rd create mode 100644 man/sc_get_metric_names.Rd diff --git a/NAMESPACE b/NAMESPACE index 495d937..4ac1597 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -3,10 +3,12 @@ export(lc_fullname) export(lc_get_comid) export(lc_get_data) +export(lc_get_metric_names) export(lc_get_params) export(lc_nlcd) export(sc_fullname) export(sc_get_comid) export(sc_get_data) +export(sc_get_metric_names) export(sc_get_params) export(sc_nlcd) diff --git a/NEWS.md b/NEWS.md index aa2d7d6..9ec6081 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,9 @@ # StreamCatTools (development version) -- Added code coverage to the package +- Added code coverage to the package +- Added two new functions - `sc_get_metric_names` and `lc_get_metric_names` + to make metric names and descriptions more searchable and slightly updated + parameters in both `sc_get_params` and `lc_get_params` functions # StreamCatTools 0.7.0 diff --git a/R/lc_get_comid.R b/R/lc_get_comid.R index 087ca56..c91331d 100644 --- a/R/lc_get_comid.R +++ b/R/lc_get_comid.R @@ -27,7 +27,7 @@ #' @return A new sf data frame with a populated 'COMID' column #' #' @examples -#' \donttest{ +#' \dontrun{ #' #' dd <- data.frame(x = c(-89.198,-114.125,-122.044), #' y = c(45.502,47.877,43.730)) diff --git a/R/lc_get_data.R b/R/lc_get_data.R index 4bd84a7..0455d2a 100644 --- a/R/lc_get_data.R +++ b/R/lc_get_data.R @@ -54,7 +54,7 @@ #' @return A tibble of desired StreamCat metrics. If data are missing for all rows of a given metric, then the column for that metric will not exist. If data are missing for only some rows, then they will be specified with NA. #' #' @examples -#' \donttest{ +#' \dontrun{ #' df <- lc_get_data(comid='23794487', aoi='cat', metric='fert') #' #' df <- lc_get_data(metric='pcturbmd2006', aoi='ws', @@ -178,7 +178,7 @@ lc_get_data <- function(comid = NULL, #' @return A tibble of desired StreamCat metrics #' #' @examples -#' \donttest{ +#' \dontrun{ #' #' df <- lc_nlcd(comid='23783629', year='2019', aoi='ws') #' diff --git a/R/lc_get_params.R b/R/lc_get_params.R index bd3b69d..39dd52e 100644 --- a/R/lc_get_params.R +++ b/R/lc_get_params.R @@ -16,12 +16,14 @@ #' @export #' #' @examples -#' \donttest{ +#' \dontrun{ #' params <- lc_get_params(param='variable_info') #' params <- lc_get_params(param='metric_names') -#' params <- lc_get_params(param='areaOfInterest') +#' params <- sc_get_params(param='categories') +#' params <- lc_get_params(param='aoi') #' params <- lc_get_params(param='state') #' params <- lc_get_params(param='county') +#' params <- sc_get_params(param='datasets') #' } lc_get_params <- function(param = NULL) { @@ -40,7 +42,7 @@ lc_get_params <- function(param = NULL) { params <- params[!duplicated(params)] params <- params[order(params)] } else if(param == 'variable_info') { - params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> + params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> httr2::req_perform() |> httr2::resp_body_string() |> readr::read_csv(show_col_types = FALSE) |> @@ -50,6 +52,20 @@ lc_get_params <- function(param = NULL) { short_description=WEBTOOL_NAME,units=METRIC_UNITS, long_description=METRIC_DESCRIPTION, dsid=DSID, source_name=SOURCE_NAME, source_URL=SOURCE_URL) + } else if(param == 'categories'){ + params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(INDICATOR_CATEGORY) + params <- sort(unique(params$INDICATOR_CATEGORY)) + } else if(param == 'datasets'){ + params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(DSNAME) + params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) } else if(param == 'region'){ params <- resp$region_options[[1]][[1]] params <- params[order(params)] @@ -93,3 +109,84 @@ lc_fullname <- function(metric = NULL) { result <- unique(resp$short_display_name[resp$metric_prefix %in% metric]) return(result) } + +#' Get LakeCat Metric Names +#' +#' @description +#' Function to filter LakeCat metrics metrics by category, area of interest, +#' dataset or year. Use `lc_get_params(categories)` or `lc_get_params(datasets)` +#' to see all the valid category or dataset options +#' +#' @author +#' Marc Weber +#' +#' @param category Filter LakeCat metrics based on the metric category +#' @param aoi Filter LakeCat metrics based on the area of interest +#' @param year Filter LakeCat metrics based on a particular year or years +#' @param dataset Filter LakeCat metrics based on the dataset name +#' +#' @return A dataframe of merics and description that match filter criteria +#' @export +#' +#' @examples +#' \dontrun{ +#' metrics <- lc_get_metric_names(category='Natural') +#' metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), +#' aoi=c('Cat','Ws')} + + +lc_get_metric_names <- function(category = NULL, + aoi = NULL, + year = NULL, + dataset = NULL) { + if (!is.null(aoi)){ + if (any(stringr::str_detect(aoi,'catchment'))) { + aoi <- gsub('catchment','Cat',aoi) + } + if (any(stringr::str_detect(aoi,'watershed'))) { + aoi <- gsub('watershed','Ws',aoi) + } + if (any(stringr::str_detect(aoi,'riparian_catchment'))) { + aoi <- gsub('riparian_catchment','CatRp100',aoi) + } + if (any(stringr::str_detect(aoi,'riparian_watershed'))) { + aoi <- gsub('riparian_watershed','WsRp100',aoi) + } + aoi <- stringr::str_to_title(aoi) + } + resp <- params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) + + filters <- list(INDICATOR_CATEGORY = category, AOI = aoi, YEAR = year, + DSNAME = dataset) + + filter_data <- function(data, filters) { + # Filter the data frame for each non-null filter + filtered_data <- purrr::reduce( + names(filters), + .init = data, + .f = function(df, col_name) { + filter_values <- filters[[col_name]] + if (!is.null(filter_values)) { + df <- df %>% + dplyr::mutate(temp_col = stringr::str_split(.data[[col_name]], ",")) %>% + dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) %>% + dplyr::select(-temp_col) + } + df + } + ) + return(filtered_data) + } + results <- filter_data(resp, filters) + results <- results |> + dplyr::select(Category = INDICATOR_CATEGORY, Metric = METRIC_NAME, + AOI,Year = YEAR, Short_Name = WEBTOOL_NAME, + Metric_Description = METRIC_DESCRIPTION, + Units = METRIC_UNITS, Source = SOURCE_NAME, + Dataset = DSNAME) + + return(results) +} \ No newline at end of file diff --git a/R/sc_get_comid.R b/R/sc_get_comid.R index 073ae6a..35bdcab 100644 --- a/R/sc_get_comid.R +++ b/R/sc_get_comid.R @@ -24,7 +24,7 @@ #' @return A new sf data frame with a populated 'COMID' column #' #' @examples -#' \donttest{ +#' \dontrun{ #' #' dd <- data.frame(x = c(-122.649,-100.348,-75.186,-106.675), #' y = c(45.085, 35.405,42.403,38.721)) diff --git a/R/sc_get_data.R b/R/sc_get_data.R index dfb0495..fb0ba72 100644 --- a/R/sc_get_data.R +++ b/R/sc_get_data.R @@ -59,7 +59,7 @@ #' @return A data frame of StreamCat metrics. If data are missing for all rows of a given metric, then the column for that metric will not exist. If data are missing for only some rows, then they will be specified with NA. #' #' @examples -#' \donttest{ +#' \dontrun{ #' df <- sc_get_data(comid='179', aoi='cat', metric='fert') #' #' df <- sc_get_data(metric='pctgrs2006', aoi='ws', region='Region01') @@ -210,7 +210,7 @@ sc_get_data <- function(comid = NULL, #' @return A tibble of desired StreamCat metrics #' #' @examples -#' \donttest{ +#' \dontrun{ #' df <- sc_nlcd(year='2001', aoi='cat',comid='179,1337,1337420') #' #' df <- sc_nlcd(year='2001', aoi='ws', region='Region01') diff --git a/R/sc_get_params.R b/R/sc_get_params.R index 19d7bd2..864bc8b 100644 --- a/R/sc_get_params.R +++ b/R/sc_get_params.R @@ -16,20 +16,22 @@ #' @export #' #' @examples -#' \donttest{ +#' \dontrun{ #' params <- sc_get_params(param='variable_info') #' params <- sc_get_params(param='metric_names') -#' params <- sc_get_params(param='areaOfInterest') +#' params <- sc_get_params(param='categories') +#' params <- sc_get_params(param='aoi') #' params <- sc_get_params(param='state') #' params <- sc_get_params(param='county') -#' } +#' params <- sc_get_params(param='datasets')} + sc_get_params <- function(param = NULL) { UUID <- DATE_DOWNLOADED <- METADATA <- FINAL_TABLE<- NULL INDICATOR_CATEGORY <- METRIC_NAME <- AOI <- YEAR <- NULL WEBTOOL_NAME <- METRIC_UNITS <- METRIC_DESCRIPTION <- DSID <- NULL SOURCE_NAME <- SOURCE_URL <- UUID <- DATE_DOWNLOADED <- NULL resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/streams/metrics")$items - if (param=='areaOfInterest'){ + if (param=='aoi'){ params <- strsplit(stringr::str_sub(resp$aoi_param_info[[1]]$options,2,-2),",")[[1]] params <- c(gsub(" ","", params),'other') params <- params[order(params)] @@ -48,7 +50,22 @@ sc_get_params <- function(param = NULL) { short_description=WEBTOOL_NAME,units=METRIC_UNITS, long_description=METRIC_DESCRIPTION, dsid=DSID, source_name=SOURCE_NAME, source_URL=SOURCE_URL) - } else if(param == 'region'){ + } else if(param == 'categories'){ + params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(INDICATOR_CATEGORY) + params <- sort(unique(params$INDICATOR_CATEGORY)) + } else if(param == 'datasets'){ + params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(DSNAME) + params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) + } + else if(param == 'region'){ params <- resp$region_options[[1]][[1]] params <- params[order(params)] } else if(param == 'state'){ @@ -91,3 +108,89 @@ sc_fullname <- function(metric = NULL) { result <- unique(resp$short_display_name[resp$metric_prefix %in% metric]) return(result) } + + +#' Get StreamCat Metric Names +#' +#' @description +#' Function to filter StreamCat metrics metrics by category, area of interest, +#' dataset or year. Use `sc_get_params(categories)` or `sc_get_params(datasets)` +#' to see all the valid category or dataset options +#' +#' @author +#' Marc Weber +#' +#' @param category Filter StreamCat metrics based on the metric category +#' @param aoi Filter StreamCat metrics based on the area of interest +#' @param year Filter StreamCat metrics based on a particular year or years +#' @param dataset Filter StreamCat metrics based on the dataset name +#' +#' @return A dataframe of merics and description that match filter criteria +#' @export +#' +#' @examples +#' \dontrun{ +#' metrics <- sc_get_metric_names(category='Wildfire') +#' metrics <- sc_get_metric_names(category = c('Deposition','Climate'), +#' aoi=c('Cat','Ws') +#' metrics <- sc_get_metric_names(aoi='Other', +#' dataset=c('Canal Density','Predicted Channel Widths Depths')) +#' +#' } + + +sc_get_metric_names <- function(category = NULL, + aoi = NULL, + year = NULL, + dataset = NULL) { + if (!is.null(aoi)){ + if (any(stringr::str_detect(aoi,'catchment'))) { + aoi <- gsub('catchment','Cat',aoi) + } + if (any(stringr::str_detect(aoi,'watershed'))) { + aoi <- gsub('watershed','Ws',aoi) + } + if (any(stringr::str_detect(aoi,'riparian_catchment'))) { + aoi <- gsub('riparian_catchment','CatRp100',aoi) + } + if (any(stringr::str_detect(aoi,'riparian_watershed'))) { + aoi <- gsub('riparian_watershed','WsRp100',aoi) + } + aoi <- stringr::str_to_title(aoi) + } + resp <- params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) + + filters <- list(INDICATOR_CATEGORY = category, AOI = aoi, YEAR = year, + DSNAME = dataset) + + filter_data <- function(data, filters) { + # Filter the data frame for each non-null filter + filtered_data <- purrr::reduce( + names(filters), + .init = data, + .f = function(df, col_name) { + filter_values <- filters[[col_name]] + if (!is.null(filter_values)) { + df <- df %>% + dplyr::mutate(temp_col = stringr::str_split(.data[[col_name]], ",")) %>% + dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) %>% + dplyr::select(-temp_col) + } + df + } + ) + return(filtered_data) + } + results <- filter_data(resp, filters) + results <- results |> + dplyr::select(Category = INDICATOR_CATEGORY, Metric = METRIC_NAME, + AOI,Year = YEAR, Short_Name = WEBTOOL_NAME, + Metric_Description = METRIC_DESCRIPTION, + Units = METRIC_UNITS, Source = SOURCE_NAME, + Dataset = DSNAME) + + return(results) +} diff --git a/README.md b/README.md index 29b3299..373894c 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![cran checks](https://badges.cranchecks.info/worst/StreamCatTools.svg)](https://cran.r-project.org/web/checks/check_results_StreamCatTools.html) [![R-CMD-check](https://github.com/USEPA/StreamCatTools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/USEPA/StreamCatTools/actions/workflows/R-CMD-check.yaml) [![Downloads](https://cranlogs.r-pkg.org/badges/StreamCatTools)](https://cran.r-project.org/package=StreamCatTools) -[![CodeCov](https://img.shields.io/badge/test%20coverage-87%25-388600.svg)](https://img.shields.io/badge/test%20coverage-87%25-388600.svg) +[![CodeCov](https://img.shields.io/badge/test%20coverage-86.9%25-388600.svg)](https://img.shields.io/badge/test%20coverage-86.9%25-388600.svg) ## StreamCatTools: Tools to work with the [StreamCat](https://www.epa.gov/national-aquatic-resource-surveys/streamcat-dataset) API within R and access the full suite of StreamCat and [LakeCat](https://www.epa.gov/national-aquatic-resource-surveys/lakecat-dataset) metrics. diff --git a/man/lc_get_comid.Rd b/man/lc_get_comid.Rd index 65fa21b..d56c481 100644 --- a/man/lc_get_comid.Rd +++ b/man/lc_get_comid.Rd @@ -38,7 +38,7 @@ sf object. The function generates a vector of NHDPlus Waterbody COMID values a user can then pass to lc_get_data function } \examples{ -\donttest{ +\dontrun{ dd <- data.frame(x = c(-89.198,-114.125,-122.044), y = c(45.502,47.877,43.730)) diff --git a/man/lc_get_data.Rd b/man/lc_get_data.Rd index 79db8dd..db08c5e 100644 --- a/man/lc_get_data.Rd +++ b/man/lc_get_data.Rd @@ -70,7 +70,7 @@ Function to return LakeCat metrics using the StreamCat API. The function allows specific metric data aggregated by area of interest, returned by comid(s), hydroregion(s), state(s), or county(ies). } \examples{ -\donttest{ +\dontrun{ df <- lc_get_data(comid='23794487', aoi='cat', metric='fert') df <- lc_get_data(metric='pcturbmd2006', aoi='ws', diff --git a/man/lc_get_metric_names.Rd b/man/lc_get_metric_names.Rd new file mode 100644 index 0000000..4668ecd --- /dev/null +++ b/man/lc_get_metric_names.Rd @@ -0,0 +1,34 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/lc_get_params.R +\name{lc_get_metric_names} +\alias{lc_get_metric_names} +\title{Get LakeCat Metric Names} +\usage{ +lc_get_metric_names(category = NULL, aoi = NULL, year = NULL, dataset = NULL) +} +\arguments{ +\item{category}{Filter LakeCat metrics based on the metric category} + +\item{aoi}{Filter LakeCat metrics based on the area of interest} + +\item{year}{Filter LakeCat metrics based on a particular year or years} + +\item{dataset}{Filter LakeCat metrics based on the dataset name} +} +\value{ +A dataframe of merics and description that match filter criteria +} +\description{ +Function to filter LakeCat metrics metrics by category, area of interest, +dataset or year. Use `lc_get_params(categories)` or `lc_get_params(datasets)` +to see all the valid category or dataset options +} +\examples{ +\dontrun{ +metrics <- lc_get_metric_names(category='Natural') +metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), +aoi=c('Cat','Ws')} +} +\author{ +Marc Weber +} diff --git a/man/lc_get_params.Rd b/man/lc_get_params.Rd index 168275a..ae76d8e 100644 --- a/man/lc_get_params.Rd +++ b/man/lc_get_params.Rd @@ -20,12 +20,14 @@ A list of all the current LakeCat values for a given parameter Function to return available LakeCat parameters using the StreamCat API. } \examples{ -\donttest{ +\dontrun{ params <- lc_get_params(param='variable_info') params <- lc_get_params(param='metric_names') -params <- lc_get_params(param='areaOfInterest') +params <- sc_get_params(param='categories') +params <- lc_get_params(param='aoi') params <- lc_get_params(param='state') params <- lc_get_params(param='county') +params <- sc_get_params(param='datasets') } } \author{ diff --git a/man/lc_nlcd.Rd b/man/lc_nlcd.Rd index 7beef4c..512be94 100644 --- a/man/lc_nlcd.Rd +++ b/man/lc_nlcd.Rd @@ -45,7 +45,7 @@ A tibble of desired StreamCat metrics Function to specifically retrieve all NLCD metrics for a given year using the StreamCat API. } \examples{ -\donttest{ +\dontrun{ df <- lc_nlcd(comid='23783629', year='2019', aoi='ws') diff --git a/man/sc_get_comid.Rd b/man/sc_get_comid.Rd index bc03c0e..d9d87fc 100644 --- a/man/sc_get_comid.Rd +++ b/man/sc_get_comid.Rd @@ -29,7 +29,7 @@ sf object. The function generates a vector of COMID values a user can then pass to sc_get_data function } \examples{ -\donttest{ +\dontrun{ dd <- data.frame(x = c(-122.649,-100.348,-75.186,-106.675), y = c(45.085, 35.405,42.403,38.721)) diff --git a/man/sc_get_data.Rd b/man/sc_get_data.Rd index 8022e01..09bccc0 100644 --- a/man/sc_get_data.Rd +++ b/man/sc_get_data.Rd @@ -75,7 +75,7 @@ Function to return StreamCat catchment and watershed metrics using the StreamCat specific metric data aggregated by area of interest, returned by comid(s), hydroregion(s), state(s), or county(ies). } \examples{ -\donttest{ +\dontrun{ df <- sc_get_data(comid='179', aoi='cat', metric='fert') df <- sc_get_data(metric='pctgrs2006', aoi='ws', region='Region01') diff --git a/man/sc_get_metric_names.Rd b/man/sc_get_metric_names.Rd new file mode 100644 index 0000000..0897bb3 --- /dev/null +++ b/man/sc_get_metric_names.Rd @@ -0,0 +1,38 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/sc_get_params.R +\name{sc_get_metric_names} +\alias{sc_get_metric_names} +\title{Get StreamCat Metric Names} +\usage{ +sc_get_metric_names(category = NULL, aoi = NULL, year = NULL, dataset = NULL) +} +\arguments{ +\item{category}{Filter StreamCat metrics based on the metric category} + +\item{aoi}{Filter StreamCat metrics based on the area of interest} + +\item{year}{Filter StreamCat metrics based on a particular year or years} + +\item{dataset}{Filter StreamCat metrics based on the dataset name} +} +\value{ +A dataframe of merics and description that match filter criteria +} +\description{ +Function to filter StreamCat metrics metrics by category, area of interest, +dataset or year. Use `sc_get_params(categories)` or `sc_get_params(datasets)` +to see all the valid category or dataset options +} +\examples{ +\dontrun{ +metrics <- sc_get_metric_names(category='Wildfire') +metrics <- sc_get_metric_names(category = c('Deposition','Climate'), +aoi=c('Cat','Ws') +metrics <- sc_get_metric_names(aoi='Other', +dataset=c('Canal Density','Predicted Channel Widths Depths')) + +} +} +\author{ +Marc Weber +} diff --git a/man/sc_get_params.Rd b/man/sc_get_params.Rd index 47a721f..34c743f 100644 --- a/man/sc_get_params.Rd +++ b/man/sc_get_params.Rd @@ -20,13 +20,14 @@ A list of all the current StreamCat values for a given parameter Function to return available StreamCat parameters using the StreamCat API. } \examples{ -\donttest{ +\dontrun{ params <- sc_get_params(param='variable_info') params <- sc_get_params(param='metric_names') -params <- sc_get_params(param='areaOfInterest') +params <- sc_get_params(param='categories') +params <- sc_get_params(param='aoi') params <- sc_get_params(param='state') params <- sc_get_params(param='county') -} +params <- sc_get_params(param='datasets')} } \author{ Marc Weber diff --git a/man/sc_nlcd.Rd b/man/sc_nlcd.Rd index 2db3bd0..6cd7d2a 100644 --- a/man/sc_nlcd.Rd +++ b/man/sc_nlcd.Rd @@ -64,7 +64,7 @@ A tibble of desired StreamCat metrics Function to retrieve all NLCD metrics for a given year using the StreamCat API. } \examples{ -\donttest{ +\dontrun{ df <- sc_nlcd(year='2001', aoi='cat',comid='179,1337,1337420') df <- sc_nlcd(year='2001', aoi='ws', region='Region01') diff --git a/tests/testthat/test-lc_get_params.R b/tests/testthat/test-lc_get_params.R index 20d2224..21d3f62 100644 --- a/tests/testthat/test-lc_get_params.R +++ b/tests/testthat/test-lc_get_params.R @@ -6,27 +6,27 @@ test_that("lc_get_params for metric_names parameters", { expect_gt(length(params),500) }) -test_that("sc_get_params for variable_info parameters", { - params <- sc_get_params(param='variable_info') +test_that("lc_get_params for variable_info parameters", { + params <- lc_get_params(param='variable_info') expect_true(exists("params")) expect_gt(nrow(params),100) }) +test_that("lc_get_metric_names", { + metrics <- lc_get_metric_names(category='Natural') + expect_true(exists("metrics")) + expect_gt(nrow(metrics),70) + expect_equal(names(metrics), c("Category","Metric","AOI","Year", + "Short_Name","Metric_Description","Units", + "Source","Dataset")) +}) + test_that("lc_get_params for area of interest parameters", { params <- lc_get_params(param='areaOfInterest') expect_true(exists("params")) expect_equal(params,c("cat","ws")) }) -test_that("lc_get_params for region parameters", { - params <- sc_get_params(param='region') - expect_true(exists("params")) - expect_equal(params,c("Region01","Region02","Region03N","Region03S","Region03W", - "Region04","Region05","Region06","Region07","Region08", - "Region09","Region10L","Region10U","Region11","Region12", - "Region13","Region14","Region15","Region16","Region17","Region18")) -}) - test_that("lc_get_params for name parameters", { params <- lc_get_params(param='metric_names') expect_true(exists("params")) diff --git a/tests/testthat/test-sc_get_params.R b/tests/testthat/test-sc_get_params.R index 4488b44..75ab546 100644 --- a/tests/testthat/test-sc_get_params.R +++ b/tests/testthat/test-sc_get_params.R @@ -2,7 +2,7 @@ context("Test that sc_get_params is pulling in StreamCat API parameters") test_that("sc_get_params for area of interest parameters", { - params <- sc_get_params(param='areaOfInterest') + params <- sc_get_params(param='aoi') expect_true(exists("params")) expect_equal(params,c("cat","catrp100","other","ws","wsrp100")) }) @@ -28,6 +28,18 @@ test_that("sc_get_params for variable_info parameters", { expect_gt(nrow(params),100) }) +test_that("sc_get_params for StreamCat metric categories", { + params <- sc_get_params(param='categories') + expect_true(exists("params")) + expect_gt(length(params),8) +}) + +test_that("sc_get_params for StreamCat datasets", { + params <- sc_get_params(param='datasets') + expect_true(exists("params")) + expect_gt(length(params),30) +}) + test_that("sc_get_params for state parameters", { params <- sc_get_params(param='state') expect_true(exists("params")) @@ -42,3 +54,22 @@ test_that("sc_get_params for county parameters", { expect_equal(names(params), c("fips","state","county_name")) }) +test_that("sc_get_metric_names for categories and AOIs", { + metrics <- sc_get_metric_names(category = c('Deposition','Climate'),aoi=c('Cat','Ws')) + expect_true(exists("metrics")) + expect_gt(nrow(metrics),10) + expect_equal(names(metrics), c("Category","Metric","AOI","Year", + "Short_Name","Metric_Description","Units", + "Source","Dataset")) +}) + +test_that("sc_get_metric_names for datasets", { + metrics <- sc_get_metric_names(aoi='Other', + dataset=c('Canal Density', + 'Predicted Channel Widths Depths')) + expect_true(exists("metrics")) + expect_lt(nrow(metrics),4) + expect_equal(names(metrics), c("Category","Metric","AOI","Year", + "Short_Name","Metric_Description","Units", + "Source","Dataset")) +}) \ No newline at end of file From bdd7fedf2ce4c3a4c0d41636976533c062dbadde Mon Sep 17 00:00:00 2001 From: Weber Date: Mon, 6 Oct 2025 16:23:31 -0700 Subject: [PATCH 05/22] Updating version --- DESCRIPTION | 2 +- NEWS.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e6b4b11..8aed21a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: StreamCatTools Type: Package Title: 'StreamCatTools' -Version: 0.7.0.9000 +Version: 0.8.0 Authors@R: c(person(given = "Marc", family = "Weber", role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 9ec6081..ad79ffb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# StreamCatTools (development version) +# StreamCatTools 0.8.0 - Added code coverage to the package - Added two new functions - `sc_get_metric_names` and `lc_get_metric_names` From c37efcaed0f39490ea8def3c7627775978ecb390 Mon Sep 17 00:00:00 2001 From: Weber Date: Wed, 8 Oct 2025 09:41:54 -0700 Subject: [PATCH 06/22] changes to sc_get_params and lc_get_params --- R/lc_get_params.R | 19 ++++++++++--------- R/sc_get_comid.R | 7 ++++--- R/sc_get_params.R | 17 +++++++++-------- tests/testthat/test-lc_get_params.R | 2 +- vignettes/Introduction.Rmd | 2 +- vignettes/LakeCat.Rmd | 2 +- 6 files changed, 26 insertions(+), 23 deletions(-) diff --git a/R/lc_get_params.R b/R/lc_get_params.R index 39dd52e..a45de44 100644 --- a/R/lc_get_params.R +++ b/R/lc_get_params.R @@ -32,7 +32,7 @@ lc_get_params <- function(param = NULL) { WEBTOOL_NAME <- METRIC_UNITS <- METRIC_DESCRIPTION <- DSID <- NULL SOURCE_NAME <- SOURCE_URL <- UUID <- DATE_DOWNLOADED <- NULL resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/lakes/metrics")$items - if (param=='areaOfInterest'){ + if (param=='aoi'){ params <- strsplit(stringr::str_sub(resp$aoi_param_info[[1]]$options,2,-2),",")[[1]] params <- c(gsub(" ","", params),'other') params <- params[order(params)] @@ -126,6 +126,7 @@ lc_fullname <- function(metric = NULL) { #' @param dataset Filter LakeCat metrics based on the dataset name #' #' @return A dataframe of merics and description that match filter criteria +#' @importFrom rlang .data #' @export #' #' @examples @@ -170,9 +171,9 @@ lc_get_metric_names <- function(category = NULL, .f = function(df, col_name) { filter_values <- filters[[col_name]] if (!is.null(filter_values)) { - df <- df %>% - dplyr::mutate(temp_col = stringr::str_split(.data[[col_name]], ",")) %>% - dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) %>% + df <- df |> + dplyr::mutate(temp_col = stringr::str_split(.data[[col_name]], ",")) |> + dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) |> dplyr::select(-temp_col) } df @@ -182,11 +183,11 @@ lc_get_metric_names <- function(category = NULL, } results <- filter_data(resp, filters) results <- results |> - dplyr::select(Category = INDICATOR_CATEGORY, Metric = METRIC_NAME, - AOI,Year = YEAR, Short_Name = WEBTOOL_NAME, - Metric_Description = METRIC_DESCRIPTION, - Units = METRIC_UNITS, Source = SOURCE_NAME, - Dataset = DSNAME) + dplyr::select(Category = .data$INDICATOR_CATEGORY, Metric = .data$METRIC_NAME, + .data$AOI,Year = .data$YEAR, Short_Name = .data$WEBTOOL_NAME, + Metric_Description = .data$METRIC_DESCRIPTION, + Units = .data$METRIC_UNITS, Source = .data$SOURCE_NAME, + Dataset = .data$DSNAME) return(results) } \ No newline at end of file diff --git a/R/sc_get_comid.R b/R/sc_get_comid.R index 35bdcab..0a22c9a 100644 --- a/R/sc_get_comid.R +++ b/R/sc_get_comid.R @@ -32,7 +32,8 @@ #' comids <- sc_get_comid(dd, xcoord='x', #' ycoord='y', crsys=4269) #' -#' dd <- sf::read_sf(system.file("shape/nc.shp", package="sf")) +#' dd <- sf::st_point_on_surface(sf::read_sf(system.file("shape/nc.shp", package="sf"))) +#' #' comids <- sc_get_comid(dd) #' #' comids <- sc_get_comid(dd, xcoord='x', @@ -53,10 +54,10 @@ sc_get_comid <- function(dd = NULL, xcoord = NULL, } else { dd <- sf::st_as_sf(dd, coords = c(xcoord, ycoord), crs = crsys, remove = FALSE) } - + geom_col <- attr(dd, "sf_column") run_for <- 1:nrow(dd) output <- do.call(rbind, lapply(1:nrow(dd), function(i){ - comid <- nhdplusTools::discover_nhdplus_id(dd[i,c('geometry')]) + comid <- nhdplusTools::discover_nhdplus_id(dd[i,c(geom_col)]) if (length(comid)==0L) comid <- NA else comid <- comid return(comid) })) diff --git a/R/sc_get_params.R b/R/sc_get_params.R index 864bc8b..8a5a096 100644 --- a/R/sc_get_params.R +++ b/R/sc_get_params.R @@ -126,6 +126,7 @@ sc_fullname <- function(metric = NULL) { #' @param dataset Filter StreamCat metrics based on the dataset name #' #' @return A dataframe of merics and description that match filter criteria +#' @importFrom rlang .data #' @export #' #' @examples @@ -174,9 +175,9 @@ sc_get_metric_names <- function(category = NULL, .f = function(df, col_name) { filter_values <- filters[[col_name]] if (!is.null(filter_values)) { - df <- df %>% - dplyr::mutate(temp_col = stringr::str_split(.data[[col_name]], ",")) %>% - dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) %>% + df <- df |> + dplyr::mutate(temp_col = stringr::str_split(.data[[col_name]], ",")) |> + dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) |> dplyr::select(-temp_col) } df @@ -186,11 +187,11 @@ sc_get_metric_names <- function(category = NULL, } results <- filter_data(resp, filters) results <- results |> - dplyr::select(Category = INDICATOR_CATEGORY, Metric = METRIC_NAME, - AOI,Year = YEAR, Short_Name = WEBTOOL_NAME, - Metric_Description = METRIC_DESCRIPTION, - Units = METRIC_UNITS, Source = SOURCE_NAME, - Dataset = DSNAME) + dplyr::select(Category = .data$INDICATOR_CATEGORY, Metric = .data$METRIC_NAME, + .data$AOI,Year = .data$YEAR, Short_Name = .data$WEBTOOL_NAME, + Metric_Description = .data$METRIC_DESCRIPTION, + Units = .data$METRIC_UNITS, Source = .data$SOURCE_NAME, + Dataset = .data$DSNAME) return(results) } diff --git a/tests/testthat/test-lc_get_params.R b/tests/testthat/test-lc_get_params.R index 21d3f62..47d62d5 100644 --- a/tests/testthat/test-lc_get_params.R +++ b/tests/testthat/test-lc_get_params.R @@ -22,7 +22,7 @@ test_that("lc_get_metric_names", { }) test_that("lc_get_params for area of interest parameters", { - params <- lc_get_params(param='areaOfInterest') + params <- lc_get_params(param='aoi') expect_true(exists("params")) expect_equal(params,c("cat","ws")) }) diff --git a/vignettes/Introduction.Rmd b/vignettes/Introduction.Rmd index 53c4aa3..37922a3 100644 --- a/vignettes/Introduction.Rmd +++ b/vignettes/Introduction.Rmd @@ -51,7 +51,7 @@ res$items ## List API parameters List StreamCat parameters: Get a list of available StreamCat values for certain parameters using the `sc_get_params` function via the API ```{r params} -region_params <- sc_get_params(param='areaOfInterest') +region_params <- sc_get_params(param='aoi') name_params <- sc_get_params(param='metric_names') diff --git a/vignettes/LakeCat.Rmd b/vignettes/LakeCat.Rmd index 382dd19..166e829 100644 --- a/vignettes/LakeCat.Rmd +++ b/vignettes/LakeCat.Rmd @@ -41,7 +41,7 @@ List LakeCat parameters: Get a list of available LakeCat values for certain para ```{r name_params} library(StreamCatTools) -region_params <- lc_get_params(param='areaOfInterest') +region_params <- lc_get_params(param='aoi') name_params <- lc_get_params(param='metric_names') From dee7c3f91d26482d1760faf473140918e7c550ea Mon Sep 17 00:00:00 2001 From: Weber Date: Wed, 8 Oct 2025 10:19:34 -0700 Subject: [PATCH 07/22] fix to allow passing vectors of metric, state, county, region to both sc_get_data and sc_get_data --- NEWS.md | 2 ++ R/lc_get_data.R | 18 +++++++++++++++--- R/sc_get_data.R | 20 ++++++++++++++++---- 3 files changed, 33 insertions(+), 7 deletions(-) diff --git a/NEWS.md b/NEWS.md index ad79ffb..3cb0c5e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,6 +4,8 @@ - Added two new functions - `sc_get_metric_names` and `lc_get_metric_names` to make metric names and descriptions more searchable and slightly updated parameters in both `sc_get_params` and `lc_get_params` functions +- Both `sc_get_data` and `lc_get_data` now accept vectors as well as comma- + separated strings for the metric, state, county and region parameters # StreamCatTools 0.7.0 diff --git a/R/lc_get_data.R b/R/lc_get_data.R index 0455d2a..3e82bf1 100644 --- a/R/lc_get_data.R +++ b/R/lc_get_data.R @@ -94,17 +94,29 @@ lc_get_data <- function(comid = NULL, # Base API URL. req <- httr2::request('https://api.epa.gov/StreamCat/lakes/metrics') # Collapse comids into a single string separated by a comma. + if ((is.null(comid) & is.null(state) & is.null(county) & is.null(region) & is.null(conus)) | is.null(metric) | is.null(aoi)){ + stop('Must provide at a minimum valid comid, metric and aoi to the function') + } + # Collapse vectors into a single string separated by a comma. if (!is.null(comid)){ comid <- paste(comid, collapse = ",") } + metric <- paste(metric, collapse = ",") + aoi <- paste(aoi, collapse = ",") + if (!is.null(state)){ + state <- paste(state, collapse = ",") + } + if (!is.null(county)){ + county <- paste(county, collapse = ",") + } + if (!is.null(region)){ + region <- paste(region, collapse = ",") + } # Force old and odd naming convention to behave correctly if (!is.null(aoi)){ if (aoi == 'catchment') aoi <- 'cat' if (aoi == 'watershed') aoi <- 'ws' } - if ((is.null(comid) & is.null(state) & is.null(county) & is.null(region) & is.null(conus)) | is.null(metric) | is.null(aoi)){ - stop('Must provide at a minimum valid comid, metric and aoi to the function') - } if (!is.null(conus) & metric=='all'){ stop('If you are requesting all metrics please request for regions, states or counties rather than all of conus') } diff --git a/R/sc_get_data.R b/R/sc_get_data.R index fb0ba72..51a83f1 100644 --- a/R/sc_get_data.R +++ b/R/sc_get_data.R @@ -100,10 +100,24 @@ sc_get_data <- function(comid = NULL, # Base API URL. base_url <- 'https://api.epa.gov/StreamCat/streams/metrics' req <- httr2::request(base_url) - # Collapse comids into a single string separated by a comma. + if ((is.null(comid) & is.null(state) & is.null(county) & is.null(region) & is.null(conus)) | is.null(metric) | is.null(aoi)){ + stop('Must provide at a minimum valid comid, metric and aoi to the function') + } + # Collapse vectors into a single string separated by a comma. if (!is.null(comid)){ comid <- paste(comid, collapse = ",") } + metric <- paste(metric, collapse = ",") + aoi <- paste(aoi, collapse = ",") + if (!is.null(state)){ + state <- paste(state, collapse = ",") + } + if (!is.null(county)){ + county <- paste(county, collapse = ",") + } + if (!is.null(region)){ + region <- paste(region, collapse = ",") + } # Force old and odd naming convention to behave correctly if (!is.null(aoi)){ if (stringr::str_detect(aoi,'catchment')) { @@ -119,9 +133,7 @@ sc_get_data <- function(comid = NULL, aoi <- gsub('riparian_watershed','wsrp100',aoi) } } - if ((is.null(comid) & is.null(state) & is.null(county) & is.null(region) & is.null(conus)) | is.null(metric) | is.null(aoi)){ - stop('Must provide at a minimum valid comid, metric and aoi to the function') - } + if (!is.null(conus) & metric=='all'){ stop('If you are requesting all metrics please request for regions, states or counties rather than all of conus') } From c57a9b7ef9077d061343a0048bfe547858728493 Mon Sep 17 00:00:00 2001 From: Michael Dumelle Date: Wed, 8 Oct 2025 11:18:14 -0700 Subject: [PATCH 08/22] remove global variables messages --- R/lc_get_params.R | 63 +++++++++++++++++++++++++++------------------- R/sc_get_params.R | 64 +++++++++++++++++++++++++++-------------------- 2 files changed, 74 insertions(+), 53 deletions(-) diff --git a/R/lc_get_params.R b/R/lc_get_params.R index a45de44..22cd0ed 100644 --- a/R/lc_get_params.R +++ b/R/lc_get_params.R @@ -8,7 +8,7 @@ #' #' @param param List of available parameters in the API for the following options: #' name, areaofInterest, region, state, county. State and county return a data -#' frame that includes FIPS codes, names and state abbreviations +#' frame that includes FIPS codes, names and state abbreviations #' Syntax: param=, #' Values: name|area #' @@ -31,6 +31,7 @@ lc_get_params <- function(param = NULL) { INDICATOR_CATEGORY <- METRIC_NAME <- AOI <- YEAR <- NULL WEBTOOL_NAME <- METRIC_UNITS <- METRIC_DESCRIPTION <- DSID <- NULL SOURCE_NAME <- SOURCE_URL <- UUID <- DATE_DOWNLOADED <- NULL + DSNAME <- NULL resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/lakes/metrics")$items if (param=='aoi'){ params <- strsplit(stringr::str_sub(resp$aoi_param_info[[1]]$options,2,-2),",")[[1]] @@ -45,10 +46,10 @@ lc_get_params <- function(param = NULL) { params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> httr2::req_perform() |> httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> - dplyr::select(-UUID,-DATE_DOWNLOADED,-METADATA) |> - dplyr::rename(dataset=FINAL_TABLE,category=INDICATOR_CATEGORY, - metric=METRIC_NAME,aoi=AOI, year=YEAR, + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(-UUID,-DATE_DOWNLOADED,-METADATA) |> + dplyr::rename(dataset=FINAL_TABLE,category=INDICATOR_CATEGORY, + metric=METRIC_NAME,aoi=AOI, year=YEAR, short_description=WEBTOOL_NAME,units=METRIC_UNITS, long_description=METRIC_DESCRIPTION, dsid=DSID, source_name=SOURCE_NAME, source_URL=SOURCE_URL) @@ -56,16 +57,16 @@ lc_get_params <- function(param = NULL) { params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> httr2::req_perform() |> httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> + readr::read_csv(show_col_types = FALSE) |> dplyr::select(INDICATOR_CATEGORY) params <- sort(unique(params$INDICATOR_CATEGORY)) } else if(param == 'datasets'){ params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> httr2::req_perform() |> httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> + readr::read_csv(show_col_types = FALSE) |> dplyr::select(DSNAME) - params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) + params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) } else if(param == 'region'){ params <- resp$region_options[[1]][[1]] params <- params[order(params)] @@ -113,27 +114,27 @@ lc_fullname <- function(metric = NULL) { #' Get LakeCat Metric Names #' #' @description -#' Function to filter LakeCat metrics metrics by category, area of interest, +#' Function to filter LakeCat metrics metrics by category, area of interest, #' dataset or year. Use `lc_get_params(categories)` or `lc_get_params(datasets)` #' to see all the valid category or dataset options #' #' @author #' Marc Weber -#' +#' #' @param category Filter LakeCat metrics based on the metric category #' @param aoi Filter LakeCat metrics based on the area of interest #' @param year Filter LakeCat metrics based on a particular year or years #' @param dataset Filter LakeCat metrics based on the dataset name #' #' @return A dataframe of merics and description that match filter criteria -#' @importFrom rlang .data +# #' @importFrom rlang .data #' @export #' #' @examples #' \dontrun{ #' metrics <- lc_get_metric_names(category='Natural') #' metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), -#' aoi=c('Cat','Ws')} +#' aoi=c('Cat','Ws')} lc_get_metric_names <- function(category = NULL, @@ -159,11 +160,12 @@ lc_get_metric_names <- function(category = NULL, httr2::req_perform() |> httr2::resp_body_string() |> readr::read_csv(show_col_types = FALSE) - + filters <- list(INDICATOR_CATEGORY = category, AOI = aoi, YEAR = year, DSNAME = dataset) - + filter_data <- function(data, filters) { + temp_col <- col_name <- NULL # Filter the data frame for each non-null filter filtered_data <- purrr::reduce( names(filters), @@ -171,10 +173,12 @@ lc_get_metric_names <- function(category = NULL, .f = function(df, col_name) { filter_values <- filters[[col_name]] if (!is.null(filter_values)) { - df <- df |> - dplyr::mutate(temp_col = stringr::str_split(.data[[col_name]], ",")) |> - dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) |> - dplyr::select(-temp_col) + temp_col <- stringr::str_split(df[[col_name]], ",") + df <- df[purrr::map_lgl(temp_col, ~ any(.x %in% filter_values)), , drop = FALSE] + # df <- df |> + # dplyr::mutate(temp_col = stringr::str_split(col_name, ",")) |> + # dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) |> + # dplyr::select(-temp_col) } df } @@ -182,12 +186,19 @@ lc_get_metric_names <- function(category = NULL, return(filtered_data) } results <- filter_data(resp, filters) - results <- results |> - dplyr::select(Category = .data$INDICATOR_CATEGORY, Metric = .data$METRIC_NAME, - .data$AOI,Year = .data$YEAR, Short_Name = .data$WEBTOOL_NAME, - Metric_Description = .data$METRIC_DESCRIPTION, - Units = .data$METRIC_UNITS, Source = .data$SOURCE_NAME, - Dataset = .data$DSNAME) - + names_keep <- c("INDICATOR_CATEGORY", "METRIC_NAME", "AOI", "YEAR", + "WEBTOOL_NAME", "METRIC_DESCRIPTION", + "METRIC_UNITS", "SOURCE_NAME", "DSNAME") + results <- results[, names_keep, drop = FALSE] + names_new <- c("Category", "Metric", "AOI", "Year", "Short_Name", + "Metric_Description", "Units", "Source", "Dataset") + names(results) <- names_new + # results <- results |> + # dplyr::select(Category = INDICATOR_CATEGORY, Metric = METRIC_NAME, + # AOI,Year = YEAR, Short_Name = WEBTOOL_NAME, + # Metric_Description = METRIC_DESCRIPTION, + # Units = METRIC_UNITS, Source = SOURCE_NAME, + # Dataset = DSNAME) + return(results) -} \ No newline at end of file +} diff --git a/R/sc_get_params.R b/R/sc_get_params.R index 8a5a096..05e60d2 100644 --- a/R/sc_get_params.R +++ b/R/sc_get_params.R @@ -8,7 +8,7 @@ #' #' @param param List of available parameters in the API for the following options: #' name, areaofInterest, region, state, county. State and county return a data -#' frame that includes FIPS codes, names and state abbreviations +#' frame that includes FIPS codes, names and state abbreviations #' Syntax: param=, #' Values: name|area #' @@ -30,6 +30,7 @@ sc_get_params <- function(param = NULL) { INDICATOR_CATEGORY <- METRIC_NAME <- AOI <- YEAR <- NULL WEBTOOL_NAME <- METRIC_UNITS <- METRIC_DESCRIPTION <- DSID <- NULL SOURCE_NAME <- SOURCE_URL <- UUID <- DATE_DOWNLOADED <- NULL + DSNAME <- NULL resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/streams/metrics")$items if (param=='aoi'){ params <- strsplit(stringr::str_sub(resp$aoi_param_info[[1]]$options,2,-2),",")[[1]] @@ -43,10 +44,10 @@ sc_get_params <- function(param = NULL) { params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> httr2::req_perform() |> httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> - dplyr::select(-UUID,-DATE_DOWNLOADED,-METADATA) |> - dplyr::rename(dataset=FINAL_TABLE,category=INDICATOR_CATEGORY, - metric=METRIC_NAME,aoi=AOI, year=YEAR, + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(-UUID,-DATE_DOWNLOADED,-METADATA) |> + dplyr::rename(dataset=FINAL_TABLE,category=INDICATOR_CATEGORY, + metric=METRIC_NAME,aoi=AOI, year=YEAR, short_description=WEBTOOL_NAME,units=METRIC_UNITS, long_description=METRIC_DESCRIPTION, dsid=DSID, source_name=SOURCE_NAME, source_URL=SOURCE_URL) @@ -54,17 +55,17 @@ sc_get_params <- function(param = NULL) { params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> httr2::req_perform() |> httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> + readr::read_csv(show_col_types = FALSE) |> dplyr::select(INDICATOR_CATEGORY) params <- sort(unique(params$INDICATOR_CATEGORY)) } else if(param == 'datasets'){ params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> httr2::req_perform() |> httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> + readr::read_csv(show_col_types = FALSE) |> dplyr::select(DSNAME) - params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) - } + params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) + } else if(param == 'region'){ params <- resp$region_options[[1]][[1]] params <- params[order(params)] @@ -113,20 +114,20 @@ sc_fullname <- function(metric = NULL) { #' Get StreamCat Metric Names #' #' @description -#' Function to filter StreamCat metrics metrics by category, area of interest, +#' Function to filter StreamCat metrics metrics by category, area of interest, #' dataset or year. Use `sc_get_params(categories)` or `sc_get_params(datasets)` #' to see all the valid category or dataset options #' #' @author #' Marc Weber -#' +#' #' @param category Filter StreamCat metrics based on the metric category #' @param aoi Filter StreamCat metrics based on the area of interest #' @param year Filter StreamCat metrics based on a particular year or years #' @param dataset Filter StreamCat metrics based on the dataset name #' #' @return A dataframe of merics and description that match filter criteria -#' @importFrom rlang .data +# #' @importFrom rlang .data #' @export #' #' @examples @@ -136,8 +137,8 @@ sc_fullname <- function(metric = NULL) { #' aoi=c('Cat','Ws') #' metrics <- sc_get_metric_names(aoi='Other', #' dataset=c('Canal Density','Predicted Channel Widths Depths')) -#' -#' } +#' +#' } sc_get_metric_names <- function(category = NULL, @@ -163,10 +164,10 @@ sc_get_metric_names <- function(category = NULL, httr2::req_perform() |> httr2::resp_body_string() |> readr::read_csv(show_col_types = FALSE) - + filters <- list(INDICATOR_CATEGORY = category, AOI = aoi, YEAR = year, DSNAME = dataset) - + filter_data <- function(data, filters) { # Filter the data frame for each non-null filter filtered_data <- purrr::reduce( @@ -175,10 +176,12 @@ sc_get_metric_names <- function(category = NULL, .f = function(df, col_name) { filter_values <- filters[[col_name]] if (!is.null(filter_values)) { - df <- df |> - dplyr::mutate(temp_col = stringr::str_split(.data[[col_name]], ",")) |> - dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) |> - dplyr::select(-temp_col) + temp_col <- stringr::str_split(df[[col_name]], ",") + df <- df[purrr::map_lgl(temp_col, ~ any(.x %in% filter_values)), , drop = FALSE] + # df <- df |> + # dplyr::mutate(temp_col = stringr::str_split(col_name, ",")) |> + # dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) |> + # dplyr::select(-temp_col) } df } @@ -186,12 +189,19 @@ sc_get_metric_names <- function(category = NULL, return(filtered_data) } results <- filter_data(resp, filters) - results <- results |> - dplyr::select(Category = .data$INDICATOR_CATEGORY, Metric = .data$METRIC_NAME, - .data$AOI,Year = .data$YEAR, Short_Name = .data$WEBTOOL_NAME, - Metric_Description = .data$METRIC_DESCRIPTION, - Units = .data$METRIC_UNITS, Source = .data$SOURCE_NAME, - Dataset = .data$DSNAME) - + names_keep <- c("INDICATOR_CATEGORY", "METRIC_NAME", "AOI", "YEAR", + "WEBTOOL_NAME", "METRIC_DESCRIPTION", + "METRIC_UNITS", "SOURCE_NAME", "DSNAME") + results <- results[, names_keep, drop = FALSE] + names_new <- c("Category", "Metric", "AOI", "Year", "Short_Name", + "Metric_Description", "Units", "Source", "Dataset") + names(results) <- names_new + # results |> + # dplyr::select(Category = INDICATOR_CATEGORY, Metric = METRIC_NAME, + # AOI,Year = YEAR, Short_Name = WEBTOOL_NAME, + # Metric_Description = METRIC_DESCRIPTION, + # Units = METRIC_UNITS, Source = SOURCE_NAME, + # Dataset = DSNAME) + return(results) } From 979ea71b5683c983a5a82f10b8e7d74b07201bee Mon Sep 17 00:00:00 2001 From: Weber Date: Wed, 8 Oct 2025 12:34:23 -0700 Subject: [PATCH 09/22] couple more updates to get_params functions and adding Mike as contributor --- DESCRIPTION | 4 ++++ R/lc_get_params.R | 10 ---------- R/sc_get_params.R | 10 ---------- 3 files changed, 4 insertions(+), 20 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 8aed21a..e77e1b7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -22,6 +22,10 @@ Authors@R: c(person(given = "Marc", family = "Rebhuhn", role = "ctb", email = "rebhuhnd@gmail.com"), + person(given = "Michael", + family = "Dumelle", + role = "ctb", + email = "dumelle.michael@epa.gov"), person(given = "Zachary", family = "Smith", role = "ctb")) diff --git a/R/lc_get_params.R b/R/lc_get_params.R index 22cd0ed..8fd05f8 100644 --- a/R/lc_get_params.R +++ b/R/lc_get_params.R @@ -175,10 +175,6 @@ lc_get_metric_names <- function(category = NULL, if (!is.null(filter_values)) { temp_col <- stringr::str_split(df[[col_name]], ",") df <- df[purrr::map_lgl(temp_col, ~ any(.x %in% filter_values)), , drop = FALSE] - # df <- df |> - # dplyr::mutate(temp_col = stringr::str_split(col_name, ",")) |> - # dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) |> - # dplyr::select(-temp_col) } df } @@ -193,12 +189,6 @@ lc_get_metric_names <- function(category = NULL, names_new <- c("Category", "Metric", "AOI", "Year", "Short_Name", "Metric_Description", "Units", "Source", "Dataset") names(results) <- names_new - # results <- results |> - # dplyr::select(Category = INDICATOR_CATEGORY, Metric = METRIC_NAME, - # AOI,Year = YEAR, Short_Name = WEBTOOL_NAME, - # Metric_Description = METRIC_DESCRIPTION, - # Units = METRIC_UNITS, Source = SOURCE_NAME, - # Dataset = DSNAME) return(results) } diff --git a/R/sc_get_params.R b/R/sc_get_params.R index 05e60d2..4d024fa 100644 --- a/R/sc_get_params.R +++ b/R/sc_get_params.R @@ -178,10 +178,6 @@ sc_get_metric_names <- function(category = NULL, if (!is.null(filter_values)) { temp_col <- stringr::str_split(df[[col_name]], ",") df <- df[purrr::map_lgl(temp_col, ~ any(.x %in% filter_values)), , drop = FALSE] - # df <- df |> - # dplyr::mutate(temp_col = stringr::str_split(col_name, ",")) |> - # dplyr::filter(purrr::map_lgl(temp_col, ~ any(.x %in% filter_values))) |> - # dplyr::select(-temp_col) } df } @@ -196,12 +192,6 @@ sc_get_metric_names <- function(category = NULL, names_new <- c("Category", "Metric", "AOI", "Year", "Short_Name", "Metric_Description", "Units", "Source", "Dataset") names(results) <- names_new - # results |> - # dplyr::select(Category = INDICATOR_CATEGORY, Metric = METRIC_NAME, - # AOI,Year = YEAR, Short_Name = WEBTOOL_NAME, - # Metric_Description = METRIC_DESCRIPTION, - # Units = METRIC_UNITS, Source = SOURCE_NAME, - # Dataset = DSNAME) return(results) } From 7f53b7c507c4a75d8001a890531c325ae2e9b408 Mon Sep 17 00:00:00 2001 From: Weber Date: Wed, 8 Oct 2025 12:34:56 -0700 Subject: [PATCH 10/22] updated documentation --- DESCRIPTION | 2 +- man/lc_get_metric_names.Rd | 4 ++-- man/lc_get_params.Rd | 2 +- man/sc_get_comid.Rd | 3 ++- man/sc_get_metric_names.Rd | 4 ++-- man/sc_get_params.Rd | 2 +- 6 files changed, 9 insertions(+), 8 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e77e1b7..72a92be 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -59,6 +59,6 @@ URL: https://usepa.github.io/StreamCatTools/, https://github.com/USEPA/StreamCat BugReports: https://github.com/USEPA/StreamCatTools/issues VignetteBuilder: knitr,rmarkdown LazyData: true -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 License: CC0 NeedsCompilation: no diff --git a/man/lc_get_metric_names.Rd b/man/lc_get_metric_names.Rd index 4668ecd..523ee82 100644 --- a/man/lc_get_metric_names.Rd +++ b/man/lc_get_metric_names.Rd @@ -19,7 +19,7 @@ lc_get_metric_names(category = NULL, aoi = NULL, year = NULL, dataset = NULL) A dataframe of merics and description that match filter criteria } \description{ -Function to filter LakeCat metrics metrics by category, area of interest, +Function to filter LakeCat metrics metrics by category, area of interest, dataset or year. Use `lc_get_params(categories)` or `lc_get_params(datasets)` to see all the valid category or dataset options } @@ -27,7 +27,7 @@ to see all the valid category or dataset options \dontrun{ metrics <- lc_get_metric_names(category='Natural') metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), -aoi=c('Cat','Ws')} +aoi=c('Cat','Ws')} } \author{ Marc Weber diff --git a/man/lc_get_params.Rd b/man/lc_get_params.Rd index ae76d8e..3195dc0 100644 --- a/man/lc_get_params.Rd +++ b/man/lc_get_params.Rd @@ -9,7 +9,7 @@ lc_get_params(param = NULL) \arguments{ \item{param}{List of available parameters in the API for the following options: name, areaofInterest, region, state, county. State and county return a data -frame that includes FIPS codes, names and state abbreviations +frame that includes FIPS codes, names and state abbreviations Syntax: param=, Values: name|area} } diff --git a/man/sc_get_comid.Rd b/man/sc_get_comid.Rd index d9d87fc..db36764 100644 --- a/man/sc_get_comid.Rd +++ b/man/sc_get_comid.Rd @@ -37,7 +37,8 @@ y = c(45.085, 35.405,42.403,38.721)) comids <- sc_get_comid(dd, xcoord='x', ycoord='y', crsys=4269) -dd <- sf::read_sf(system.file("shape/nc.shp", package="sf")) +dd <- sf::st_point_on_surface(sf::read_sf(system.file("shape/nc.shp", package="sf"))) + comids <- sc_get_comid(dd) comids <- sc_get_comid(dd, xcoord='x', diff --git a/man/sc_get_metric_names.Rd b/man/sc_get_metric_names.Rd index 0897bb3..1f11eb1 100644 --- a/man/sc_get_metric_names.Rd +++ b/man/sc_get_metric_names.Rd @@ -19,7 +19,7 @@ sc_get_metric_names(category = NULL, aoi = NULL, year = NULL, dataset = NULL) A dataframe of merics and description that match filter criteria } \description{ -Function to filter StreamCat metrics metrics by category, area of interest, +Function to filter StreamCat metrics metrics by category, area of interest, dataset or year. Use `sc_get_params(categories)` or `sc_get_params(datasets)` to see all the valid category or dataset options } @@ -31,7 +31,7 @@ aoi=c('Cat','Ws') metrics <- sc_get_metric_names(aoi='Other', dataset=c('Canal Density','Predicted Channel Widths Depths')) -} +} } \author{ Marc Weber diff --git a/man/sc_get_params.Rd b/man/sc_get_params.Rd index 34c743f..bbb59a5 100644 --- a/man/sc_get_params.Rd +++ b/man/sc_get_params.Rd @@ -9,7 +9,7 @@ sc_get_params(param = NULL) \arguments{ \item{param}{List of available parameters in the API for the following options: name, areaofInterest, region, state, county. State and county return a data -frame that includes FIPS codes, names and state abbreviations +frame that includes FIPS codes, names and state abbreviations Syntax: param=, Values: name|area} } From 56f96cd7fc9716b88824c377c5d48c80c8292b0e Mon Sep 17 00:00:00 2001 From: Weber Date: Thu, 9 Oct 2025 09:54:36 -0700 Subject: [PATCH 11/22] Increment develop branch --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 72a92be..d647b4f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: StreamCatTools Type: Package Title: 'StreamCatTools' -Version: 0.8.0 +Version: 0.8.0.9000 Authors@R: c(person(given = "Marc", family = "Weber", role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 3cb0c5e..67a5a34 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# StreamCatTools (development version) + # StreamCatTools 0.8.0 - Added code coverage to the package From 276494d4fefea3771b4b15bd4fbc4d4adeae8100 Mon Sep 17 00:00:00 2001 From: Weber Date: Tue, 14 Oct 2025 17:03:42 -0700 Subject: [PATCH 12/22] added try catch to functions to fail gracefully and fixed column separator in get_metric_names --- R/lc_get_data.R | 27 +++++++--- R/lc_get_params.R | 127 +++++++++++++++++++++++++-------------------- R/sc_get_data.R | 15 +++++- R/sc_get_params.R | 128 ++++++++++++++++++++++++++-------------------- 4 files changed, 177 insertions(+), 120 deletions(-) diff --git a/R/lc_get_data.R b/R/lc_get_data.R index 3e82bf1..4d3200f 100644 --- a/R/lc_get_data.R +++ b/R/lc_get_data.R @@ -136,7 +136,8 @@ lc_get_data <- function(comid = NULL, state=state,county=county,region=region,conus=conus, countOnly=countOnly ) - df <- req |> + df <- tryCatch({ + req |> httr2::req_method("POST") |> httr2::req_headers("Content-Type" = "application/x-www-form-urlencoded") |> httr2::req_method("POST") |> @@ -146,12 +147,24 @@ lc_get_data <- function(comid = NULL, httr2::req_perform() |> httr2::resp_body_string() |> jsonlite::fromJSON() - # Return a data frame - if (is.null(countOnly)){ - df <- df$items |> - dplyr::select(comid, dplyr::everything()) - return(df) - } else return(df$items) + },error = function(e) { + message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message) + return(NULL) + }) + # Return a data frame if success + if (exists("df") && !is.null(df)){ + # Return a data frame + if (is.null(countOnly)){ + df <- df$items |> + dplyr::select(comid, dplyr::everything()) + return(df) + } else return(df$items) + if (is.null(countOnly)){ + df <- df$items |> + dplyr::select(comid, dplyr::everything()) + return(df) + } else return(df$items) + } } diff --git a/R/lc_get_params.R b/R/lc_get_params.R index 8fd05f8..369e0ad 100644 --- a/R/lc_get_params.R +++ b/R/lc_get_params.R @@ -32,58 +32,63 @@ lc_get_params <- function(param = NULL) { WEBTOOL_NAME <- METRIC_UNITS <- METRIC_DESCRIPTION <- DSID <- NULL SOURCE_NAME <- SOURCE_URL <- UUID <- DATE_DOWNLOADED <- NULL DSNAME <- NULL - resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/lakes/metrics")$items - if (param=='aoi'){ - params <- strsplit(stringr::str_sub(resp$aoi_param_info[[1]]$options,2,-2),",")[[1]] - params <- c(gsub(" ","", params),'other') - params <- params[order(params)] - params <- params[!params %in% c('catrp100','wsrp100','other')] - } else if(param == 'metric_names') { - params <- resp$name_options[[1]][[1]] - params <- params[!duplicated(params)] - params <- params[order(params)] - } else if(param == 'variable_info') { - params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> - httr2::req_perform() |> - httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> - dplyr::select(-UUID,-DATE_DOWNLOADED,-METADATA) |> - dplyr::rename(dataset=FINAL_TABLE,category=INDICATOR_CATEGORY, - metric=METRIC_NAME,aoi=AOI, year=YEAR, - short_description=WEBTOOL_NAME,units=METRIC_UNITS, - long_description=METRIC_DESCRIPTION, dsid=DSID, - source_name=SOURCE_NAME, source_URL=SOURCE_URL) - } else if(param == 'categories'){ - params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> - httr2::req_perform() |> - httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> - dplyr::select(INDICATOR_CATEGORY) - params <- sort(unique(params$INDICATOR_CATEGORY)) - } else if(param == 'datasets'){ - params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> - httr2::req_perform() |> - httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> - dplyr::select(DSNAME) - params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) - } else if(param == 'region'){ - params <- resp$region_options[[1]][[1]] - params <- params[order(params)] - } else if(param == 'state'){ - params <- resp$state_options[[1]] - params <- params[!params$st_abbr %in% c('AK','HI','PR'),] - params$st_fips <- as.character(params$st_fips) - params$st_fips[nchar(params$st_fips) < 2] <- paste0('0',params$st_fips[nchar(params$st_fips) < 2]) - params <- params[order(params$st_name),] - rownames(params) <- 1:nrow(params) - } else if(param == 'county'){ - params <- resp$county_options[[1]] - params$fips <- as.character(params$fips) - params$fips[nchar(params$fips) < 5] <- paste0('0',params$fips[nchar(params$fips) < 5]) - params <- params[with(params,order(state,county_name)),] - rownames(params) <- 1:nrow(params) - } + resp <- tryCatch({ + jsonlite::fromJSON("https://api.epa.gov/StreamCat/lakes/metrics")$items + if (param=='aoi'){ + params <- strsplit(stringr::str_sub(resp$aoi_param_info[[1]]$options,2,-2),",")[[1]] + params <- c(gsub(" ","", params),'other') + params <- params[order(params)] + params <- params[!params %in% c('catrp100','wsrp100','other')] + } else if(param == 'metric_names') { + params <- resp$name_options[[1]][[1]] + params <- params[!duplicated(params)] + params <- params[order(params)] + } else if(param == 'variable_info') { + params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(-UUID,-DATE_DOWNLOADED,-METADATA) |> + dplyr::rename(dataset=FINAL_TABLE,category=INDICATOR_CATEGORY, + metric=METRIC_NAME,aoi=AOI, year=YEAR, + short_description=WEBTOOL_NAME,units=METRIC_UNITS, + long_description=METRIC_DESCRIPTION, dsid=DSID, + source_name=SOURCE_NAME, source_URL=SOURCE_URL) + } else if(param == 'categories'){ + params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(INDICATOR_CATEGORY) + params <- sort(unique(params$INDICATOR_CATEGORY)) + } else if(param == 'datasets'){ + params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(DSNAME) + params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) + } else if(param == 'region'){ + params <- resp$region_options[[1]][[1]] + params <- params[order(params)] + } else if(param == 'state'){ + params <- resp$state_options[[1]] + params <- params[!params$st_abbr %in% c('AK','HI','PR'),] + params$st_fips <- as.character(params$st_fips) + params$st_fips[nchar(params$st_fips) < 2] <- paste0('0',params$st_fips[nchar(params$st_fips) < 2]) + params <- params[order(params$st_name),] + rownames(params) <- 1:nrow(params) + } else if(param == 'county'){ + params <- resp$county_options[[1]] + params$fips <- as.character(params$fips) + params$fips[nchar(params$fips) < 5] <- paste0('0',params$fips[nchar(params$fips) < 5]) + params <- params[with(params,order(state,county_name)),] + rownames(params) <- 1:nrow(params) + } + },error = function(e) { + message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message) + return(NULL) + }) return(params) } @@ -106,8 +111,13 @@ lc_get_params <- function(param = NULL) { #' fullname <- lc_fullname(metric='clay') lc_fullname <- function(metric = NULL) { - resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/lakes/datadictionary")$items - result <- unique(resp$short_display_name[resp$metric_prefix %in% metric]) + result <- tryCatch({ + resp <-jsonlite::fromJSON("https://api.epa.gov/StreamCat/lakes/datadictionary")$items + resp <- unique(resp$short_display_name[resp$metric_prefix %in% metric]) + },error = function(e) { + message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message) + return(NULL) + }) return(result) } @@ -156,10 +166,15 @@ lc_get_metric_names <- function(category = NULL, } aoi <- stringr::str_to_title(aoi) } - resp <- params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> + resp <- tryCatch({ + params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |> httr2::req_perform() |> httr2::resp_body_string() |> readr::read_csv(show_col_types = FALSE) + },error = function(e) { + message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message) + return(NULL) + }) filters <- list(INDICATOR_CATEGORY = category, AOI = aoi, YEAR = year, DSNAME = dataset) @@ -173,7 +188,7 @@ lc_get_metric_names <- function(category = NULL, .f = function(df, col_name) { filter_values <- filters[[col_name]] if (!is.null(filter_values)) { - temp_col <- stringr::str_split(df[[col_name]], ",") + temp_col <- stringr::str_split(df[[col_name]], ", ") df <- df[purrr::map_lgl(temp_col, ~ any(.x %in% filter_values)), , drop = FALSE] } df diff --git a/R/sc_get_data.R b/R/sc_get_data.R index 51a83f1..906be8f 100644 --- a/R/sc_get_data.R +++ b/R/sc_get_data.R @@ -153,7 +153,8 @@ sc_get_data <- function(comid = NULL, state=state,county=county,region=region,conus=conus, countOnly=countOnly ) - df <- req |> + df <- tryCatch({ + req |> httr2::req_method("POST") |> httr2::req_headers("Content-Type" = "application/x-www-form-urlencoded") |> httr2::req_method("POST") |> @@ -163,12 +164,24 @@ sc_get_data <- function(comid = NULL, httr2::req_perform() |> httr2::resp_body_string() |> jsonlite::fromJSON() + },error = function(e) { + message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message) + return(NULL) + }) + # Return a data frame if success + if (exists("df") && !is.null(df)){ # Return a data frame + if (is.null(countOnly)){ + df <- df$items |> + dplyr::select(comid, dplyr::everything()) + return(df) + } else return(df$items) if (is.null(countOnly)){ df <- df$items |> dplyr::select(comid, dplyr::everything()) return(df) } else return(df$items) + } } diff --git a/R/sc_get_params.R b/R/sc_get_params.R index 4d024fa..d5802d3 100644 --- a/R/sc_get_params.R +++ b/R/sc_get_params.R @@ -31,58 +31,63 @@ sc_get_params <- function(param = NULL) { WEBTOOL_NAME <- METRIC_UNITS <- METRIC_DESCRIPTION <- DSID <- NULL SOURCE_NAME <- SOURCE_URL <- UUID <- DATE_DOWNLOADED <- NULL DSNAME <- NULL - resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/streams/metrics")$items - if (param=='aoi'){ - params <- strsplit(stringr::str_sub(resp$aoi_param_info[[1]]$options,2,-2),",")[[1]] - params <- c(gsub(" ","", params),'other') - params <- params[order(params)] - } else if(param == 'metric_names') { - params <- resp$name_options[[1]][[1]] - params <- params[!duplicated(params)] - params <- params[order(params)] - } else if(param == 'variable_info') { - params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> - httr2::req_perform() |> - httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> - dplyr::select(-UUID,-DATE_DOWNLOADED,-METADATA) |> - dplyr::rename(dataset=FINAL_TABLE,category=INDICATOR_CATEGORY, - metric=METRIC_NAME,aoi=AOI, year=YEAR, - short_description=WEBTOOL_NAME,units=METRIC_UNITS, - long_description=METRIC_DESCRIPTION, dsid=DSID, - source_name=SOURCE_NAME, source_URL=SOURCE_URL) - } else if(param == 'categories'){ - params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> - httr2::req_perform() |> - httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> - dplyr::select(INDICATOR_CATEGORY) - params <- sort(unique(params$INDICATOR_CATEGORY)) - } else if(param == 'datasets'){ - params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> - httr2::req_perform() |> - httr2::resp_body_string() |> - readr::read_csv(show_col_types = FALSE) |> - dplyr::select(DSNAME) - params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) - } - else if(param == 'region'){ - params <- resp$region_options[[1]][[1]] - params <- params[order(params)] - } else if(param == 'state'){ - params <- resp$state_options[[1]] - params <- params[!params$st_abbr %in% c('AK','HI','PR'),] - params$st_fips <- as.character(params$st_fips) - params$st_fips[nchar(params$st_fips) < 2] <- paste0('0',params$st_fips[nchar(params$st_fips) < 2]) - params <- params[order(params$st_name),] - rownames(params) <- 1:nrow(params) - } else if(param == 'county'){ - params <- resp$county_options[[1]] - params$fips <- as.character(params$fips) - params$fips[nchar(params$fips) < 5] <- paste0('0',params$fips[nchar(params$fips) < 5]) - params <- params[with(params,order(state,county_name)),] - rownames(params) <- 1:nrow(params) - } + resp <- tryCatch({ + jsonlite::fromJSON("https://api.epa.gov/StreamCat/streams/metrics")$items + if (param=='aoi'){ + params <- strsplit(stringr::str_sub(resp$aoi_param_info[[1]]$options,2,-2),",")[[1]] + params <- c(gsub(" ","", params),'other') + params <- params[order(params)] + } else if(param == 'metric_names') { + params <- resp$name_options[[1]][[1]] + params <- params[!duplicated(params)] + params <- params[order(params)] + } else if(param == 'variable_info') { + params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(-UUID,-DATE_DOWNLOADED,-METADATA) |> + dplyr::rename(dataset=FINAL_TABLE,category=INDICATOR_CATEGORY, + metric=METRIC_NAME,aoi=AOI, year=YEAR, + short_description=WEBTOOL_NAME,units=METRIC_UNITS, + long_description=METRIC_DESCRIPTION, dsid=DSID, + source_name=SOURCE_NAME, source_URL=SOURCE_URL) + } else if(param == 'categories'){ + params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(INDICATOR_CATEGORY) + params <- sort(unique(params$INDICATOR_CATEGORY)) + } else if(param == 'datasets'){ + params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> + httr2::req_perform() |> + httr2::resp_body_string() |> + readr::read_csv(show_col_types = FALSE) |> + dplyr::select(DSNAME) + params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) + } + else if(param == 'region'){ + params <- resp$region_options[[1]][[1]] + params <- params[order(params)] + } else if(param == 'state'){ + params <- resp$state_options[[1]] + params <- params[!params$st_abbr %in% c('AK','HI','PR'),] + params$st_fips <- as.character(params$st_fips) + params$st_fips[nchar(params$st_fips) < 2] <- paste0('0',params$st_fips[nchar(params$st_fips) < 2]) + params <- params[order(params$st_name),] + rownames(params) <- 1:nrow(params) + } else if(param == 'county'){ + params <- resp$county_options[[1]] + params$fips <- as.character(params$fips) + params$fips[nchar(params$fips) < 5] <- paste0('0',params$fips[nchar(params$fips) < 5]) + params <- params[with(params,order(state,county_name)),] + rownames(params) <- 1:nrow(params) + } + },error = function(e) { + message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message) + return(NULL) + }) return(params) } @@ -105,8 +110,13 @@ sc_get_params <- function(param = NULL) { #' fullname <- sc_fullname(metric='clay') sc_fullname <- function(metric = NULL) { - resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/streams/datadictionary")$items - result <- unique(resp$short_display_name[resp$metric_prefix %in% metric]) + result <- tryCatch({ + resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/streams/datadictionary")$items + resp <- unique(resp$short_display_name[resp$metric_prefix %in% metric]) + },error = function(e) { + message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message) + return(NULL) + }) return(result) } @@ -160,10 +170,15 @@ sc_get_metric_names <- function(category = NULL, } aoi <- stringr::str_to_title(aoi) } - resp <- params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> + resp <- tryCatch({ + params <- httr2::request('https://api.epa.gov/StreamCat/streams/variable_info') |> httr2::req_perform() |> httr2::resp_body_string() |> readr::read_csv(show_col_types = FALSE) + },error = function(e) { + message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message) + return(NULL) + }) filters <- list(INDICATOR_CATEGORY = category, AOI = aoi, YEAR = year, DSNAME = dataset) @@ -176,7 +191,8 @@ sc_get_metric_names <- function(category = NULL, .f = function(df, col_name) { filter_values <- filters[[col_name]] if (!is.null(filter_values)) { - temp_col <- stringr::str_split(df[[col_name]], ",") + # Split the column values by comma + temp_col <- stringr::str_split(df[[col_name]], ", ") df <- df[purrr::map_lgl(temp_col, ~ any(.x %in% filter_values)), , drop = FALSE] } df From c867a2bcca4e3757de8d1834d2b3a68be847e403 Mon Sep 17 00:00:00 2001 From: Weber Date: Wed, 15 Oct 2025 10:00:42 -0700 Subject: [PATCH 13/22] added new get_metric_names example to Vignettes and last fixes to tryCatch in functions --- R/lc_get_params.R | 12 +++++------- R/sc_get_params.R | 13 +++++-------- tests/testthat/test-lc_get_params.R | 2 +- vignettes/Introduction.Rmd | 8 ++++++++ 4 files changed, 19 insertions(+), 16 deletions(-) diff --git a/R/lc_get_params.R b/R/lc_get_params.R index 369e0ad..22a3e1e 100644 --- a/R/lc_get_params.R +++ b/R/lc_get_params.R @@ -32,14 +32,14 @@ lc_get_params <- function(param = NULL) { WEBTOOL_NAME <- METRIC_UNITS <- METRIC_DESCRIPTION <- DSID <- NULL SOURCE_NAME <- SOURCE_URL <- UUID <- DATE_DOWNLOADED <- NULL DSNAME <- NULL - resp <- tryCatch({ - jsonlite::fromJSON("https://api.epa.gov/StreamCat/lakes/metrics")$items + result <- tryCatch({ + resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/lakes/metrics")$items if (param=='aoi'){ params <- strsplit(stringr::str_sub(resp$aoi_param_info[[1]]$options,2,-2),",")[[1]] params <- c(gsub(" ","", params),'other') params <- params[order(params)] params <- params[!params %in% c('catrp100','wsrp100','other')] - } else if(param == 'metric_names') { + } else if(param == 'metric_names') { params <- resp$name_options[[1]][[1]] params <- params[!duplicated(params)] params <- params[order(params)] @@ -77,19 +77,17 @@ lc_get_params <- function(param = NULL) { params$st_fips <- as.character(params$st_fips) params$st_fips[nchar(params$st_fips) < 2] <- paste0('0',params$st_fips[nchar(params$st_fips) < 2]) params <- params[order(params$st_name),] - rownames(params) <- 1:nrow(params) } else if(param == 'county'){ params <- resp$county_options[[1]] params$fips <- as.character(params$fips) params$fips[nchar(params$fips) < 5] <- paste0('0',params$fips[nchar(params$fips) < 5]) params <- params[with(params,order(state,county_name)),] - rownames(params) <- 1:nrow(params) } },error = function(e) { message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message) return(NULL) }) - return(params) + return(result) } #' @title Lookup Full Metric Name @@ -144,7 +142,7 @@ lc_fullname <- function(metric = NULL) { #' \dontrun{ #' metrics <- lc_get_metric_names(category='Natural') #' metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), -#' aoi=c('Cat','Ws')} +#' aoi=c('Cat','Ws'))} lc_get_metric_names <- function(category = NULL, diff --git a/R/sc_get_params.R b/R/sc_get_params.R index d5802d3..2941822 100644 --- a/R/sc_get_params.R +++ b/R/sc_get_params.R @@ -31,8 +31,8 @@ sc_get_params <- function(param = NULL) { WEBTOOL_NAME <- METRIC_UNITS <- METRIC_DESCRIPTION <- DSID <- NULL SOURCE_NAME <- SOURCE_URL <- UUID <- DATE_DOWNLOADED <- NULL DSNAME <- NULL - resp <- tryCatch({ - jsonlite::fromJSON("https://api.epa.gov/StreamCat/streams/metrics")$items + result <- tryCatch({ + resp <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/streams/metrics")$items if (param=='aoi'){ params <- strsplit(stringr::str_sub(resp$aoi_param_info[[1]]$options,2,-2),",")[[1]] params <- c(gsub(" ","", params),'other') @@ -66,8 +66,7 @@ sc_get_params <- function(param = NULL) { readr::read_csv(show_col_types = FALSE) |> dplyr::select(DSNAME) params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)])) - } - else if(param == 'region'){ + } else if(param == 'region'){ params <- resp$region_options[[1]][[1]] params <- params[order(params)] } else if(param == 'state'){ @@ -76,19 +75,17 @@ sc_get_params <- function(param = NULL) { params$st_fips <- as.character(params$st_fips) params$st_fips[nchar(params$st_fips) < 2] <- paste0('0',params$st_fips[nchar(params$st_fips) < 2]) params <- params[order(params$st_name),] - rownames(params) <- 1:nrow(params) } else if(param == 'county'){ params <- resp$county_options[[1]] params$fips <- as.character(params$fips) params$fips[nchar(params$fips) < 5] <- paste0('0',params$fips[nchar(params$fips) < 5]) params <- params[with(params,order(state,county_name)),] - rownames(params) <- 1:nrow(params) } },error = function(e) { message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message) return(NULL) }) - return(params) + return(result) } #' @title Lookup Full Metric Name @@ -144,7 +141,7 @@ sc_fullname <- function(metric = NULL) { #' \dontrun{ #' metrics <- sc_get_metric_names(category='Wildfire') #' metrics <- sc_get_metric_names(category = c('Deposition','Climate'), -#' aoi=c('Cat','Ws') +#' aoi=c('Cat','Ws')) #' metrics <- sc_get_metric_names(aoi='Other', #' dataset=c('Canal Density','Predicted Channel Widths Depths')) #' diff --git a/tests/testthat/test-lc_get_params.R b/tests/testthat/test-lc_get_params.R index 47d62d5..55eccc6 100644 --- a/tests/testthat/test-lc_get_params.R +++ b/tests/testthat/test-lc_get_params.R @@ -15,7 +15,7 @@ test_that("lc_get_params for variable_info parameters", { test_that("lc_get_metric_names", { metrics <- lc_get_metric_names(category='Natural') expect_true(exists("metrics")) - expect_gt(nrow(metrics),70) + expect_gt(nrow(metrics),20) expect_equal(names(metrics), c("Category","Metric","AOI","Year", "Short_Name","Metric_Description","Units", "Source","Dataset")) diff --git a/vignettes/Introduction.Rmd b/vignettes/Introduction.Rmd index 37922a3..42ce618 100644 --- a/vignettes/Introduction.Rmd +++ b/vignettes/Introduction.Rmd @@ -76,6 +76,7 @@ metric='pctdecid2019,fert' fullname <- sc_fullname(metric) fullname ``` + We can additionally get a data frame of state FIPS codes, abbreviations and names, and the same information for counties as well using `sc_get_params`: ```{r states} states <- sc_get_params(param='state') @@ -87,6 +88,13 @@ counties <- sc_get_params(param='county') head(counties) ``` +## Filter metric information by criteria +We can also filter metric names and information by the metric year(s), the indicator categories for metrics, the metric data set names, or the Areas of Interest the metrics are available for. +```{r get_metric_names} +metrics <- sc_get_metric_names(category = c('Deposition','Climate'),aoi=c('Cat','Ws')) +head(metrics) +``` + ## Get data for COMIDs In this example we access several variables, for several areas of interest, and for several COMIDs using the `sc_get_data` function. Loads data into a tibble we can view. ```{r get_data} From 4a400675e93bcec66ec43fb4302dacbb723de01c Mon Sep 17 00:00:00 2001 From: Weber Date: Wed, 15 Oct 2025 10:17:11 -0700 Subject: [PATCH 14/22] document new functions --- man/lc_get_metric_names.Rd | 2 +- man/sc_get_metric_names.Rd | 2 +- vignettes/LakeCat.Rmd | 7 +++++++ 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/man/lc_get_metric_names.Rd b/man/lc_get_metric_names.Rd index 523ee82..edaeb8f 100644 --- a/man/lc_get_metric_names.Rd +++ b/man/lc_get_metric_names.Rd @@ -27,7 +27,7 @@ to see all the valid category or dataset options \dontrun{ metrics <- lc_get_metric_names(category='Natural') metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), -aoi=c('Cat','Ws')} +aoi=c('Cat','Ws'))} } \author{ Marc Weber diff --git a/man/sc_get_metric_names.Rd b/man/sc_get_metric_names.Rd index 1f11eb1..89c5791 100644 --- a/man/sc_get_metric_names.Rd +++ b/man/sc_get_metric_names.Rd @@ -27,7 +27,7 @@ to see all the valid category or dataset options \dontrun{ metrics <- sc_get_metric_names(category='Wildfire') metrics <- sc_get_metric_names(category = c('Deposition','Climate'), -aoi=c('Cat','Ws') +aoi=c('Cat','Ws')) metrics <- sc_get_metric_names(aoi='Other', dataset=c('Canal Density','Predicted Channel Widths Depths')) diff --git a/vignettes/LakeCat.Rmd b/vignettes/LakeCat.Rmd index 166e829..5894270 100644 --- a/vignettes/LakeCat.Rmd +++ b/vignettes/LakeCat.Rmd @@ -68,6 +68,13 @@ fullname <- lc_fullname(metric) fullname ``` +## Filter metric information by criteria +We can also filter metric names and information by the metric year(s), the indicator categories for metrics, the metric data set names, or the Areas of Interest the metrics are available for. +```{r get_metric_names} +metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), aoi=c('Cat','Ws')) +head(metrics) +``` + ## Get Waterbody COMIDs In this example we use the `lc_get_comid` function to find COMIDs for a set of example lake locations we load into R.`lc_get_comid` is just a simple wrapper for `get_waterbodies` in the [nhdplusTools](https://doi-usgs.github.io/nhdplusTools/) R package. We can then use the COMIDs we derive for our lake locations to get LakeCat metrics for these lakes as we show in after this. ```{r comids, warning=FALSE, message=FALSE} From f70a18649d03c8221adef4a5257db4b725729dbd Mon Sep 17 00:00:00 2001 From: Weber Date: Wed, 15 Oct 2025 11:35:15 -0700 Subject: [PATCH 15/22] updated CRAN comments --- cran-comments.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index f8d18b2..499faf5 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,8 +1,10 @@ -This is a minor update that +This is a minor update that: -- Adds code covereage to the package -- Adds two new functions to the package -- Allows passing of vectors as parameters to two of the package functions +- Addresses CRAN error noted by Dr. Brian Ripley generated by tests that is + required to be fixed by 10/25/25 +- Adds tryCatch handling for functions calling web services in order to fail + gracefully and not produce errors +- Adds documentation to vignettes for two new functions added to the package ------- From f6f3b788d5c83e78bd2ade152d81995de0101dd2 Mon Sep 17 00:00:00 2001 From: Weber Date: Thu, 16 Oct 2025 09:21:22 -0700 Subject: [PATCH 16/22] Ordered vignettes in github pages --- DESCRIPTION | 2 +- NEWS.md | 2 ++ _pkgdown.yml | 7 +++++++ docs/404.html | 6 +++--- docs/LICENSE.html | 6 +++--- docs/articles/Applications.html | 6 +++--- docs/articles/Introduction.html | 6 +++--- docs/articles/LakeCat.html | 6 +++--- docs/articles/index.html | 14 +++++++------- docs/authors.html | 10 +++++----- docs/index.html | 6 +++--- docs/news/index.html | 12 +++++++++--- docs/pkgdown.yml | 2 +- docs/reference/index.html | 6 +++--- docs/reference/lc_fullname.html | 6 +++--- docs/reference/lc_get_comid.html | 6 +++--- docs/reference/lc_get_data.html | 6 +++--- docs/reference/lc_get_metric_names.html | 6 +++--- docs/reference/lc_get_params.html | 6 +++--- docs/reference/lc_nlcd.html | 6 +++--- docs/reference/sc_fullname.html | 6 +++--- docs/reference/sc_get_comid.html | 6 +++--- docs/reference/sc_get_data.html | 6 +++--- docs/reference/sc_get_metric_names.html | 6 +++--- docs/reference/sc_get_params.html | 6 +++--- docs/reference/sc_nlcd.html | 6 +++--- docs/search.json | 2 +- 27 files changed, 90 insertions(+), 75 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 93b9297..d84b6a3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: StreamCatTools Type: Package Title: 'StreamCatTools' -Version: 0.9.0 +Version: 0.9.0.9000 Authors@R: c(person(given = "Marc", family = "Weber", role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 17c9643..ef3cdcb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# StreamCatTools (development version) + # StreamCatTools 0.9.0 - Addresses CRAN error generated by tests that is diff --git a/_pkgdown.yml b/_pkgdown.yml index 64e3756..e2b3f5d 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,11 @@ url: https://usepa.github.io/StreamCatTools/ template: bootstrap: 5 +articles: +- title: Articles + navbar: ~ + contents: + - Introduction + - LakeCat + - Applications diff --git a/docs/404.html b/docs/404.html index 0730f52..38c9e01 100644 --- a/docs/404.html +++ b/docs/404.html @@ -26,7 +26,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000
  • Changelog
    • diff --git a/docs/LICENSE.html b/docs/LICENSE.html index c519551..250b0d2 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
    • Changelog
      • diff --git a/docs/articles/Introduction.html b/docs/articles/Introduction.html index 96ab64e..80b87ea 100644 --- a/docs/articles/Introduction.html +++ b/docs/articles/Introduction.html @@ -25,7 +25,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000
    • Changelog
      • diff --git a/docs/articles/LakeCat.html b/docs/articles/LakeCat.html index e998f27..79c404b 100644 --- a/docs/articles/LakeCat.html +++ b/docs/articles/LakeCat.html @@ -25,7 +25,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000
    • Changelog
      • diff --git a/docs/articles/index.html b/docs/articles/index.html index 228d7f0..b4ee587 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
      • @@ -37,15 +37,15 @@
        -

        All vignettes

        +

        Articles

        -
        Applications
        -
        -
        Getting Started
        +
        Getting Started
        Working with LakeCat data
        +
        Applications
        +
        diff --git a/docs/authors.html b/docs/authors.html index 347a031..22213e7 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
        • @@ -75,13 +75,13 @@

          Citation

          Weber M (2025). StreamCatTools: 'StreamCatTools'. -R package version 0.8.0.9000, https://github.com/USEPA/StreamCatTools, https://usepa.github.io/StreamCatTools/. +R package version 0.9.0.9000, https://github.com/USEPA/StreamCatTools, https://usepa.github.io/StreamCatTools/. 

          @Manual{,
   title = {StreamCatTools: 'StreamCatTools'},
   author = {Marc Weber},
   year = {2025},
-  note = {R package version 0.8.0.9000, https://github.com/USEPA/StreamCatTools},
+  note = {R package version 0.9.0.9000, https://github.com/USEPA/StreamCatTools},
   url = {https://usepa.github.io/StreamCatTools/},
 }
          diff --git a/docs/index.html b/docs/index.html index d73a3b5..ad43f9c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -28,7 +28,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000
        • Changelog
          • diff --git a/docs/news/index.html b/docs/news/index.html index ee5a638..f593f58 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
          • @@ -41,6 +41,12 @@

            StreamCatTools (development version)

            +

            StreamCatTools 0.9.0

            CRAN release: 2025-10-15

            +
            • Addresses CRAN error generated by tests that is
              • +
            • Adds tryCatch handling for functions calling web services in order to fail gracefully and not produce errors
              • +
            • Adds documentation to vignettes for two new functions added to the package
              • +
            +

            StreamCatTools 0.8.0

            CRAN release: 2025-10-09

            • Added code coverage to the package
            • Added two new functions - sc_get_metric_names and lc_get_metric_names to make metric names and descriptions more searchable and slightly updated parameters in both sc_get_params and lc_get_params functions
              • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9fe7ede..c6f2eb9 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -5,7 +5,7 @@ articles: Applications: Applications.html Introduction: Introduction.html LakeCat: LakeCat.html -last_built: 2025-10-15T19:02Z +last_built: 2025-10-16T16:17Z urls: reference: https://usepa.github.io/StreamCatTools/reference article: https://usepa.github.io/StreamCatTools/articles diff --git a/docs/reference/index.html b/docs/reference/index.html index f93c3c6..9eb77db 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
              • diff --git a/docs/reference/lc_fullname.html b/docs/reference/lc_fullname.html index ccab799..9cfbb7c 100644 --- a/docs/reference/lc_fullname.html +++ b/docs/reference/lc_fullname.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                • diff --git a/docs/reference/lc_get_comid.html b/docs/reference/lc_get_comid.html index b88b018..3434636 100644 --- a/docs/reference/lc_get_comid.html +++ b/docs/reference/lc_get_comid.html @@ -13,7 +13,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                  • diff --git a/docs/reference/lc_get_data.html b/docs/reference/lc_get_data.html index b4fb769..0edd4f4 100644 --- a/docs/reference/lc_get_data.html +++ b/docs/reference/lc_get_data.html @@ -9,7 +9,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                    • diff --git a/docs/reference/lc_get_metric_names.html b/docs/reference/lc_get_metric_names.html index f138ce4..8c59184 100644 --- a/docs/reference/lc_get_metric_names.html +++ b/docs/reference/lc_get_metric_names.html @@ -11,7 +11,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                      • diff --git a/docs/reference/lc_get_params.html b/docs/reference/lc_get_params.html index 9084335..1989e41 100644 --- a/docs/reference/lc_get_params.html +++ b/docs/reference/lc_get_params.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                        • diff --git a/docs/reference/lc_nlcd.html b/docs/reference/lc_nlcd.html index 50a0d86..481435d 100644 --- a/docs/reference/lc_nlcd.html +++ b/docs/reference/lc_nlcd.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                          • diff --git a/docs/reference/sc_fullname.html b/docs/reference/sc_fullname.html index fb7b97a..6d57fa8 100644 --- a/docs/reference/sc_fullname.html +++ b/docs/reference/sc_fullname.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                            • diff --git a/docs/reference/sc_get_comid.html b/docs/reference/sc_get_comid.html index 2f267d0..b92ee0b 100644 --- a/docs/reference/sc_get_comid.html +++ b/docs/reference/sc_get_comid.html @@ -13,7 +13,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                              • diff --git a/docs/reference/sc_get_data.html b/docs/reference/sc_get_data.html index 80087ed..906aa22 100644 --- a/docs/reference/sc_get_data.html +++ b/docs/reference/sc_get_data.html @@ -9,7 +9,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                                • diff --git a/docs/reference/sc_get_metric_names.html b/docs/reference/sc_get_metric_names.html index 1d245bf..5ac8e91 100644 --- a/docs/reference/sc_get_metric_names.html +++ b/docs/reference/sc_get_metric_names.html @@ -11,7 +11,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                                  • diff --git a/docs/reference/sc_get_params.html b/docs/reference/sc_get_params.html index 119b7a0..ce53e2e 100644 --- a/docs/reference/sc_get_params.html +++ b/docs/reference/sc_get_params.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                                    • diff --git a/docs/reference/sc_nlcd.html b/docs/reference/sc_nlcd.html index 3dfe6c8..c5fbbae 100644 --- a/docs/reference/sc_nlcd.html +++ b/docs/reference/sc_nlcd.html @@ -7,7 +7,7 @@ StreamCatTools - 0.8.0.9000 + 0.9.0.9000 -
                                      • diff --git a/docs/search.json b/docs/search.json index 319167d..a258823 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"https://usepa.github.io/StreamCatTools/articles/Applications.html","id":"plotting-watershed-data","dir":"Articles","previous_headings":"","what":"Plotting watershed data","title":"Applications","text":"example access single variable Calapooia River using sc_get_data function. use nhdplusTools library grab flowlines watershed Calapooia, plot selected StreamCat metric Calapooia River show watershed.","code":"library(StreamCatTools) start_comid = 23763517 nldi_feature <- list(featureSource = \"comid\", featureID = start_comid) flowline_nldi <- nhdplusTools::navigate_nldi(nldi_feature, mode = \"UT\", data_source = \"flowlines\", distance=5000) # get StreamCat metrics df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=flowline_nldi$UT_flowlines$nhdplus_comid) # We can also pull out comids the following way: # comids <- paste(as.integer(flowline_nldi$UT_flowlines$nhdplus_comid), collapse=\",\",sep=\"\") # df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=comids) flowline_nldi <- flowline_nldi$UT_flowlines flowline_nldi$PCTIMP2011CAT <- df$pctimp2011cat[match(flowline_nldi$nhdplus_comid, df$comid)] basin <- nhdplusTools::get_nldi_basin(nldi_feature = nldi_feature) library(mapview) mapview::mapviewOptions(fgb=FALSE) mapview::mapview(basin, alpha.regions=.08) + mapview::mapview(flowline_nldi, zcol = \"PCTIMP2011CAT\", legend = TRUE)"},{"path":"https://usepa.github.io/StreamCatTools/articles/Applications.html","id":"working-with-nars-data","dir":"Articles","previous_headings":"","what":"Working with NARS data","title":"Applications","text":"example demonstrate data ‘mashup’ grabbing NRSA data EPA National Aquatic Resource Surveys (NARS) website directly R, pull particular StreamCat metrics sites using sc_get_data, compare landscape metrics NRSA metrics","code":"nrsa <- readr::read_csv(\"https://www.epa.gov/sites/production/files/2015-09/siteinfo_0.csv\") dplyr::glimpse(nrsa) # Promote data frame to sf spatial points data frame nrsa_sf <- sf::st_as_sf(nrsa, coords = c(\"LON_DD83\", \"LAT_DD83\"), crs = 4269) # Get COMIDs using nhdplusTools package # nrsa$COMID<- NA # for (i in 1:nrow(nrsa_sf)){ # print (i) # nrsa_sf[i,'COMID'] <- discover_nhdplus_id(nrsa_sf[i,c('geometry')]) # } load(system.file(\"extdata\", \"sample_nrsa_data.rda\", package=\"StreamCatTools\")) # get particular StreamCat data for all these NRSA sites # nrsa_sf$COMID <- as.character(nrsa_sf$COMID) comids <- nrsa_sf$COMID comids <- comids[!is.na(comids)] comids <- comids[c(1:700)] comids <- paste(comids,collapse=',') df <- sc_get_data(metric='pctcrop2006', aoi='ws', comid=comids) # glimpse(df) df$COMID <- as.integer(df$comid) nrsa_sf <- dplyr::left_join(nrsa_sf, df, by='COMID') # download mmi from NARS web page library(dplyr) library(ggplot2) mmi <- readr::read_csv(\"https://www.epa.gov/sites/production/files/2015-09/bentcond.csv\") # dplyr::glimpse(mmi) # join mmi to NARS info data frame with StreamCat PctCrop metric nrsa_sf <- dplyr::left_join(nrsa_sf, mmi[,c('SITE_ID','BENT_MMI_COND')], by='SITE_ID') bxplt <- nrsa_sf %>% tidyr::drop_na(BENT_MMI_COND) %>% ggplot2::ggplot(aes(x=pctcrop2006ws, y=BENT_MMI_COND))+ ggplot2::geom_boxplot()+ ggplot2::ggtitle('NRSA Benthic MMI versus % Crop in Watershed from 2006 NLCD') suppressWarnings(print(bxplt))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"installing-and-loading-streamcattools","dir":"Articles","previous_headings":"","what":"Installing and loading StreamCatTools","title":"Getting Started","text":"install, currently need install GitHub using devtools installing load library","code":"library(devtools) install_github('USEPA/StreamCatTools') library(StreamCatTools)"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"background","dir":"Articles","previous_headings":"","what":"Background","title":"Getting Started","text":"StreamCatTools package designed simplify use StreamCat data R, leveraging new API StreamCat.","code":""},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"streamcat-api","dir":"Articles","previous_headings":"","what":"StreamCat API","title":"Getting Started","text":"can pull data R StreamCat API simply passing URL extract json. hard-wire parameters though limited number records returned GET request.","code":"res <- jsonlite::fromJSON(\"https://api.epa.gov/StreamCat/streams/metrics?name=fert&areaOfInterest=cat&comid=179\") res$items #> fertws fertcat comid #> 1 1.438 1.438 179"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"list-api-parameters","dir":"Articles","previous_headings":"","what":"List API parameters","title":"Getting Started","text":"List StreamCat parameters: Get list available StreamCat values certain parameters using sc_get_params function via API can also see metrics available areas interest years using sc_get_params function (returns tibble information StreamCat metrics): can look display name names metric using sc_fullname function via API can additionally get data frame state FIPS codes, abbreviations names, information counties well using sc_get_params:","code":"region_params <- sc_get_params(param='aoi') name_params <- sc_get_params(param='metric_names') print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) #> [1] \"region parameters are: cat, catrp100, other, ws, wsrp100\" print(paste0('A selection of available StreamCat metrics include: ',paste(name_params[1:10],collapse = ', '))) #> [1] \"A selection of available StreamCat metrics include: agkffact, al2o3, bankfulldepth, bankfullwidth, bfi, canaldens, cao, cbnf, chem, clay\" var_info <- sc_get_params(param='variable_info') head(var_info) #> # A tibble: 6 × 13 #> category metric aoi year short_description long_description units dsid #> #> 1 Anthropogen… NABD_… Cat,… NA NABD Dam Density Density of geor… Coun… 33 #> 2 Anthropogen… NABD_… Cat,… NA NABD NID Reservo… Volume all rese… Cubi… 33 #> 3 Anthropogen… NABD_… Cat,… NA NABD Normal Rese… Volume all rese… Cubi… 33 #> 4 Natural Preci… Cat,… NA Surplus Precipit… This dataset re… Kilo… 75 #> 5 Soils Rckde… Cat,… NA Mean Bedrock Dep… Mean depth (cm)… Cent… 56 #> 6 Soils agkff… Cat,… NA Ag Soil Erodibil… Mean of STATSGO… Unit… 28 #> # ℹ 5 more variables: dataset , source_name , source_URL , #> # ACTIVE , DSNAME metric='pcthbwet2011' fullname <- sc_fullname(metric) fullname #> [1] \"Herbaceous Wetland Percentage 2011\" metric='pctdecid2019,fert' fullname <- sc_fullname(metric) fullname #> character(0) states <- sc_get_params(param='state') head(states) #> st_fips st_abbr st_name #> 30 01 AL Alabama #> 8 04 AZ Arizona #> 25 05 AR Arkansas #> 6 06 CA California #> 15 08 CO Colorado #> 50 09 CT Connecticut counties <- sc_get_params(param='county') head(counties) #> fips state county_name #> 752 01001 AL Autauga County #> 713 01003 AL Baldwin County #> 655 01005 AL Barbour County #> 755 01007 AL Bibb County #> 748 01009 AL Blount County #> 656 01011 AL Bullock County"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"filter-metric-information-by-criteria","dir":"Articles","previous_headings":"","what":"Filter metric information by criteria","title":"Getting Started","text":"can also filter metric names information metric year(s), indicator categories metrics, metric data set names, Areas Interest metrics available .","code":"metrics <- sc_get_metric_names(category = c('Deposition','Climate'),aoi=c('Cat','Ws')) head(metrics) #> # A tibble: 6 × 9 #> Category Metric AOI Year Short_Name Metric_Description Units Source Dataset #> #> 1 Climate bfi[A… Cat,… NA Base Flow… Base flow is the … Perc… USGS … Base F… #> 2 Deposit… inorg… Cat,… 2008 Mean Annu… Annual gradient m… Kilo… NADP NADP #> 3 Deposit… nh4[Y… Cat,… 2008 Mean annu… Annual gradient m… Kilo… NADP NADP #> 4 Deposit… no3[Y… Cat,… 2008 Mean Annu… Annual gradient m… Kilo… NADP NADP #> 5 Climate preci… Cat,… NA 30-year M… PRISM climate dat… Mill… PRISM PRISM #> 6 Climate preci… Cat,… 1991… 30-year M… PRISM climate dat… Mill… PRISM PRISM"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-data-for-comids","dir":"Articles","previous_headings":"","what":"Get data for COMIDs","title":"Getting Started","text":"example access several variables, several areas interest, several COMIDs using sc_get_data function. Loads data tibble can view.","code":"df <- sc_get_data(metric='pcturbmd2006,damdens,tridens', aoi='rp100cat,cat,ws', comid='179,1337,1337420') knitr::kable(df)"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-data-for-county","dir":"Articles","previous_headings":"","what":"Get data for county","title":"Getting Started","text":"example access couple variables watershed scale area interest county (Benton County case) using sc_get_data function.","code":"df <- sc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-all-metrics-for-comids-or-an-area-of-interest","dir":"Articles","previous_headings":"","what":"Get all metrics for COMIDs or an Area of Interest","title":"Getting Started","text":"can also get StreamCat metrics set COMIDs area interest. Please request metric=‘’ aoi=‘conus’ order overload requests server. Requesting metric=‘’ state multiple states hydroregions also take long time process.","code":"df <- sc_get_data(comid='179', aoi='cat', metric='all') knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-nlcd-data","dir":"Articles","previous_headings":"","what":"Get NLCD data","title":"Getting Started","text":"example access National Land Cover Dataset (NLCD) data 2001, just catchment level several COMIDs using sc_nlcd function. Loads data tibble can view. can also pass couple years different area interest another region like county.","code":"df <- sc_nlcd(year='2001', aoi='cat', comid='179,1337,1337420') knitr::kable(df) df <- sc_nlcd(year='2006, 2019', aoi='ws', county='41003') knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-comids","dir":"Articles","previous_headings":"","what":"Get COMIDs","title":"Getting Started","text":"example use sc_get_comid function find COMIDs USGS stream gages load R. use .csv file coordinate columns known coordinate reference system.","code":"gages = readr::read_csv(system.file(\"extdata\",\"Gages_flowdata.csv\", package = \"StreamCatTools\"),show_col_types = FALSE) # we'll just grab a few variables to keep things simple gages <- gages[,c('SOURCE_FEA','STATION_NM','LON_SITE','LAT_SITE')] gages_coms <- sc_get_comid(gages, xcoord='LON_SITE', ycoord='LAT_SITE', crsys=4269) # Add the COMID we found back to gages data frame gages$COMID <- strsplit(gages_coms, \",\")[[1]] df <- sc_get_data(metric='huden2010', aoi='ws', comid=gages_coms) df$COMID <- as.character(df$comid) gages <- dplyr::left_join(gages, df, by='COMID') knitr::kable(head(gages))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-data-for-a-hydroregion","dir":"Articles","previous_headings":"","what":"Get data for a hydroregion","title":"Getting Started","text":"example access couple watershed-metrics particular NHDPlus hydroregion using sc_get_data function.","code":"df <- sc_get_data(metric='pctwdwet2006', aoi='ws', region='Region17') knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-data-for-conus","dir":"Articles","previous_headings":"","what":"Get data for CONUS","title":"Getting Started","text":"example access metric conus using sc_get_data function - shown demonstration run takes bit time","code":"# df <- sc_get_data(metric='om', aoi='ws', conus='true') # knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"accessing-and-working-with-lakecat","dir":"Articles","previous_headings":"","what":"Accessing and working with LakeCat","title":"Working with LakeCat data","text":"StreamCatTools package designed simplify use StreamCat data R, leveraging new API StreamCat. now functionality StreamCat API accessing working LakeCat data added functions StreamCatTools access LakeCata data R using API. can actually pull data R LakeCat simply passing URL extract json. hard-wire parameters limited number records returned GET request.","code":"res <- jsonlite::fromJSON(\"https://api.epa.gov/StreamCat/lakes/metrics?name=pcturbmd2006&areaOfInterest=cat&comid=22538788\") res$items"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"list-lakecat-api-parameters","dir":"Articles","previous_headings":"","what":"List LakeCat API parameters","title":"Working with LakeCat data","text":"List LakeCat parameters: Get list available LakeCat values certain parameters using lc_get_params function (right now just metric names areas interest function) via API can also see metrics available areas interest years using sc_get_params function (returns tibble information StreamCat metrics): Look display name names metric using lc_fullname function via API","code":"library(StreamCatTools) region_params <- lc_get_params(param='aoi') name_params <- lc_get_params(param='metric_names') print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) #> [1] \"region parameters are: cat, ws\" print(paste0('A selection of available LakrCat metrics include: ',paste(name_params[1:10],collapse = ', '))) #> [1] \"A selection of available LakrCat metrics include: agkffact, al2o3, bfi, canaldens, cao, cbnf, clay, coalminedens, compstrgth, damdens\" var_info <- lc_get_params(param='variable_info') head(var_info) #> # A tibble: 6 × 13 #> category metric aoi year short_description long_description units dsid #> #> 1 Soils agkff… Cat,… NA Ag Soil Erodibil… Mean of STATSGO… Unit… 10 #> 2 Natural al2o3… Cat,… NA Mean Lithologica… Mean % of litho… Perc… 11 #> 3 Base areas… Ws NA Watershed Area S… Watershed area … Squa… NA #> 4 Climate bfi[A… Cat,… NA Base Flow Index Base flow is th… Perc… 12 #> 5 Anthropogen… canal… Cat,… NA Canal Density Density of NHDP… Kilo… 13 #> 6 Natural cao[A… Cat,… NA Mean Lithologica… Mean % of litho… Perc… 11 #> # ℹ 5 more variables: dataset , source_name , source_URL , #> # ACTIVE , DSNAME metric='pcthbwet2016' fullname <- lc_fullname(metric) fullname #> [1] \"Herbaceous Wetland Percentage 2016\" metric=c('pctdecid2019','fert') fullname <- lc_fullname(metric) fullname #> [1] \"Deciduous Forest Percentage 2019\" #> [2] \"Synthetic Nitrogen Fertilizer Application Mean Rate\""},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"filter-metric-information-by-criteria","dir":"Articles","previous_headings":"","what":"Filter metric information by criteria","title":"Working with LakeCat data","text":"can also filter metric names information metric year(s), indicator categories metrics, metric data set names, Areas Interest metrics available .","code":"metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), aoi=c('Cat','Ws')) head(metrics) #> # A tibble: 6 × 9 #> Category Metric AOI Year Short_Name Metric_Description Units Source Dataset #> #> 1 Natural al2o3… Cat,… NA Mean Lith… Mean % of litholo… Perc… USGS … USGS G… #> 2 Anthrop… canal… Cat,… NA Canal Den… Density of NHDPlu… Kilo… Falco… Canal … #> 3 Natural cao[A… Cat,… NA Mean Lith… Mean % of litholo… Perc… USGS … USGS G… #> 4 Anthrop… cbnf[… Cat,… NA Cultivate… Mean rate of biol… Kilo… Envir… Agricu… #> 5 Anthrop… coalm… Cat,… NA Coal Mine… Density of coal m… Coun… USGS … Coal M… #> 6 Natural comps… Cat,… NA Mean Lith… Mean lithological… Perc… USGS … USGS G…"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"get-waterbody-comids","dir":"Articles","previous_headings":"","what":"Get Waterbody COMIDs","title":"Working with LakeCat data","text":"example use lc_get_comid function find COMIDs set example lake locations load R.lc_get_comid just simple wrapper get_waterbodies nhdplusTools R package. can use COMIDs derive lake locations get LakeCat metrics lakes show .","code":"dd <- data.frame(x = c(-89.198,-114.125,-122.044), y = c(45.502,47.877,43.730)) |> sf::st_as_sf(coords = c('x', 'y'), crs = 4326) comids <- lc_get_comid(dd)"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"get-data-for-comids","dir":"Articles","previous_headings":"","what":"Get data for COMIDs","title":"Working with LakeCat data","text":"example access several variables, several areas interest, several COMIDs using lc_get_data function. ’ll show using COMIDS derived lc_get_comid function previous chunk well known COMIDS NHDPlus waterbodies. Loads data tibble can view.","code":"df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid=comids) knitr::kable(df) df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='23783629,23794487,23812618') knitr::kable(df)"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"get-data-for-county","dir":"Articles","previous_headings":"","what":"Get data for county","title":"Working with LakeCat data","text":"example access couple variables watershed scale area interest county (Benton County case) using sc_get_data function.","code":"df <- lc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"get-nlcd-data","dir":"Articles","previous_headings":"","what":"Get NLCD data","title":"Working with LakeCat data","text":"example access National Land Cover Dataset (NLCD) data 2019, just catchment level several COMIDs using lc_nlcd function. Loads data tibble can view.","code":"df <- lc_nlcd(comid='23783629,23794487,23812618', year='2019', aoi='ws') knitr::kable(df)"},{"path":"https://usepa.github.io/StreamCatTools/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Marc Weber. Author, maintainer. Ryan Hill. Contributor. Travis Hudson. Contributor. Allen Brookes. Contributor. David Rebhuhn. Contributor. Michael Dumelle. Contributor. Zachary Smith. Contributor.","code":""},{"path":"https://usepa.github.io/StreamCatTools/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Weber M (2025). StreamCatTools: 'StreamCatTools'. R package version 0.8.0.9000, https://github.com/USEPA/StreamCatTools, https://usepa.github.io/StreamCatTools/.","code":"@Manual{, title = {StreamCatTools: 'StreamCatTools'}, author = {Marc Weber}, year = {2025}, note = {R package version 0.8.0.9000, https://github.com/USEPA/StreamCatTools}, url = {https://usepa.github.io/StreamCatTools/}, }"},{"path":[]},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"streamcattools-tools-to-work-with-the-streamcat-api-within-r-and-access-the-full-suite-of-streamcat-and-lakecat-metrics","dir":"","previous_headings":"","what":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","title":"StreamCatTools","text":"StreamCatTools R package accessing StreamCat LakeCat data via StreamCat API working site data conjunction StreamCat NHDPlus.","code":""},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"installation","dir":"","previous_headings":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","what":"Installation","title":"StreamCatTools","text":"can install load recent approved version CRAN running can install load recent development version GitHub running: view vignettes RStudio, run","code":"# install the most recent approved version from CRAN install.packages(\"StreamCatTools\") # load the most recent approved version from CRAN library(StreamCatTools) library(remotes) install_github(\"USEPA/StreamCatTools\", build_vignettes=TRUE) library(StreamCatTools) vignette(\"Introduction\", \"StreamCatTools\") vignette(\"Applications\", \"StreamCatTools\") vignette(\"LakeCat\", \"StreamCatTools\")"},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"contributing","dir":"","previous_headings":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","what":"Contributing","title":"StreamCatTools","text":"Contributions development package welcome encouraged. Please consider following guidlelines contributing StreamCatTools: encourage package users submit bugs enhancement requests submitting issues - see Quickstart GitHub Issues page new GitHub issues Contributions use standard GitHub fork - pull-request workflow encourage use tidyverse style guide contributions Contributions ideally tested using testthat Make sure use roxygen run Check contributing contribute documentation, running devtools::document() pkgdown::build_site() refresh help docs pkgdown pages (push packagedown changes - verify changes locally)","code":""},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"python-implementation-of-streamcat-api","dir":"","previous_headings":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","what":"Python Implementation of StreamCat API","title":"StreamCatTools","text":"PyNHD, part HyRiver suite Python packages, also provides access StreamCat data via API Python, along NHDPlus value-added attributes catchments catchment network accumulated values catchments available via USGS ScienceBase","code":""},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"recommended-citation","dir":"","previous_headings":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","what":"Recommended Citation:","title":"StreamCatTools","text":"","code":"Weber, Marc H, Hill, Ryan A., Brookes, Allen F. 2024, StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics, https://usepa.github.io/StreamCatTools"},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"disclaimer","dir":"","previous_headings":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","what":"Disclaimer","title":"StreamCatTools","text":"United States Environmental Protection Agency (EPA) GitHub project code provided “” basis user assumes responsibility use. EPA relinquished control information longer responsibility protect integrity , confidentiality, availability information. reference specific commercial products, processes, services service mark, trademark, manufacturer, otherwise, constitute imply endorsement, recommendation favoring EPA. EPA seal logo shall used manner imply endorsement commercial product activity EPA United States Government.","code":""},{"path":[]},{"path":"https://usepa.github.io/StreamCatTools/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"CC0 1.0 Universal","title":"CC0 1.0 Universal","text":"CREATIVE COMMONS CORPORATION LAW FIRM PROVIDE LEGAL SERVICES. DISTRIBUTION DOCUMENT CREATE ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES INFORMATION “-” BASIS. 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Affirmer understands acknowledges Creative Commons party document duty obligation respect CC0 use Work.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":null,"dir":"Reference","previous_headings":"","what":"Lookup Full Metric Name — lc_fullname","title":"Lookup Full Metric Name — lc_fullname","text":"Function retrieve full metric name based short name using LakeCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lookup Full Metric Name — lc_fullname","text":"","code":"lc_fullname(metric = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lookup Full Metric Name — lc_fullname","text":"metric Short metric name Syntax: metric=value1 Values: metric","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lookup Full Metric Name — lc_fullname","text":"lookup full name given LakeCat metric","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Lookup Full Metric Name — lc_fullname","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lookup Full Metric Name — lc_fullname","text":"","code":"fullname <- lc_fullname(metric='clay')"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Lake COMIDs — lc_get_comid","title":"Get Lake COMIDs — lc_get_comid","text":"Function return NHDPlusV2 Waterbody COMIDS using either dataframe coordinates specified CRS sf object. function generates vector NHDPlus Waterbody COMID values user can pass lc_get_data function","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Lake COMIDs — lc_get_comid","text":"","code":"lc_get_comid( dd = NULL, xcoord = NULL, ycoord = NULL, crsys = NULL, buffer = NULL )"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Lake COMIDs — lc_get_comid","text":"dd Name data frame object. Can simple data frame coordinate columns known CRS sf points data frame xcoord x coordinate column using raw data frame ycoord y coordinate column using raw data frame crsys epsg code using raw data frame buffer amount buffer use extend search waterbody (simply passed nhdplusTools::get_waterbodies)","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Lake COMIDs — lc_get_comid","text":"new sf data frame populated 'COMID' column","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get Lake COMIDs — lc_get_comid","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Lake COMIDs — lc_get_comid","text":"","code":"if (FALSE) { # \\dontrun{ dd <- data.frame(x = c(-89.198,-114.125,-122.044), y = c(45.502,47.877,43.730)) comids <- lc_get_comid(dd, xcoord='x', ycoord='y', crsys=4269) dd <- data.frame(x = c(-89.198,-114.125,-122.044), y = c(45.502,47.877,43.730)) |> sf::st_as_sf(coords = c('x', 'y'), crs = 4326) comids <- lc_get_comid(dd) } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get LakeCat data — lc_get_data","title":"Get LakeCat data — lc_get_data","text":"Function return LakeCat metrics using StreamCat API. function allows user get specific metric data aggregated area interest, returned comid(s), hydroregion(s), state(s), county(ies).","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get LakeCat data — lc_get_data","text":"","code":"lc_get_data( comid = NULL, metric = NULL, aoi = NULL, showAreaSqKm = NULL, showPctFull = NULL, state = NULL, county = NULL, region = NULL, conus = NULL, countOnly = NULL )"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get LakeCat data — lc_get_data","text":"comid Return metric information specific COMIDs. Can comma-delimited list, character vector, object can coerced comma-delimited list paste. One comid, county, state, region required unless conus='true'. Syntax: comid=, metric Name(s) metrics query. Must character string comma-delimited list metrics. case-sensitive. Syntax: name=, aoi Specify area interest described metric. default, available areas interest given metric returned. Case-sensitive. Syntax: areaOfInterest=, Values: catchment|watershed| showAreaSqKm Return area square kilometers given area interest. default value false. Values: true|false showPctFull Return pctfull dataset. default value false. Values: true|false state Return metric information COMIDs within specific state. Use state's abbreviation query given state. One comid, county, state, region required unless conus='true'. specified valid, comid county ignored. Case-sensitive. Syntax: state=, county Return metric information COMIDs within specific county. Users must use FIPS code, county name, way disambiguate counties. One comid, county, state, region required unless conus='true'. specified valid, comid ignored. Syntax: county=, region Return metric information COMIDs within specified hydroregion. Hydroregions specified using full name .e. 'Region01', 'Region03N', 'Region10L' One comid, county, state, region required unless conus='true'. specified valid, comid, county, state ignored. Case-sensitive. Syntax: region=, conus Return COMIDs conterminous United States. Character string (case-sensitive) logical. default value false. true, comid, county, state, region ignored. Values: true|false countOnly Return CSV containing row count (ROWCOUNT) column count (COLUMNCOUNT) server expects return request. default value false. Values: true|false","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get LakeCat data — lc_get_data","text":"tibble desired StreamCat metrics. data missing rows given metric, column metric exist. data missing rows, specified NA.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get LakeCat data — lc_get_data","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get LakeCat data — lc_get_data","text":"","code":"if (FALSE) { # \\dontrun{ df <- lc_get_data(comid='23794487', aoi='cat', metric='fert') df <- lc_get_data(metric='pcturbmd2006', aoi='ws', comid='24083377') df <- lc_get_data(metric='pctgrs2006', aoi='ws', region='Region01') df <- lc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') df <- lc_get_data(metric='pcturbmd2006', aoi='ws', comid='24083377', showAreaSqKm=FALSE, showPctFull=TRUE) df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='23783629,23794487,23812618') df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid=c('23783629','23794487','23812618')) df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='23783629,23794487,23812618', countOnly=TRUE) } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Get LakeCat Metric Names — lc_get_metric_names","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"Function filter LakeCat metrics metrics category, area interest, dataset year. Use `lc_get_params(categories)` `lc_get_params(datasets)` see valid category dataset options","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"","code":"lc_get_metric_names(category = NULL, aoi = NULL, year = NULL, dataset = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"category Filter LakeCat metrics based metric category aoi Filter LakeCat metrics based area interest year Filter LakeCat metrics based particular year years dataset Filter LakeCat metrics based dataset name","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"dataframe merics description match filter criteria","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"","code":"if (FALSE) { # \\dontrun{ metrics <- lc_get_metric_names(category='Natural') metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), aoi=c('Cat','Ws'))} # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Get LakeCat Parameters — lc_get_params","title":"Get LakeCat Parameters — lc_get_params","text":"Function return available LakeCat parameters using StreamCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get LakeCat Parameters — lc_get_params","text":"","code":"lc_get_params(param = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get LakeCat Parameters — lc_get_params","text":"param List available parameters API following options: name, areaofInterest, region, state, county. State county return data frame includes FIPS codes, names state abbreviations Syntax: param=, Values: name|area","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get LakeCat Parameters — lc_get_params","text":"list current LakeCat values given parameter","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get LakeCat Parameters — lc_get_params","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get LakeCat Parameters — lc_get_params","text":"","code":"if (FALSE) { # \\dontrun{ params <- lc_get_params(param='variable_info') params <- lc_get_params(param='metric_names') params <- sc_get_params(param='categories') params <- lc_get_params(param='aoi') params <- lc_get_params(param='state') params <- lc_get_params(param='county') params <- sc_get_params(param='datasets') } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":null,"dir":"Reference","previous_headings":"","what":"Get NLCD Data — lc_nlcd","title":"Get NLCD Data — lc_nlcd","text":"Function specifically retrieve NLCD metrics given year using StreamCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get NLCD Data — lc_nlcd","text":"","code":"lc_nlcd( year = \"2019\", aoi = NULL, comid = NULL, showAreaSqKm = NULL, showPctFull = NULL, countOnly = NULL )"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get NLCD Data — lc_nlcd","text":"year Years(s) NLCD metrics query. valid NLCD years accepted (.e. 2001, 2004, 2006, 2008, 2011, 2013, 2016, 2019) Syntax: year=, aoi Specify area interest described metric. default, available areas interest given metric returned. Syntax: areaOfInterest=, Values: catchment|watershed|riparian_catchment|riparian_watershed|comid Return metric information specific COMIDs Syntax: comid=, showAreaSqKm Return area square kilometers given area interest. default value false. Values: true|false showPctFull Return pctfull dataset. default value false. Values: true|false countOnly Return CSV containing row count (ROWCOUNT) column count (COLUMNCOUNT) server expects return request. default value false. Values: true|false","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get NLCD Data — lc_nlcd","text":"tibble desired StreamCat metrics","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get NLCD Data — lc_nlcd","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get NLCD Data — lc_nlcd","text":"","code":"if (FALSE) { # \\dontrun{ df <- lc_nlcd(comid='23783629', year='2019', aoi='ws') df <- lc_nlcd(year='2016', aoi='cat', comid='23783629,23794487,23812618', showAreaSqKm=FALSE, showPctFull=TRUE) df <- lc_nlcd(year='2016', aoi='cat', comid='23783629,23794487,23812618', countOnly=TRUE) df <- lc_nlcd(year='2016, 2019', aoi='cat,ws', comid='23783629,23794487,23812618') } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":null,"dir":"Reference","previous_headings":"","what":"Lookup Full Metric Name — sc_fullname","title":"Lookup Full Metric Name — sc_fullname","text":"Function retrieve full metric name based short name using StreamCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lookup Full Metric Name — sc_fullname","text":"","code":"sc_fullname(metric = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lookup Full Metric Name — sc_fullname","text":"metric Short metric name Syntax: metric=value1 Values: metric","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lookup Full Metric Name — sc_fullname","text":"lookup full name given StreamCat metric","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Lookup Full Metric Name — sc_fullname","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lookup Full Metric Name — sc_fullname","text":"","code":"fullname <- sc_fullname(metric='clay')"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":null,"dir":"Reference","previous_headings":"","what":"Get COMIDs — sc_get_comid","title":"Get COMIDs — sc_get_comid","text":"Function return NHDPlusV2 COMIDS using either dataframe coordinates specified CRS sf object. function generates vector COMID values user can pass sc_get_data function","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get COMIDs — sc_get_comid","text":"","code":"sc_get_comid(dd = NULL, xcoord = NULL, ycoord = NULL, crsys = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get COMIDs — sc_get_comid","text":"dd Name data frame object. Can simple data frame coordinate columns known CRS sf points data frame xcoord x coordinate column using raw data frame ycoord y coordinate column using raw data frame crsys epsg code using raw data frame","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get COMIDs — sc_get_comid","text":"new sf data frame populated 'COMID' column","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get COMIDs — sc_get_comid","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get COMIDs — sc_get_comid","text":"","code":"if (FALSE) { # \\dontrun{ dd <- data.frame(x = c(-122.649,-100.348,-75.186,-106.675), y = c(45.085, 35.405,42.403,38.721)) comids <- sc_get_comid(dd, xcoord='x', ycoord='y', crsys=4269) dd <- sf::st_point_on_surface(sf::read_sf(system.file(\"shape/nc.shp\", package=\"sf\"))) comids <- sc_get_comid(dd) comids <- sc_get_comid(dd, xcoord='x', ycoord='y', crsys=4269) dd <- sf::read_sf(system.file(\"shape/nc.shp\", package=\"sf\")) comids <- sc_get_comid(dd) } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get StreamCat data — sc_get_data","title":"Get StreamCat data — sc_get_data","text":"Function return StreamCat catchment watershed metrics using StreamCat API. function allows user get specific metric data aggregated area interest, returned comid(s), hydroregion(s), state(s), county(ies).","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get StreamCat data — sc_get_data","text":"","code":"sc_get_data( comid = NULL, metric = NULL, aoi = NULL, showAreaSqKm = NULL, showPctFull = NULL, state = NULL, county = NULL, region = NULL, conus = NULL, countOnly = NULL )"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get StreamCat data — sc_get_data","text":"comid Return metric information specific COMIDs. Can comma-delimited list, character vector, object can coerced comma-delimited list paste. One comid, county, state, region required unless conus='true'. Syntax: comid=, metric Name(s) metrics query. Must character string comma-delimited list metrics, , metric='' metrics queried. case-sensitive. Syntax: name=, aoi Name(s) areas interest query. metric data given AOI, data returned AOI. Certain metrics AOI specified StreamCat need AOI specified ''. metrics include: BankfullDepth, BankfullWidth, ThalwagDepth (sic), CHEM_V2_1, CONN, HABT, HYD, ICI, IWI, TEMP, WettedWidth, prg_bmmi, mast, msst, mwst metrics. Case-sensitive. Syntax: areaOfInterest=, Values: cat|ws|catrp100|wsrp100|showAreaSqKm Return area square kilometers given area interest. default value false. Values: true|false showPctFull Return pctfull dataset. default value false. Values: true|false state Return metric information COMIDs within specific state. Use state's abbreviation query given state. One comid, county, state, region required unless conus='true'. specified valid, comid county ignored. Case-sensitive. Syntax: state=, county Return metric information COMIDs within specific county. Users must use FIPS code, county name, way disambiguate counties. One comid, county, state, region required unless conus='true'. specified valid, comid ignored. Syntax: county=, region Return metric information COMIDs within specified hydroregion. Hydroregions specified using full name .e. 'Region01', 'Region03N', 'Region10L' One comid, county, state, region required unless conus='true'. specified valid, comid, county, state ignored. Case-sensitive. Syntax: region=, conus Return COMIDs conterminous United States. Character string (case-sensitive) logical. default value false. true, comid, county, state, region ignored. Values: true|false countOnly Return CSV containing row count (ROWCOUNT) column count (COLUMNCOUNT) server expects return request. default value false. Values: true|false","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get StreamCat data — sc_get_data","text":"data frame StreamCat metrics. data missing rows given metric, column metric exist. data missing rows, specified NA.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get StreamCat data — sc_get_data","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get StreamCat data — sc_get_data","text":"","code":"if (FALSE) { # \\dontrun{ df <- sc_get_data(comid='179', aoi='cat', metric='fert') df <- sc_get_data(metric='pctgrs2006', aoi='ws', region='Region01') df <- sc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') df <- sc_get_data(metric='pcturbmd2006', aoi='wsrp100', comid='1337420') df <- sc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='179,1337,1337420') df <- sc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='179,1337,1337420', showAreaSqKm='true', showPctFull='true') df <- sc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='179,1337,1337420', countOnly='true') df <- sc_get_data(metric='thalwagdepth', comid='179,1337,1337420', aoi='other') df <- sc_get_data(metric='thalwagdepth', comid=c('179','1337','1337420'), aoi='other') df <- sc_get_data(comid='179', aoi='ws', metric='all') } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Get StreamCat Metric Names — sc_get_metric_names","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"Function filter StreamCat metrics metrics category, area interest, dataset year. Use `sc_get_params(categories)` `sc_get_params(datasets)` see valid category dataset options","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"","code":"sc_get_metric_names(category = NULL, aoi = NULL, year = NULL, dataset = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"category Filter StreamCat metrics based metric category aoi Filter StreamCat metrics based area interest year Filter StreamCat metrics based particular year years dataset Filter StreamCat metrics based dataset name","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"dataframe merics description match filter criteria","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"","code":"if (FALSE) { # \\dontrun{ metrics <- sc_get_metric_names(category='Wildfire') metrics <- sc_get_metric_names(category = c('Deposition','Climate'), aoi=c('Cat','Ws')) metrics <- sc_get_metric_names(aoi='Other', dataset=c('Canal Density','Predicted Channel Widths Depths')) } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Get StreamCat Parameters — sc_get_params","title":"Get StreamCat Parameters — sc_get_params","text":"Function return available StreamCat parameters using StreamCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get StreamCat Parameters — sc_get_params","text":"","code":"sc_get_params(param = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get StreamCat Parameters — sc_get_params","text":"param List available parameters API following options: name, areaofInterest, region, state, county. State county return data frame includes FIPS codes, names state abbreviations Syntax: param=, Values: name|area","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get StreamCat Parameters — sc_get_params","text":"list current StreamCat values given parameter","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get StreamCat Parameters — sc_get_params","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get StreamCat Parameters — sc_get_params","text":"","code":"if (FALSE) { # \\dontrun{ params <- sc_get_params(param='variable_info') params <- sc_get_params(param='metric_names') params <- sc_get_params(param='categories') params <- sc_get_params(param='aoi') params <- sc_get_params(param='state') params <- sc_get_params(param='county') params <- sc_get_params(param='datasets')} # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":null,"dir":"Reference","previous_headings":"","what":"Get NLCD Data — sc_nlcd","title":"Get NLCD Data — sc_nlcd","text":"Function retrieve NLCD metrics given year using StreamCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get NLCD Data — sc_nlcd","text":"","code":"sc_nlcd( year = \"2019\", comid = NULL, aoi = NULL, showAreaSqKm = NULL, showPctFull = NULL, state = NULL, county = NULL, region = NULL, conus = NULL, countOnly = NULL )"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get NLCD Data — sc_nlcd","text":"year Years(s) NLCD metrics query. valid NLCD years accepted (.e. 2001, 2004, 2006, 2008, 2011, 2013, 2016, 2019) Syntax: year=, comid Return metric information specific COMIDs Syntax: comid=, aoi Specify area interest described metric. default, available areas interest given metric returned. Syntax: areaOfInterest=, Values: catchment|watershed|riparian_catchment|riparian_watershed|showAreaSqKm Return area square kilometers given area interest. default value false. Values: true|false showPctFull Return pctfull dataset. default value false. Values: true|false state Return metric information COMIDs within specific state. Use state's abbreviation query given state. Syntax: state=, county Return metric information COMIDs within specific county. Users must use FIPS code, county name, way disambiguate counties. Syntax: county=, region Return metric information COMIDs within specified hydroregion. Syntax: region=, conus Return COMIDs conterminous United States. default value false. Values: true|false countOnly Return CSV containing row count (ROWCOUNT) column count (COLUMNCOUNT) server expects return request. default value false. Values: true|false","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get NLCD Data — sc_nlcd","text":"tibble desired StreamCat metrics","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get NLCD Data — sc_nlcd","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get NLCD Data — sc_nlcd","text":"","code":"if (FALSE) { # \\dontrun{ df <- sc_nlcd(year='2001', aoi='cat',comid='179,1337,1337420') df <- sc_nlcd(year='2001', aoi='ws', region='Region01') df <- sc_nlcd(year='2001', aoi='ws', region='Region01', countOnly=TRUE) df <- sc_nlcd(year='2001', aoi='ws', region='Region01', showAreaSqKm=FALSE, showPctFull=TRUE) df <- sc_nlcd(year='2001, 2006', aoi='cat,ws', comid='179,1337,1337420') } # }"},{"path":[]},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-080","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.8.0","title":"StreamCatTools 0.8.0","text":"CRAN release: 2025-10-09 Added code coverage package Added two new functions - sc_get_metric_names lc_get_metric_names make metric names descriptions searchable slightly updated parameters sc_get_params lc_get_params functions sc_get_data lc_get_data now accept vectors well comma- separated strings metric, state, county region parameters","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-070","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.7.0","title":"StreamCatTools 0.7.0","text":"CRAN release: 2025-09-15 Updated sc_get_data lc_get_data pass parameters POST request body rather header, providing ability pass lengthy lists COMIDS requests Fixed bug package tests causing error running testthat","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-060","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.6.0","title":"StreamCatTools 0.6.0","text":"CRAN release: 2025-09-02 Added functionality sc_get_data lc_get_data accommodate large numbers (e.g. > 700) COMIDs header POST request","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-050","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.5.0","title":"StreamCatTools 0.5.0","text":"Overhauled sc_get_data lc_get_data functions able pull metrics StreamCat LakeCat area interest Updated sc_get_data lc_get_data able pass hundreds COMIDs time function parameter error call server Updated sc_get_params lc_get_params now return variable information, well just metric names full names, return tables state county abbreviations, names FIPS codes","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-040","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.4.0","title":"StreamCatTools 0.4.0","text":"Overhauled functions use new api.epa.gov endpoints StreamCat described swagger documentation Streamlined sc_get_data lc_get_data requests httr2 Adopted functionality package functions use Oracle ORDs Database REST API rather previous JAVA REST service","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-030","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.3.0","title":"StreamCatTools 0.3.0","text":"Incorporated POST requests httr2 requests deal many COMIDs requests Added documentation vignette working LakeCat data package","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-020","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.2.0","title":"StreamCatTools 0.2.0","text":"lc_get_data lc_get_params Changed lifecycle stable","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-0119002","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.1.1.9002","title":"StreamCatTools 0.1.1.9002","text":"Fixed sc_get_data pass COMIDs function robustly Added sc_nlcd helper function easily grab NLCD based metrics StreamCat Updated package documentation","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-0119001","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.1.1.9001","title":"StreamCatTools 0.1.1.9001","text":"API publicly released package works now everyone (just inside EPA network)","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-0119000","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.1.1.9000","title":"StreamCatTools 0.1.1.9000","text":"Added NEWS.md file track changes package.","code":""}] +[{"path":"https://usepa.github.io/StreamCatTools/articles/Applications.html","id":"plotting-watershed-data","dir":"Articles","previous_headings":"","what":"Plotting watershed data","title":"Applications","text":"example access single variable Calapooia River using sc_get_data function. use nhdplusTools library grab flowlines watershed Calapooia, plot selected StreamCat metric Calapooia River show watershed.","code":"library(StreamCatTools) start_comid = 23763517 nldi_feature <- list(featureSource = \"comid\", featureID = start_comid) flowline_nldi <- nhdplusTools::navigate_nldi(nldi_feature, mode = \"UT\", data_source = \"flowlines\", distance=5000) # get StreamCat metrics df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=flowline_nldi$UT_flowlines$nhdplus_comid) # We can also pull out comids the following way: # comids <- paste(as.integer(flowline_nldi$UT_flowlines$nhdplus_comid), collapse=\",\",sep=\"\") # df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=comids) flowline_nldi <- flowline_nldi$UT_flowlines flowline_nldi$PCTIMP2011CAT <- df$pctimp2011cat[match(flowline_nldi$nhdplus_comid, df$comid)] basin <- nhdplusTools::get_nldi_basin(nldi_feature = nldi_feature) library(mapview) mapview::mapviewOptions(fgb=FALSE) mapview::mapview(basin, alpha.regions=.08) + mapview::mapview(flowline_nldi, zcol = \"PCTIMP2011CAT\", legend = TRUE)"},{"path":"https://usepa.github.io/StreamCatTools/articles/Applications.html","id":"working-with-nars-data","dir":"Articles","previous_headings":"","what":"Working with NARS data","title":"Applications","text":"example demonstrate data ‘mashup’ grabbing NRSA data EPA National Aquatic Resource Surveys (NARS) website directly R, pull particular StreamCat metrics sites using sc_get_data, compare landscape metrics NRSA metrics","code":"nrsa <- readr::read_csv(\"https://www.epa.gov/sites/production/files/2015-09/siteinfo_0.csv\") dplyr::glimpse(nrsa) # Promote data frame to sf spatial points data frame nrsa_sf <- sf::st_as_sf(nrsa, coords = c(\"LON_DD83\", \"LAT_DD83\"), crs = 4269) # Get COMIDs using nhdplusTools package # nrsa$COMID<- NA # for (i in 1:nrow(nrsa_sf)){ # print (i) # nrsa_sf[i,'COMID'] <- discover_nhdplus_id(nrsa_sf[i,c('geometry')]) # } load(system.file(\"extdata\", \"sample_nrsa_data.rda\", package=\"StreamCatTools\")) # get particular StreamCat data for all these NRSA sites # nrsa_sf$COMID <- as.character(nrsa_sf$COMID) comids <- nrsa_sf$COMID comids <- comids[!is.na(comids)] comids <- comids[c(1:700)] comids <- paste(comids,collapse=',') df <- sc_get_data(metric='pctcrop2006', aoi='ws', comid=comids) # glimpse(df) df$COMID <- as.integer(df$comid) nrsa_sf <- dplyr::left_join(nrsa_sf, df, by='COMID') # download mmi from NARS web page library(dplyr) library(ggplot2) mmi <- readr::read_csv(\"https://www.epa.gov/sites/production/files/2015-09/bentcond.csv\") # dplyr::glimpse(mmi) # join mmi to NARS info data frame with StreamCat PctCrop metric nrsa_sf <- dplyr::left_join(nrsa_sf, mmi[,c('SITE_ID','BENT_MMI_COND')], by='SITE_ID') bxplt <- nrsa_sf %>% tidyr::drop_na(BENT_MMI_COND) %>% ggplot2::ggplot(aes(x=pctcrop2006ws, y=BENT_MMI_COND))+ ggplot2::geom_boxplot()+ ggplot2::ggtitle('NRSA Benthic MMI versus % Crop in Watershed from 2006 NLCD') suppressWarnings(print(bxplt))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"installing-and-loading-streamcattools","dir":"Articles","previous_headings":"","what":"Installing and loading StreamCatTools","title":"Getting Started","text":"install, currently need install GitHub using devtools installing load library","code":"library(devtools) install_github('USEPA/StreamCatTools') library(StreamCatTools)"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"background","dir":"Articles","previous_headings":"","what":"Background","title":"Getting Started","text":"StreamCatTools package designed simplify use StreamCat data R, leveraging new API StreamCat.","code":""},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"streamcat-api","dir":"Articles","previous_headings":"","what":"StreamCat API","title":"Getting Started","text":"can pull data R StreamCat API simply passing URL extract json. hard-wire parameters though limited number records returned GET request.","code":"res <- jsonlite::fromJSON(\"https://api.epa.gov/StreamCat/streams/metrics?name=fert&areaOfInterest=cat&comid=179\") res$items #> fertws fertcat comid #> 1 1.438 1.438 179"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"list-api-parameters","dir":"Articles","previous_headings":"","what":"List API parameters","title":"Getting Started","text":"List StreamCat parameters: Get list available StreamCat values certain parameters using sc_get_params function via API can also see metrics available areas interest years using sc_get_params function (returns tibble information StreamCat metrics): can look display name names metric using sc_fullname function via API can additionally get data frame state FIPS codes, abbreviations names, information counties well using sc_get_params:","code":"region_params <- sc_get_params(param='aoi') name_params <- sc_get_params(param='metric_names') print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) #> [1] \"region parameters are: cat, catrp100, other, ws, wsrp100\" print(paste0('A selection of available StreamCat metrics include: ',paste(name_params[1:10],collapse = ', '))) #> [1] \"A selection of available StreamCat metrics include: agkffact, al2o3, bankfulldepth, bankfullwidth, bfi, canaldens, cao, cbnf, chem, clay\" var_info <- sc_get_params(param='variable_info') head(var_info) #> # A tibble: 6 × 13 #> category metric aoi year short_description long_description units dsid #> #> 1 Anthropogen… NABD_… Cat,… NA NABD Dam Density Density of geor… Coun… 33 #> 2 Anthropogen… NABD_… Cat,… NA NABD NID Reservo… Volume all rese… Cubi… 33 #> 3 Anthropogen… NABD_… Cat,… NA NABD Normal Rese… Volume all rese… Cubi… 33 #> 4 Natural Preci… Cat,… NA Surplus Precipit… This dataset re… Kilo… 75 #> 5 Soils Rckde… Cat,… NA Mean Bedrock Dep… Mean depth (cm)… Cent… 56 #> 6 Soils agkff… Cat,… NA Ag Soil Erodibil… Mean of STATSGO… Unit… 28 #> # ℹ 5 more variables: dataset , source_name , source_URL , #> # ACTIVE , DSNAME metric='pcthbwet2011' fullname <- sc_fullname(metric) fullname #> [1] \"Herbaceous Wetland Percentage 2011\" metric='pctdecid2019,fert' fullname <- sc_fullname(metric) fullname #> character(0) states <- sc_get_params(param='state') head(states) #> st_fips st_abbr st_name #> 30 01 AL Alabama #> 8 04 AZ Arizona #> 25 05 AR Arkansas #> 6 06 CA California #> 15 08 CO Colorado #> 50 09 CT Connecticut counties <- sc_get_params(param='county') head(counties) #> fips state county_name #> 752 01001 AL Autauga County #> 713 01003 AL Baldwin County #> 655 01005 AL Barbour County #> 755 01007 AL Bibb County #> 748 01009 AL Blount County #> 656 01011 AL Bullock County"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"filter-metric-information-by-criteria","dir":"Articles","previous_headings":"","what":"Filter metric information by criteria","title":"Getting Started","text":"can also filter metric names information metric year(s), indicator categories metrics, metric data set names, Areas Interest metrics available .","code":"metrics <- sc_get_metric_names(category = c('Deposition','Climate'),aoi=c('Cat','Ws')) head(metrics) #> # A tibble: 6 × 9 #> Category Metric AOI Year Short_Name Metric_Description Units Source Dataset #> #> 1 Climate bfi[A… Cat,… NA Base Flow… Base flow is the … Perc… USGS … Base F… #> 2 Deposit… inorg… Cat,… 2008 Mean Annu… Annual gradient m… Kilo… NADP NADP #> 3 Deposit… nh4[Y… Cat,… 2008 Mean annu… Annual gradient m… Kilo… NADP NADP #> 4 Deposit… no3[Y… Cat,… 2008 Mean Annu… Annual gradient m… Kilo… NADP NADP #> 5 Climate preci… Cat,… NA 30-year M… PRISM climate dat… Mill… PRISM PRISM #> 6 Climate preci… Cat,… 1991… 30-year M… PRISM climate dat… Mill… PRISM PRISM"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-data-for-comids","dir":"Articles","previous_headings":"","what":"Get data for COMIDs","title":"Getting Started","text":"example access several variables, several areas interest, several COMIDs using sc_get_data function. Loads data tibble can view.","code":"df <- sc_get_data(metric='pcturbmd2006,damdens,tridens', aoi='rp100cat,cat,ws', comid='179,1337,1337420') knitr::kable(df)"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-data-for-county","dir":"Articles","previous_headings":"","what":"Get data for county","title":"Getting Started","text":"example access couple variables watershed scale area interest county (Benton County case) using sc_get_data function.","code":"df <- sc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-all-metrics-for-comids-or-an-area-of-interest","dir":"Articles","previous_headings":"","what":"Get all metrics for COMIDs or an Area of Interest","title":"Getting Started","text":"can also get StreamCat metrics set COMIDs area interest. Please request metric=‘’ aoi=‘conus’ order overload requests server. Requesting metric=‘’ state multiple states hydroregions also take long time process.","code":"df <- sc_get_data(comid='179', aoi='cat', metric='all') knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-nlcd-data","dir":"Articles","previous_headings":"","what":"Get NLCD data","title":"Getting Started","text":"example access National Land Cover Dataset (NLCD) data 2001, just catchment level several COMIDs using sc_nlcd function. Loads data tibble can view. can also pass couple years different area interest another region like county.","code":"df <- sc_nlcd(year='2001', aoi='cat', comid='179,1337,1337420') knitr::kable(df) df <- sc_nlcd(year='2006, 2019', aoi='ws', county='41003') knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-comids","dir":"Articles","previous_headings":"","what":"Get COMIDs","title":"Getting Started","text":"example use sc_get_comid function find COMIDs USGS stream gages load R. use .csv file coordinate columns known coordinate reference system.","code":"gages = readr::read_csv(system.file(\"extdata\",\"Gages_flowdata.csv\", package = \"StreamCatTools\"),show_col_types = FALSE) # we'll just grab a few variables to keep things simple gages <- gages[,c('SOURCE_FEA','STATION_NM','LON_SITE','LAT_SITE')] gages_coms <- sc_get_comid(gages, xcoord='LON_SITE', ycoord='LAT_SITE', crsys=4269) # Add the COMID we found back to gages data frame gages$COMID <- strsplit(gages_coms, \",\")[[1]] df <- sc_get_data(metric='huden2010', aoi='ws', comid=gages_coms) df$COMID <- as.character(df$comid) gages <- dplyr::left_join(gages, df, by='COMID') knitr::kable(head(gages))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-data-for-a-hydroregion","dir":"Articles","previous_headings":"","what":"Get data for a hydroregion","title":"Getting Started","text":"example access couple watershed-metrics particular NHDPlus hydroregion using sc_get_data function.","code":"df <- sc_get_data(metric='pctwdwet2006', aoi='ws', region='Region17') knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/Introduction.html","id":"get-data-for-conus","dir":"Articles","previous_headings":"","what":"Get data for CONUS","title":"Getting Started","text":"example access metric conus using sc_get_data function - shown demonstration run takes bit time","code":"# df <- sc_get_data(metric='om', aoi='ws', conus='true') # knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"accessing-and-working-with-lakecat","dir":"Articles","previous_headings":"","what":"Accessing and working with LakeCat","title":"Working with LakeCat data","text":"StreamCatTools package designed simplify use StreamCat data R, leveraging new API StreamCat. now functionality StreamCat API accessing working LakeCat data added functions StreamCatTools access LakeCata data R using API. can actually pull data R LakeCat simply passing URL extract json. hard-wire parameters limited number records returned GET request.","code":"res <- jsonlite::fromJSON(\"https://api.epa.gov/StreamCat/lakes/metrics?name=pcturbmd2006&areaOfInterest=cat&comid=22538788\") res$items"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"list-lakecat-api-parameters","dir":"Articles","previous_headings":"","what":"List LakeCat API parameters","title":"Working with LakeCat data","text":"List LakeCat parameters: Get list available LakeCat values certain parameters using lc_get_params function (right now just metric names areas interest function) via API can also see metrics available areas interest years using sc_get_params function (returns tibble information StreamCat metrics): Look display name names metric using lc_fullname function via API","code":"library(StreamCatTools) region_params <- lc_get_params(param='aoi') name_params <- lc_get_params(param='metric_names') print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) #> [1] \"region parameters are: cat, ws\" print(paste0('A selection of available LakrCat metrics include: ',paste(name_params[1:10],collapse = ', '))) #> [1] \"A selection of available LakrCat metrics include: agkffact, al2o3, bfi, canaldens, cao, cbnf, clay, coalminedens, compstrgth, damdens\" var_info <- lc_get_params(param='variable_info') head(var_info) #> # A tibble: 6 × 13 #> category metric aoi year short_description long_description units dsid #> #> 1 Soils agkff… Cat,… NA Ag Soil Erodibil… Mean of STATSGO… Unit… 10 #> 2 Natural al2o3… Cat,… NA Mean Lithologica… Mean % of litho… Perc… 11 #> 3 Base areas… Ws NA Watershed Area S… Watershed area … Squa… NA #> 4 Climate bfi[A… Cat,… NA Base Flow Index Base flow is th… Perc… 12 #> 5 Anthropogen… canal… Cat,… NA Canal Density Density of NHDP… Kilo… 13 #> 6 Natural cao[A… Cat,… NA Mean Lithologica… Mean % of litho… Perc… 11 #> # ℹ 5 more variables: dataset , source_name , source_URL , #> # ACTIVE , DSNAME metric='pcthbwet2016' fullname <- lc_fullname(metric) fullname #> [1] \"Herbaceous Wetland Percentage 2016\" metric=c('pctdecid2019','fert') fullname <- lc_fullname(metric) fullname #> [1] \"Deciduous Forest Percentage 2019\" #> [2] \"Synthetic Nitrogen Fertilizer Application Mean Rate\""},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"filter-metric-information-by-criteria","dir":"Articles","previous_headings":"","what":"Filter metric information by criteria","title":"Working with LakeCat data","text":"can also filter metric names information metric year(s), indicator categories metrics, metric data set names, Areas Interest metrics available .","code":"metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), aoi=c('Cat','Ws')) head(metrics) #> # A tibble: 6 × 9 #> Category Metric AOI Year Short_Name Metric_Description Units Source Dataset #> #> 1 Natural al2o3… Cat,… NA Mean Lith… Mean % of litholo… Perc… USGS … USGS G… #> 2 Anthrop… canal… Cat,… NA Canal Den… Density of NHDPlu… Kilo… Falco… Canal … #> 3 Natural cao[A… Cat,… NA Mean Lith… Mean % of litholo… Perc… USGS … USGS G… #> 4 Anthrop… cbnf[… Cat,… NA Cultivate… Mean rate of biol… Kilo… Envir… Agricu… #> 5 Anthrop… coalm… Cat,… NA Coal Mine… Density of coal m… Coun… USGS … Coal M… #> 6 Natural comps… Cat,… NA Mean Lith… Mean lithological… Perc… USGS … USGS G…"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"get-waterbody-comids","dir":"Articles","previous_headings":"","what":"Get Waterbody COMIDs","title":"Working with LakeCat data","text":"example use lc_get_comid function find COMIDs set example lake locations load R.lc_get_comid just simple wrapper get_waterbodies nhdplusTools R package. can use COMIDs derive lake locations get LakeCat metrics lakes show .","code":"dd <- data.frame(x = c(-89.198,-114.125,-122.044), y = c(45.502,47.877,43.730)) |> sf::st_as_sf(coords = c('x', 'y'), crs = 4326) comids <- lc_get_comid(dd)"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"get-data-for-comids","dir":"Articles","previous_headings":"","what":"Get data for COMIDs","title":"Working with LakeCat data","text":"example access several variables, several areas interest, several COMIDs using lc_get_data function. ’ll show using COMIDS derived lc_get_comid function previous chunk well known COMIDS NHDPlus waterbodies. Loads data tibble can view.","code":"df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid=comids) knitr::kable(df) df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='23783629,23794487,23812618') knitr::kable(df)"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"get-data-for-county","dir":"Articles","previous_headings":"","what":"Get data for county","title":"Working with LakeCat data","text":"example access couple variables watershed scale area interest county (Benton County case) using sc_get_data function.","code":"df <- lc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') knitr::kable(head(df))"},{"path":"https://usepa.github.io/StreamCatTools/articles/LakeCat.html","id":"get-nlcd-data","dir":"Articles","previous_headings":"","what":"Get NLCD data","title":"Working with LakeCat data","text":"example access National Land Cover Dataset (NLCD) data 2019, just catchment level several COMIDs using lc_nlcd function. Loads data tibble can view.","code":"df <- lc_nlcd(comid='23783629,23794487,23812618', year='2019', aoi='ws') knitr::kable(df)"},{"path":"https://usepa.github.io/StreamCatTools/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Marc Weber. Author, maintainer. Ryan Hill. Contributor. Travis Hudson. Contributor. Allen Brookes. Contributor. David Rebhuhn. Contributor. Michael Dumelle. Contributor. Zachary Smith. Contributor.","code":""},{"path":"https://usepa.github.io/StreamCatTools/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Weber M (2025). StreamCatTools: 'StreamCatTools'. R package version 0.9.0.9000, https://github.com/USEPA/StreamCatTools, https://usepa.github.io/StreamCatTools/.","code":"@Manual{, title = {StreamCatTools: 'StreamCatTools'}, author = {Marc Weber}, year = {2025}, note = {R package version 0.9.0.9000, https://github.com/USEPA/StreamCatTools}, url = {https://usepa.github.io/StreamCatTools/}, }"},{"path":[]},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"streamcattools-tools-to-work-with-the-streamcat-api-within-r-and-access-the-full-suite-of-streamcat-and-lakecat-metrics","dir":"","previous_headings":"","what":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","title":"StreamCatTools","text":"StreamCatTools R package accessing StreamCat LakeCat data via StreamCat API working site data conjunction StreamCat NHDPlus.","code":""},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"installation","dir":"","previous_headings":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","what":"Installation","title":"StreamCatTools","text":"can install load recent approved version CRAN running can install load recent development version GitHub running: view vignettes RStudio, run","code":"# install the most recent approved version from CRAN install.packages(\"StreamCatTools\") # load the most recent approved version from CRAN library(StreamCatTools) library(remotes) install_github(\"USEPA/StreamCatTools\", build_vignettes=TRUE) library(StreamCatTools) vignette(\"Introduction\", \"StreamCatTools\") vignette(\"Applications\", \"StreamCatTools\") vignette(\"LakeCat\", \"StreamCatTools\")"},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"contributing","dir":"","previous_headings":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","what":"Contributing","title":"StreamCatTools","text":"Contributions development package welcome encouraged. Please consider following guidlelines contributing StreamCatTools: encourage package users submit bugs enhancement requests submitting issues - see Quickstart GitHub Issues page new GitHub issues Contributions use standard GitHub fork - pull-request workflow encourage use tidyverse style guide contributions Contributions ideally tested using testthat Make sure use roxygen run Check contributing contribute documentation, running devtools::document() pkgdown::build_site() refresh help docs pkgdown pages (push packagedown changes - verify changes locally)","code":""},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"python-implementation-of-streamcat-api","dir":"","previous_headings":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","what":"Python Implementation of StreamCat API","title":"StreamCatTools","text":"PyNHD, part HyRiver suite Python packages, also provides access StreamCat data via API Python, along NHDPlus value-added attributes catchments catchment network accumulated values catchments available via USGS ScienceBase","code":""},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"recommended-citation","dir":"","previous_headings":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","what":"Recommended Citation:","title":"StreamCatTools","text":"","code":"Weber, Marc H, Hill, Ryan A., Brookes, Allen F. 2024, StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics, https://usepa.github.io/StreamCatTools"},{"path":"https://usepa.github.io/StreamCatTools/index.html","id":"disclaimer","dir":"","previous_headings":"StreamCatTools: Tools to work with the StreamCat API within R and access the full suite of StreamCat and LakeCat metrics.","what":"Disclaimer","title":"StreamCatTools","text":"United States Environmental Protection Agency (EPA) GitHub project code provided “” basis user assumes responsibility use. EPA relinquished control information longer responsibility protect integrity , confidentiality, availability information. reference specific commercial products, processes, services service mark, trademark, manufacturer, otherwise, constitute imply endorsement, recommendation favoring EPA. EPA seal logo shall used manner imply endorsement commercial product activity EPA United States Government.","code":""},{"path":[]},{"path":"https://usepa.github.io/StreamCatTools/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"CC0 1.0 Universal","title":"CC0 1.0 Universal","text":"CREATIVE COMMONS CORPORATION LAW FIRM PROVIDE LEGAL SERVICES. DISTRIBUTION DOCUMENT CREATE ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES INFORMATION “-” BASIS. CREATIVE COMMONS MAKES WARRANTIES REGARDING USE DOCUMENT INFORMATION WORKS PROVIDED HEREUNDER, DISCLAIMS LIABILITY DAMAGES RESULTING USE DOCUMENT INFORMATION WORKS PROVIDED HEREUNDER.","code":""},{"path":"https://usepa.github.io/StreamCatTools/LICENSE.html","id":"statement-of-purpose","dir":"","previous_headings":"","what":"Statement of Purpose","title":"CC0 1.0 Universal","text":"laws jurisdictions throughout world automatically confer exclusive Copyright Related Rights (defined ) upon creator subsequent owner(s) (, “owner”) original work authorship /database (, “Work”). 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Affirmer understands acknowledges Creative Commons party document duty obligation respect CC0 use Work.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":null,"dir":"Reference","previous_headings":"","what":"Lookup Full Metric Name — lc_fullname","title":"Lookup Full Metric Name — lc_fullname","text":"Function retrieve full metric name based short name using LakeCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lookup Full Metric Name — lc_fullname","text":"","code":"lc_fullname(metric = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lookup Full Metric Name — lc_fullname","text":"metric Short metric name Syntax: metric=value1 Values: metric","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lookup Full Metric Name — lc_fullname","text":"lookup full name given LakeCat metric","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Lookup Full Metric Name — lc_fullname","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_fullname.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lookup Full Metric Name — lc_fullname","text":"","code":"fullname <- lc_fullname(metric='clay')"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Lake COMIDs — lc_get_comid","title":"Get Lake COMIDs — lc_get_comid","text":"Function return NHDPlusV2 Waterbody COMIDS using either dataframe coordinates specified CRS sf object. function generates vector NHDPlus Waterbody COMID values user can pass lc_get_data function","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Lake COMIDs — lc_get_comid","text":"","code":"lc_get_comid( dd = NULL, xcoord = NULL, ycoord = NULL, crsys = NULL, buffer = NULL )"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Lake COMIDs — lc_get_comid","text":"dd Name data frame object. Can simple data frame coordinate columns known CRS sf points data frame xcoord x coordinate column using raw data frame ycoord y coordinate column using raw data frame crsys epsg code using raw data frame buffer amount buffer use extend search waterbody (simply passed nhdplusTools::get_waterbodies)","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Lake COMIDs — lc_get_comid","text":"new sf data frame populated 'COMID' column","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get Lake COMIDs — lc_get_comid","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_comid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Lake COMIDs — lc_get_comid","text":"","code":"if (FALSE) { # \\dontrun{ dd <- data.frame(x = c(-89.198,-114.125,-122.044), y = c(45.502,47.877,43.730)) comids <- lc_get_comid(dd, xcoord='x', ycoord='y', crsys=4269) dd <- data.frame(x = c(-89.198,-114.125,-122.044), y = c(45.502,47.877,43.730)) |> sf::st_as_sf(coords = c('x', 'y'), crs = 4326) comids <- lc_get_comid(dd) } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get LakeCat data — lc_get_data","title":"Get LakeCat data — lc_get_data","text":"Function return LakeCat metrics using StreamCat API. function allows user get specific metric data aggregated area interest, returned comid(s), hydroregion(s), state(s), county(ies).","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get LakeCat data — lc_get_data","text":"","code":"lc_get_data( comid = NULL, metric = NULL, aoi = NULL, showAreaSqKm = NULL, showPctFull = NULL, state = NULL, county = NULL, region = NULL, conus = NULL, countOnly = NULL )"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get LakeCat data — lc_get_data","text":"comid Return metric information specific COMIDs. Can comma-delimited list, character vector, object can coerced comma-delimited list paste. One comid, county, state, region required unless conus='true'. Syntax: comid=, metric Name(s) metrics query. Must character string comma-delimited list metrics. case-sensitive. Syntax: name=, aoi Specify area interest described metric. default, available areas interest given metric returned. Case-sensitive. Syntax: areaOfInterest=, Values: catchment|watershed| showAreaSqKm Return area square kilometers given area interest. default value false. Values: true|false showPctFull Return pctfull dataset. default value false. Values: true|false state Return metric information COMIDs within specific state. Use state's abbreviation query given state. One comid, county, state, region required unless conus='true'. specified valid, comid county ignored. Case-sensitive. Syntax: state=, county Return metric information COMIDs within specific county. Users must use FIPS code, county name, way disambiguate counties. One comid, county, state, region required unless conus='true'. specified valid, comid ignored. Syntax: county=, region Return metric information COMIDs within specified hydroregion. Hydroregions specified using full name .e. 'Region01', 'Region03N', 'Region10L' One comid, county, state, region required unless conus='true'. specified valid, comid, county, state ignored. Case-sensitive. Syntax: region=, conus Return COMIDs conterminous United States. Character string (case-sensitive) logical. default value false. true, comid, county, state, region ignored. Values: true|false countOnly Return CSV containing row count (ROWCOUNT) column count (COLUMNCOUNT) server expects return request. default value false. Values: true|false","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get LakeCat data — lc_get_data","text":"tibble desired StreamCat metrics. data missing rows given metric, column metric exist. data missing rows, specified NA.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get LakeCat data — lc_get_data","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get LakeCat data — lc_get_data","text":"","code":"if (FALSE) { # \\dontrun{ df <- lc_get_data(comid='23794487', aoi='cat', metric='fert') df <- lc_get_data(metric='pcturbmd2006', aoi='ws', comid='24083377') df <- lc_get_data(metric='pctgrs2006', aoi='ws', region='Region01') df <- lc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') df <- lc_get_data(metric='pcturbmd2006', aoi='ws', comid='24083377', showAreaSqKm=FALSE, showPctFull=TRUE) df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='23783629,23794487,23812618') df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid=c('23783629','23794487','23812618')) df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='23783629,23794487,23812618', countOnly=TRUE) } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Get LakeCat Metric Names — lc_get_metric_names","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"Function filter LakeCat metrics metrics category, area interest, dataset year. Use `lc_get_params(categories)` `lc_get_params(datasets)` see valid category dataset options","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"","code":"lc_get_metric_names(category = NULL, aoi = NULL, year = NULL, dataset = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"category Filter LakeCat metrics based metric category aoi Filter LakeCat metrics based area interest year Filter LakeCat metrics based particular year years dataset Filter LakeCat metrics based dataset name","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"dataframe merics description match filter criteria","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_metric_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get LakeCat Metric Names — lc_get_metric_names","text":"","code":"if (FALSE) { # \\dontrun{ metrics <- lc_get_metric_names(category='Natural') metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), aoi=c('Cat','Ws'))} # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Get LakeCat Parameters — lc_get_params","title":"Get LakeCat Parameters — lc_get_params","text":"Function return available LakeCat parameters using StreamCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get LakeCat Parameters — lc_get_params","text":"","code":"lc_get_params(param = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get LakeCat Parameters — lc_get_params","text":"param List available parameters API following options: name, areaofInterest, region, state, county. State county return data frame includes FIPS codes, names state abbreviations Syntax: param=, Values: name|area","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get LakeCat Parameters — lc_get_params","text":"list current LakeCat values given parameter","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get LakeCat Parameters — lc_get_params","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_get_params.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get LakeCat Parameters — lc_get_params","text":"","code":"if (FALSE) { # \\dontrun{ params <- lc_get_params(param='variable_info') params <- lc_get_params(param='metric_names') params <- sc_get_params(param='categories') params <- lc_get_params(param='aoi') params <- lc_get_params(param='state') params <- lc_get_params(param='county') params <- sc_get_params(param='datasets') } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":null,"dir":"Reference","previous_headings":"","what":"Get NLCD Data — lc_nlcd","title":"Get NLCD Data — lc_nlcd","text":"Function specifically retrieve NLCD metrics given year using StreamCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get NLCD Data — lc_nlcd","text":"","code":"lc_nlcd( year = \"2019\", aoi = NULL, comid = NULL, showAreaSqKm = NULL, showPctFull = NULL, countOnly = NULL )"},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get NLCD Data — lc_nlcd","text":"year Years(s) NLCD metrics query. valid NLCD years accepted (.e. 2001, 2004, 2006, 2008, 2011, 2013, 2016, 2019) Syntax: year=, aoi Specify area interest described metric. default, available areas interest given metric returned. Syntax: areaOfInterest=, Values: catchment|watershed|riparian_catchment|riparian_watershed|comid Return metric information specific COMIDs Syntax: comid=, showAreaSqKm Return area square kilometers given area interest. default value false. Values: true|false showPctFull Return pctfull dataset. default value false. Values: true|false countOnly Return CSV containing row count (ROWCOUNT) column count (COLUMNCOUNT) server expects return request. default value false. Values: true|false","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get NLCD Data — lc_nlcd","text":"tibble desired StreamCat metrics","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get NLCD Data — lc_nlcd","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/lc_nlcd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get NLCD Data — lc_nlcd","text":"","code":"if (FALSE) { # \\dontrun{ df <- lc_nlcd(comid='23783629', year='2019', aoi='ws') df <- lc_nlcd(year='2016', aoi='cat', comid='23783629,23794487,23812618', showAreaSqKm=FALSE, showPctFull=TRUE) df <- lc_nlcd(year='2016', aoi='cat', comid='23783629,23794487,23812618', countOnly=TRUE) df <- lc_nlcd(year='2016, 2019', aoi='cat,ws', comid='23783629,23794487,23812618') } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":null,"dir":"Reference","previous_headings":"","what":"Lookup Full Metric Name — sc_fullname","title":"Lookup Full Metric Name — sc_fullname","text":"Function retrieve full metric name based short name using StreamCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lookup Full Metric Name — sc_fullname","text":"","code":"sc_fullname(metric = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lookup Full Metric Name — sc_fullname","text":"metric Short metric name Syntax: metric=value1 Values: metric","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lookup Full Metric Name — sc_fullname","text":"lookup full name given StreamCat metric","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Lookup Full Metric Name — sc_fullname","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_fullname.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lookup Full Metric Name — sc_fullname","text":"","code":"fullname <- sc_fullname(metric='clay')"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":null,"dir":"Reference","previous_headings":"","what":"Get COMIDs — sc_get_comid","title":"Get COMIDs — sc_get_comid","text":"Function return NHDPlusV2 COMIDS using either dataframe coordinates specified CRS sf object. function generates vector COMID values user can pass sc_get_data function","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get COMIDs — sc_get_comid","text":"","code":"sc_get_comid(dd = NULL, xcoord = NULL, ycoord = NULL, crsys = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get COMIDs — sc_get_comid","text":"dd Name data frame object. Can simple data frame coordinate columns known CRS sf points data frame xcoord x coordinate column using raw data frame ycoord y coordinate column using raw data frame crsys epsg code using raw data frame","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get COMIDs — sc_get_comid","text":"new sf data frame populated 'COMID' column","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get COMIDs — sc_get_comid","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_comid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get COMIDs — sc_get_comid","text":"","code":"if (FALSE) { # \\dontrun{ dd <- data.frame(x = c(-122.649,-100.348,-75.186,-106.675), y = c(45.085, 35.405,42.403,38.721)) comids <- sc_get_comid(dd, xcoord='x', ycoord='y', crsys=4269) dd <- sf::st_point_on_surface(sf::read_sf(system.file(\"shape/nc.shp\", package=\"sf\"))) comids <- sc_get_comid(dd) comids <- sc_get_comid(dd, xcoord='x', ycoord='y', crsys=4269) dd <- sf::read_sf(system.file(\"shape/nc.shp\", package=\"sf\")) comids <- sc_get_comid(dd) } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Get StreamCat data — sc_get_data","title":"Get StreamCat data — sc_get_data","text":"Function return StreamCat catchment watershed metrics using StreamCat API. function allows user get specific metric data aggregated area interest, returned comid(s), hydroregion(s), state(s), county(ies).","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get StreamCat data — sc_get_data","text":"","code":"sc_get_data( comid = NULL, metric = NULL, aoi = NULL, showAreaSqKm = NULL, showPctFull = NULL, state = NULL, county = NULL, region = NULL, conus = NULL, countOnly = NULL )"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get StreamCat data — sc_get_data","text":"comid Return metric information specific COMIDs. Can comma-delimited list, character vector, object can coerced comma-delimited list paste. One comid, county, state, region required unless conus='true'. Syntax: comid=, metric Name(s) metrics query. Must character string comma-delimited list metrics, , metric='' metrics queried. case-sensitive. Syntax: name=, aoi Name(s) areas interest query. metric data given AOI, data returned AOI. Certain metrics AOI specified StreamCat need AOI specified ''. metrics include: BankfullDepth, BankfullWidth, ThalwagDepth (sic), CHEM_V2_1, CONN, HABT, HYD, ICI, IWI, TEMP, WettedWidth, prg_bmmi, mast, msst, mwst metrics. Case-sensitive. Syntax: areaOfInterest=, Values: cat|ws|catrp100|wsrp100|showAreaSqKm Return area square kilometers given area interest. default value false. Values: true|false showPctFull Return pctfull dataset. default value false. Values: true|false state Return metric information COMIDs within specific state. Use state's abbreviation query given state. One comid, county, state, region required unless conus='true'. specified valid, comid county ignored. Case-sensitive. Syntax: state=, county Return metric information COMIDs within specific county. Users must use FIPS code, county name, way disambiguate counties. One comid, county, state, region required unless conus='true'. specified valid, comid ignored. Syntax: county=, region Return metric information COMIDs within specified hydroregion. Hydroregions specified using full name .e. 'Region01', 'Region03N', 'Region10L' One comid, county, state, region required unless conus='true'. specified valid, comid, county, state ignored. Case-sensitive. Syntax: region=, conus Return COMIDs conterminous United States. Character string (case-sensitive) logical. default value false. true, comid, county, state, region ignored. Values: true|false countOnly Return CSV containing row count (ROWCOUNT) column count (COLUMNCOUNT) server expects return request. default value false. Values: true|false","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get StreamCat data — sc_get_data","text":"data frame StreamCat metrics. data missing rows given metric, column metric exist. data missing rows, specified NA.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get StreamCat data — sc_get_data","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get StreamCat data — sc_get_data","text":"","code":"if (FALSE) { # \\dontrun{ df <- sc_get_data(comid='179', aoi='cat', metric='fert') df <- sc_get_data(metric='pctgrs2006', aoi='ws', region='Region01') df <- sc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') df <- sc_get_data(metric='pcturbmd2006', aoi='wsrp100', comid='1337420') df <- sc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='179,1337,1337420') df <- sc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='179,1337,1337420', showAreaSqKm='true', showPctFull='true') df <- sc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='179,1337,1337420', countOnly='true') df <- sc_get_data(metric='thalwagdepth', comid='179,1337,1337420', aoi='other') df <- sc_get_data(metric='thalwagdepth', comid=c('179','1337','1337420'), aoi='other') df <- sc_get_data(comid='179', aoi='ws', metric='all') } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Get StreamCat Metric Names — sc_get_metric_names","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"Function filter StreamCat metrics metrics category, area interest, dataset year. Use `sc_get_params(categories)` `sc_get_params(datasets)` see valid category dataset options","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"","code":"sc_get_metric_names(category = NULL, aoi = NULL, year = NULL, dataset = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"category Filter StreamCat metrics based metric category aoi Filter StreamCat metrics based area interest year Filter StreamCat metrics based particular year years dataset Filter StreamCat metrics based dataset name","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"dataframe merics description match filter criteria","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_metric_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get StreamCat Metric Names — sc_get_metric_names","text":"","code":"if (FALSE) { # \\dontrun{ metrics <- sc_get_metric_names(category='Wildfire') metrics <- sc_get_metric_names(category = c('Deposition','Climate'), aoi=c('Cat','Ws')) metrics <- sc_get_metric_names(aoi='Other', dataset=c('Canal Density','Predicted Channel Widths Depths')) } # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Get StreamCat Parameters — sc_get_params","title":"Get StreamCat Parameters — sc_get_params","text":"Function return available StreamCat parameters using StreamCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get StreamCat Parameters — sc_get_params","text":"","code":"sc_get_params(param = NULL)"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get StreamCat Parameters — sc_get_params","text":"param List available parameters API following options: name, areaofInterest, region, state, county. State county return data frame includes FIPS codes, names state abbreviations Syntax: param=, Values: name|area","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get StreamCat Parameters — sc_get_params","text":"list current StreamCat values given parameter","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get StreamCat Parameters — sc_get_params","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_get_params.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get StreamCat Parameters — sc_get_params","text":"","code":"if (FALSE) { # \\dontrun{ params <- sc_get_params(param='variable_info') params <- sc_get_params(param='metric_names') params <- sc_get_params(param='categories') params <- sc_get_params(param='aoi') params <- sc_get_params(param='state') params <- sc_get_params(param='county') params <- sc_get_params(param='datasets')} # }"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":null,"dir":"Reference","previous_headings":"","what":"Get NLCD Data — sc_nlcd","title":"Get NLCD Data — sc_nlcd","text":"Function retrieve NLCD metrics given year using StreamCat API.","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get NLCD Data — sc_nlcd","text":"","code":"sc_nlcd( year = \"2019\", comid = NULL, aoi = NULL, showAreaSqKm = NULL, showPctFull = NULL, state = NULL, county = NULL, region = NULL, conus = NULL, countOnly = NULL )"},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get NLCD Data — sc_nlcd","text":"year Years(s) NLCD metrics query. valid NLCD years accepted (.e. 2001, 2004, 2006, 2008, 2011, 2013, 2016, 2019) Syntax: year=, comid Return metric information specific COMIDs Syntax: comid=, aoi Specify area interest described metric. default, available areas interest given metric returned. Syntax: areaOfInterest=, Values: catchment|watershed|riparian_catchment|riparian_watershed|showAreaSqKm Return area square kilometers given area interest. default value false. Values: true|false showPctFull Return pctfull dataset. default value false. Values: true|false state Return metric information COMIDs within specific state. Use state's abbreviation query given state. Syntax: state=, county Return metric information COMIDs within specific county. Users must use FIPS code, county name, way disambiguate counties. Syntax: county=, region Return metric information COMIDs within specified hydroregion. Syntax: region=, conus Return COMIDs conterminous United States. default value false. Values: true|false countOnly Return CSV containing row count (ROWCOUNT) column count (COLUMNCOUNT) server expects return request. default value false. Values: true|false","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get NLCD Data — sc_nlcd","text":"tibble desired StreamCat metrics","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get NLCD Data — sc_nlcd","text":"Marc Weber","code":""},{"path":"https://usepa.github.io/StreamCatTools/reference/sc_nlcd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get NLCD Data — sc_nlcd","text":"","code":"if (FALSE) { # \\dontrun{ df <- sc_nlcd(year='2001', aoi='cat',comid='179,1337,1337420') df <- sc_nlcd(year='2001', aoi='ws', region='Region01') df <- sc_nlcd(year='2001', aoi='ws', region='Region01', countOnly=TRUE) df <- sc_nlcd(year='2001', aoi='ws', region='Region01', showAreaSqKm=FALSE, showPctFull=TRUE) df <- sc_nlcd(year='2001, 2006', aoi='cat,ws', comid='179,1337,1337420') } # }"},{"path":[]},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-090","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.9.0","title":"StreamCatTools 0.9.0","text":"CRAN release: 2025-10-15 Addresses CRAN error generated tests Adds tryCatch handling functions calling web services order fail gracefully produce errors Adds documentation vignettes two new functions added package","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-080","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.8.0","title":"StreamCatTools 0.8.0","text":"CRAN release: 2025-10-09 Added code coverage package Added two new functions - sc_get_metric_names lc_get_metric_names make metric names descriptions searchable slightly updated parameters sc_get_params lc_get_params functions sc_get_data lc_get_data now accept vectors well comma- separated strings metric, state, county region parameters","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-070","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.7.0","title":"StreamCatTools 0.7.0","text":"CRAN release: 2025-09-15 Updated sc_get_data lc_get_data pass parameters POST request body rather header, providing ability pass lengthy lists COMIDS requests Fixed bug package tests causing error running testthat","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-060","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.6.0","title":"StreamCatTools 0.6.0","text":"CRAN release: 2025-09-02 Added functionality sc_get_data lc_get_data accommodate large numbers (e.g. > 700) COMIDs header POST request","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-050","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.5.0","title":"StreamCatTools 0.5.0","text":"Overhauled sc_get_data lc_get_data functions able pull metrics StreamCat LakeCat area interest Updated sc_get_data lc_get_data able pass hundreds COMIDs time function parameter error call server Updated sc_get_params lc_get_params now return variable information, well just metric names full names, return tables state county abbreviations, names FIPS codes","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-040","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.4.0","title":"StreamCatTools 0.4.0","text":"Overhauled functions use new api.epa.gov endpoints StreamCat described swagger documentation Streamlined sc_get_data lc_get_data requests httr2 Adopted functionality package functions use Oracle ORDs Database REST API rather previous JAVA REST service","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-030","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.3.0","title":"StreamCatTools 0.3.0","text":"Incorporated POST requests httr2 requests deal many COMIDs requests Added documentation vignette working LakeCat data package","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-020","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.2.0","title":"StreamCatTools 0.2.0","text":"lc_get_data lc_get_params Changed lifecycle stable","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-0119002","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.1.1.9002","title":"StreamCatTools 0.1.1.9002","text":"Fixed sc_get_data pass COMIDs function robustly Added sc_nlcd helper function easily grab NLCD based metrics StreamCat Updated package documentation","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-0119001","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.1.1.9001","title":"StreamCatTools 0.1.1.9001","text":"API publicly released package works now everyone (just inside EPA network)","code":""},{"path":"https://usepa.github.io/StreamCatTools/news/index.html","id":"streamcattools-0119000","dir":"Changelog","previous_headings":"","what":"StreamCatTools 0.1.1.9000","title":"StreamCatTools 0.1.1.9000","text":"Added NEWS.md file track changes package.","code":""}] From b5cb3ae9f0904bf361dc463504a0b04e46ff8e2a Mon Sep 17 00:00:00 2001 From: Weber Date: Mon, 20 Oct 2025 14:46:06 -0700 Subject: [PATCH 17/22] handling in vignettes for web service being down --- R/sc_get_params.R | 20 +++--- tests/testthat/test-lc_get_params.R | 7 +++ tests/testthat/test-lc_getdata.R | 27 ++++---- tests/testthat/test-lc_nlcd.R | 20 +++--- tests/testthat/test-sc_get_params.R | 18 ++++-- tests/testthat/test-sc_getdata.R | 3 + tests/testthat/test-sc_nlcd.R | 20 +++--- vignettes/Applications.Rmd | 29 +++++---- vignettes/Introduction.Rmd | 97 +++++++++++++++++++++++------ vignettes/LakeCat.Rmd | 53 ++++++++++++---- 10 files changed, 211 insertions(+), 83 deletions(-) diff --git a/R/sc_get_params.R b/R/sc_get_params.R index 2941822..afcf51e 100644 --- a/R/sc_get_params.R +++ b/R/sc_get_params.R @@ -179,7 +179,6 @@ sc_get_metric_names <- function(category = NULL, filters <- list(INDICATOR_CATEGORY = category, AOI = aoi, YEAR = year, DSNAME = dataset) - filter_data <- function(data, filters) { # Filter the data frame for each non-null filter filtered_data <- purrr::reduce( @@ -197,14 +196,17 @@ sc_get_metric_names <- function(category = NULL, ) return(filtered_data) } - results <- filter_data(resp, filters) - names_keep <- c("INDICATOR_CATEGORY", "METRIC_NAME", "AOI", "YEAR", - "WEBTOOL_NAME", "METRIC_DESCRIPTION", - "METRIC_UNITS", "SOURCE_NAME", "DSNAME") - results <- results[, names_keep, drop = FALSE] - names_new <- c("Category", "Metric", "AOI", "Year", "Short_Name", - "Metric_Description", "Units", "Source", "Dataset") - names(results) <- names_new + if (exists('resp') & !is.null(resp)){ + results <- filter_data(resp, filters) + names_keep <- c("INDICATOR_CATEGORY", "METRIC_NAME", "AOI", "YEAR", + "WEBTOOL_NAME", "METRIC_DESCRIPTION", + "METRIC_UNITS", "SOURCE_NAME", "DSNAME") + results <- results[, names_keep, drop = FALSE] + names_new <- c("Category", "Metric", "AOI", "Year", "Short_Name", + "Metric_Description", "Units", "Source", "Dataset") + names(results) <- names_new + } else + results <- 'the service appears to be down currently' return(results) } diff --git a/tests/testthat/test-lc_get_params.R b/tests/testthat/test-lc_get_params.R index 55eccc6..beb0d25 100644 --- a/tests/testthat/test-lc_get_params.R +++ b/tests/testthat/test-lc_get_params.R @@ -1,18 +1,21 @@ context("Test that lc_get_params is pulling in StreamCat API parameters") test_that("lc_get_params for metric_names parameters", { + testthat::skip_on_cran() params <- lc_get_params(param='metric_names') expect_true(exists("params")) expect_gt(length(params),500) }) test_that("lc_get_params for variable_info parameters", { + testthat::skip_on_cran() params <- lc_get_params(param='variable_info') expect_true(exists("params")) expect_gt(nrow(params),100) }) test_that("lc_get_metric_names", { + testthat::skip_on_cran() metrics <- lc_get_metric_names(category='Natural') expect_true(exists("metrics")) expect_gt(nrow(metrics),20) @@ -22,18 +25,21 @@ test_that("lc_get_metric_names", { }) test_that("lc_get_params for area of interest parameters", { + testthat::skip_on_cran() params <- lc_get_params(param='aoi') expect_true(exists("params")) expect_equal(params,c("cat","ws")) }) test_that("lc_get_params for name parameters", { + testthat::skip_on_cran() params <- lc_get_params(param='metric_names') expect_true(exists("params")) expect_equal(length(params),517) }) test_that("lc_get_params for state parameters", { + testthat::skip_on_cran() params <- lc_get_params(param='state') expect_true(exists("params")) expect_equal(nrow(params),49) @@ -41,6 +47,7 @@ test_that("lc_get_params for state parameters", { }) test_that("lc_get_params for county parameters", { + testthat::skip_on_cran() params <- lc_get_params(param='county') expect_true(exists("params")) expect_equal(nrow(params),3108) diff --git a/tests/testthat/test-lc_getdata.R b/tests/testthat/test-lc_getdata.R index 71ab6d0..f4efa3e 100644 --- a/tests/testthat/test-lc_getdata.R +++ b/tests/testthat/test-lc_getdata.R @@ -2,23 +2,25 @@ context("Test that sc_get_data is pulling in StreamCat API data") test_that("lc_get_data for a sample COMID returns a data frame", { - df <- lc_get_data(metric='pcturbmd2006,pctconif2008,rddens', - aoi='cat,ws', - comid='23783629,23794487,23812618') - expect_true(exists("df")) - expect_equal(nrow(df), 3) - expect_equal(ncol(df), 7) + testthat::skip_on_cran() + df <- lc_get_data(metric='pcturbmd2006,pctconif2008,rddens', + aoi='cat,ws',comid='23783629,23794487,23812618') + expect_true(exists("df")) + expect_equal(nrow(df), 3) + expect_equal(ncol(df), 7) }) test_that("lc_get_data for a county and ws metrics returns a data frame", { - df <- lc_get_data(metric='pctwdwet2006', aoi='ws', - comid='23794487',showAreaSqKm=TRUE, showPctFull=TRUE) - expect_true(exists("df")) - expect_equal(nrow(df), 1) - expect_equal(ncol(df), 5) - }) + testthat::skip_on_cran() + df <- lc_get_data(metric='pctwdwet2006', aoi='ws', + comid='23794487',showAreaSqKm=TRUE, showPctFull=TRUE) + expect_true(exists("df")) + expect_equal(nrow(df), 1) + expect_equal(ncol(df), 5) + }) test_that("lc_get_data for a hydroregion and ws metrics returns a data frame", { + testthat::skip_on_cran() df <- lc_get_data(metric='pctwdwet2006', aoi='ws', region='Region01') expect_true(exists("df")) @@ -27,6 +29,7 @@ test_that("lc_get_data for a hydroregion and ws metrics returns a data frame", { }) test_that("lc_get_data for a county and ws metrics returns a data frame", { + testthat::skip_on_cran() df <- lc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') expect_true(exists("df")) diff --git a/tests/testthat/test-lc_nlcd.R b/tests/testthat/test-lc_nlcd.R index 3f5d7a2..546aec2 100644 --- a/tests/testthat/test-lc_nlcd.R +++ b/tests/testthat/test-lc_nlcd.R @@ -2,17 +2,19 @@ context("Test that lc_nlcd is pulling in StreamCat API data") test_that("lc_get_data for a sample COMID returns a data frame", { - df <- lc_nlcd(year='2019', aoi='catchment', - comid='23783629,23794487,23812618') - expect_true(exists("df")) - expect_equal(nrow(df), 3) - expect_equal(ncol(df), 17) + testthat::skip_on_cran() + df <- lc_nlcd(year='2019', aoi='catchment', + comid='23783629,23794487,23812618') + expect_true(exists("df")) + expect_equal(nrow(df), 3) + expect_equal(ncol(df), 17) }) test_that("lc_get_data for a county and ws metrics returns a data frame", { + testthat::skip_on_cran() df <- lc_nlcd(year='2006, 2019', aoi='watershed', comid='23794487',showAreaSqKm=TRUE, showPctFull=TRUE) - expect_true(exists("df")) - expect_equal(nrow(df), 1) - expect_equal(ncol(df), 36) - }) + expect_true(exists("df")) + expect_equal(nrow(df), 1) + expect_equal(ncol(df), 36) +}) diff --git a/tests/testthat/test-sc_get_params.R b/tests/testthat/test-sc_get_params.R index 75ab546..be665aa 100644 --- a/tests/testthat/test-sc_get_params.R +++ b/tests/testthat/test-sc_get_params.R @@ -2,12 +2,14 @@ context("Test that sc_get_params is pulling in StreamCat API parameters") test_that("sc_get_params for area of interest parameters", { - params <- sc_get_params(param='aoi') - expect_true(exists("params")) - expect_equal(params,c("cat","catrp100","other","ws","wsrp100")) - }) + testthat::skip_on_cran() + params <- sc_get_params(param='aoi') + expect_true(exists("params")) + expect_equal(params,c("cat","catrp100","other","ws","wsrp100")) +}) test_that("sc_get_params for region parameters", { + testthat::skip_on_cran() params <- sc_get_params(param='region') expect_true(exists("params")) expect_equal(params,c("Region01","Region02","Region03N","Region03S","Region03W", @@ -17,30 +19,35 @@ test_that("sc_get_params for region parameters", { }) test_that("sc_get_params for metric_names parameters", { + testthat::skip_on_cran() params <- sc_get_params(param='metric_names') expect_true(exists("params")) expect_gt(length(params),1000) }) test_that("sc_get_params for variable_info parameters", { + testthat::skip_on_cran() params <- sc_get_params(param='variable_info') expect_true(exists("params")) expect_gt(nrow(params),100) }) test_that("sc_get_params for StreamCat metric categories", { + testthat::skip_on_cran() params <- sc_get_params(param='categories') expect_true(exists("params")) expect_gt(length(params),8) }) test_that("sc_get_params for StreamCat datasets", { + testthat::skip_on_cran() params <- sc_get_params(param='datasets') expect_true(exists("params")) expect_gt(length(params),30) }) test_that("sc_get_params for state parameters", { + testthat::skip_on_cran() params <- sc_get_params(param='state') expect_true(exists("params")) expect_equal(nrow(params),49) @@ -48,6 +55,7 @@ test_that("sc_get_params for state parameters", { }) test_that("sc_get_params for county parameters", { + testthat::skip_on_cran() params <- sc_get_params(param='county') expect_true(exists("params")) expect_equal(nrow(params),3108) @@ -55,6 +63,7 @@ test_that("sc_get_params for county parameters", { }) test_that("sc_get_metric_names for categories and AOIs", { + testthat::skip_on_cran() metrics <- sc_get_metric_names(category = c('Deposition','Climate'),aoi=c('Cat','Ws')) expect_true(exists("metrics")) expect_gt(nrow(metrics),10) @@ -64,6 +73,7 @@ test_that("sc_get_metric_names for categories and AOIs", { }) test_that("sc_get_metric_names for datasets", { + testthat::skip_on_cran() metrics <- sc_get_metric_names(aoi='Other', dataset=c('Canal Density', 'Predicted Channel Widths Depths')) diff --git a/tests/testthat/test-sc_getdata.R b/tests/testthat/test-sc_getdata.R index d5a4376..b6f2436 100644 --- a/tests/testthat/test-sc_getdata.R +++ b/tests/testthat/test-sc_getdata.R @@ -1,6 +1,7 @@ context("Test that sc_get_data is pulling in StreamCat API data") test_that("sc_get_data for a sample COMID returns a data frame", { + testthat::skip_on_cran() df <- sc_get_data(comid='179', aoi='cat', metric='fert') expect_true(exists("df")) expect_equal(nrow(df), 1) @@ -17,6 +18,7 @@ test_that("sc_get_data for multiple COMIDs and areas and metrics returns a data }) test_that("sc_get_data for showAreaSqKm and showPctFull returns a data frame", { + testthat::skip_on_cran() df <- sc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='179,1337,1337420',showAreaSqKm=TRUE, showPctFull=TRUE) expect_true(exists("df")) @@ -41,6 +43,7 @@ test_that("sc_get_data for a county and ws metrics returns a data frame", { }) test_that("sc_get_data for all ws metrics for a COMID returns a data frame", { + testthat::skip_on_cran() df <- sc_get_data(comid='1337420',metric='all', aoi='ws') expect_true(exists("df")) }) \ No newline at end of file diff --git a/tests/testthat/test-sc_nlcd.R b/tests/testthat/test-sc_nlcd.R index 75697df..3005001 100644 --- a/tests/testthat/test-sc_nlcd.R +++ b/tests/testthat/test-sc_nlcd.R @@ -2,17 +2,19 @@ context("Test that sc_nlcd is pulling in StreamCat API data") test_that("sc_get_data for a sample COMID returns a data frame", { - df <- sc_nlcd(year='2019', aoi='cat', - comid='179,1337,1337420') - expect_true(exists("df")) - expect_equal(nrow(df), 3) - expect_equal(ncol(df), 17) + testthat::skip_on_cran() + df <- sc_nlcd(year='2019', aoi='cat', + comid='179,1337,1337420') + expect_true(exists("df")) + expect_equal(nrow(df), 3) + expect_equal(ncol(df), 17) }) test_that("sc_get_data for a county and ws metrics returns a data frame", { + testthat::skip_on_cran() df <- sc_nlcd(year='2006, 2019', aoi='ws', county='41003') - expect_true(exists("df")) - expect_equal(nrow(df), 632) - expect_equal(ncol(df), 33) - }) + expect_true(exists("df")) + expect_equal(nrow(df), 632) + expect_equal(ncol(df), 33) +}) diff --git a/vignettes/Applications.Rmd b/vignettes/Applications.Rmd index 074e1c2..3fcfab2 100644 --- a/vignettes/Applications.Rmd +++ b/vignettes/Applications.Rmd @@ -37,21 +37,28 @@ flowline_nldi <- nhdplusTools::navigate_nldi(nldi_feature, mode = "UT", data_sou # get StreamCat metrics df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=flowline_nldi$UT_flowlines$nhdplus_comid) - -# We can also pull out comids the following way: -# comids <- paste(as.integer(flowline_nldi$UT_flowlines$nhdplus_comid), collapse=",",sep="") -# df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=comids) - -flowline_nldi <- flowline_nldi$UT_flowlines -flowline_nldi$PCTIMP2011CAT <- df$pctimp2011cat[match(flowline_nldi$nhdplus_comid, df$comid)] - -basin <- nhdplusTools::get_nldi_basin(nldi_feature = nldi_feature) +if (exists('flowline_nldi')){ + if (!is.null(flowline_nldi)){ + # We can also pull out comids the following way: + # comids <- paste(as.integer(flowline_nldi$UT_flowlines$nhdplus_comid), collapse=",",sep="") + # df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=comids) + + flowline_nldi <- flowline_nldi$UT_flowlines + flowline_nldi$PCTIMP2011CAT <- df$pctimp2011cat[match(flowline_nldi$nhdplus_comid, df$comid)] + + basin <- nhdplusTools::get_nldi_basin(nldi_feature = nldi_feature) + } +} else print('the service appears to be down currently') ``` ```{r wshd pt2} library(mapview) -mapview::mapviewOptions(fgb=FALSE) -mapview::mapview(basin, alpha.regions=.08) + mapview::mapview(flowline_nldi, zcol = "PCTIMP2011CAT", legend = TRUE) +if (exists('flowline_nldi')){ + if (!is.null(flowline_nldi)){ + mapview::mapviewOptions(fgb=FALSE) + mapview::mapview(basin, alpha.regions=.08) + mapview::mapview(flowline_nldi, zcol = "PCTIMP2011CAT", legend = TRUE) + } +} else print('the service appears to be down currently') ``` ### Working with NARS data diff --git a/vignettes/Introduction.Rmd b/vignettes/Introduction.Rmd index 42ce618..cf9fe88 100644 --- a/vignettes/Introduction.Rmd +++ b/vignettes/Introduction.Rmd @@ -43,7 +43,7 @@ The `StreamCatTools` package was designed to simplify the use of [StreamCat](htt ## StreamCat API We can pull data into R from the [StreamCat API](https://usepa.github.io/StreamCatWebServices_Public/#/) by simply passing a URL to extract from json. We have to hard-wire parameters though and are limited in the number of records returned through a `GET` request. -```{r API} +```{r , message=FALSE, eval=FALSE} res <- jsonlite::fromJSON("https://api.epa.gov/StreamCat/streams/metrics?name=fert&areaOfInterest=cat&comid=179") res$items ``` @@ -55,65 +55,110 @@ region_params <- sc_get_params(param='aoi') name_params <- sc_get_params(param='metric_names') -print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) -print(paste0('A selection of available StreamCat metrics include: ',paste(name_params[1:10],collapse = ', '))) +if (exists('region_params')){ + if (!is.null(region_params)){ + print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) + } +} else print('the service appears to be down currently') +if (exists('name_params')){ + if (!is.null(name_params)){ +print(paste0('A selection of available LakrCat metrics include: ',paste(name_params[1:10],collapse = ', '))) + } +} else print('the service appears to be down currently') ``` + We can also see what metrics are available for what areas of interest and what years using the `sc_get_params` function (which returns a tibble of information about StreamCat metrics): ```{r params2} var_info <- sc_get_params(param='variable_info') -head(var_info) +if (exists('var_info')){ + if (!is.null(var_info)){ + head(var_info) + } +} else print('the service appears to be down currently') ``` We can look up the display name or names for a metric using the `sc_fullname` function via the API ```{r fullnames} metric='pcthbwet2011' fullname <- sc_fullname(metric) +if (exists('fullname')){ + if (!is.null(fullname)){ fullname + } +} else print('the service appears to be down currently') ``` ```{r fullnames2} metric='pctdecid2019,fert' fullname <- sc_fullname(metric) +if (exists('fullname')){ + if (!is.null(fullname)){ fullname + } +} else print('the service appears to be down currently') ``` We can additionally get a data frame of state FIPS codes, abbreviations and names, and the same information for counties as well using `sc_get_params`: ```{r states} states <- sc_get_params(param='state') -head(states) +if (exists('states')){ + if (!is.null(states)){ + knitr::kable(head(states)) + } +} else print('the service appears to be down currently') ``` ```{r counties} counties <- sc_get_params(param='county') -head(counties) +if (exists('counties')){ + if (!is.null(counties)){ + knitr::kable(head(counties)) + } +} else print('the service appears to be down currently') ``` ## Filter metric information by criteria We can also filter metric names and information by the metric year(s), the indicator categories for metrics, the metric data set names, or the Areas of Interest the metrics are available for. ```{r get_metric_names} metrics <- sc_get_metric_names(category = c('Deposition','Climate'),aoi=c('Cat','Ws')) -head(metrics) +if (exists('metrics')){ + if (!is.null(metrics)){ + head(metrics) + } +} else print('the service appears to be down currently') ``` ## Get data for COMIDs In this example we access several variables, for several areas of interest, and for several COMIDs using the `sc_get_data` function. Loads data into a tibble we can view. ```{r get_data} df <- sc_get_data(metric='pcturbmd2006,damdens,tridens', aoi='rp100cat,cat,ws', comid='179,1337,1337420') -knitr::kable(df) +if (exists('df')){ + if (!is.null(df)){ + knitr::kable(df) + } +} else print('the service appears to be down currently') ``` ## Get data for county In this example we access a couple variables at the watershed scale for the area of interest of a county (Benton County in this case) using the `sc_get_data` function. ```{r countydata} df <- sc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') -knitr::kable(head(df)) +if (exists('df')){ + if (!is.null(df)){ + knitr::kable(head(df)) + } +} else print('the service appears to be down currently') ``` ## Get all metrics for COMIDs or an Area of Interest We can also get all StreamCat metrics for a set of COMIDs or an area of interest. **Please do not request metric='all' and aoi='conus' in order not to overload requests to the server. Requesting metric='all' for a state or multiple states or hydroregions will also take a long time to process**. ```{r all} df <- sc_get_data(comid='179', aoi='cat', metric='all') -knitr::kable(head(df)) +if (exists('df')){ + if (!is.null(df)){ + knitr::kable(head(df)) + } +} else print('the service appears to be down currently') ``` ## Get NLCD data @@ -121,14 +166,22 @@ In this example we access National Land Cover Dataset (NLCD) data for 2001, just ```{r get_nlcd} df <- sc_nlcd(year='2001', aoi='cat', comid='179,1337,1337420') -knitr::kable(df) +if (exists('df')){ + if (!is.null(df)){ + knitr::kable(df) + } +} else print('the service appears to be down currently') ``` We can also pass a couple years for a different area of interest for another region like a county. ```{r get_nlcd2} df <- sc_nlcd(year='2006, 2019', aoi='ws', county='41003') -knitr::kable(head(df)) +if (exists('df')){ + if (!is.null(df)){ + knitr::kable(head(df)) + } +} else print('the service appears to be down currently') ``` ## Get COMIDs @@ -142,22 +195,30 @@ gages_coms <- sc_get_comid(gages, xcoord='LON_SITE', ycoord='L # Add the COMID we found back to gages data frame gages$COMID <- strsplit(gages_coms, ",")[[1]] df <- sc_get_data(metric='huden2010', aoi='ws', comid=gages_coms) -df$COMID <- as.character(df$comid) -gages <- dplyr::left_join(gages, df, by='COMID') -knitr::kable(head(gages)) +if (exists('df')){ + if (!is.null(df)){ + df$COMID <- as.character(df$comid) + gages <- dplyr::left_join(gages, df, by='COMID') + knitr::kable(head(gages)) + } +} else print('the service appears to be down currently') ``` ## Get data for a hydroregion In this example we access a couple watershed-only metrics for a particular NHDPlus hydroregion using the `sc_get_data` function. ```{r hydroregion} df <- sc_get_data(metric='pctwdwet2006', aoi='ws', region='Region17') -knitr::kable(head(df)) +if (exists('df')){ + if (!is.null(df)){ + knitr::kable(head(df)) + } +} else print('the service appears to be down currently') ``` ## Get data for CONUS In this example we access a metric for conus using the `sc_get_data` function - this is shown for demonstration but not run as it takes a bit of time ```{r conus, eval=FALSE} -# df <- sc_get_data(metric='om', aoi='ws', conus='true') -# knitr::kable(head(df)) +df <- sc_get_data(metric='om', aoi='ws', conus='true') +knitr::kable(head(df)) ``` diff --git a/vignettes/LakeCat.Rmd b/vignettes/LakeCat.Rmd index 5894270..23b8231 100644 --- a/vignettes/LakeCat.Rmd +++ b/vignettes/LakeCat.Rmd @@ -44,35 +44,59 @@ library(StreamCatTools) region_params <- lc_get_params(param='aoi') name_params <- lc_get_params(param='metric_names') - -print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) +if (exists('region_params')){ + if (!is.null(region_params)){ + print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) + } +} else print('the service appears to be down currently') + +if (exists('name_params')){ + if (!is.null(name_params)){ print(paste0('A selection of available LakrCat metrics include: ',paste(name_params[1:10],collapse = ', '))) + } +} else print('the service appears to be down currently') ``` We can also see what metrics are available for what areas of interest and what years using the `sc_get_params` function (which returns a tibble of information about StreamCat metrics): ```{r params2} var_info <- lc_get_params(param='variable_info') -head(var_info) +if (exists('var_info')){ + if (!is.null(var_info)){ + head(var_info) + } +} else print('the service appears to be down currently') ``` Look up the display name or names for a metric using the `lc_fullname` function via the API ```{r fullnames} metric='pcthbwet2016' fullname <- lc_fullname(metric) +if (exists('fullname')){ + if (!is.null(fullname)){ fullname + } +} else print('the service appears to be down currently') ``` ```{r fullnames2} metric=c('pctdecid2019','fert') fullname <- lc_fullname(metric) +if (exists('fullname')){ + if (!is.null(fullname)){ fullname + } +} else print('the service appears to be down currently') ``` ## Filter metric information by criteria We can also filter metric names and information by the metric year(s), the indicator categories for metrics, the metric data set names, or the Areas of Interest the metrics are available for. ```{r get_metric_names} metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), aoi=c('Cat','Ws')) +if (exists('metrics')){ + if (!is.null(metrics)){ head(metrics) + } +} else print('the service appears to be down currently') ``` ## Get Waterbody COMIDs @@ -91,19 +115,22 @@ In this example we access several variables, for several areas of interest, and ```{r get_data} df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid=comids) -knitr::kable(df) -``` - -```{r get_data2} -df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='23783629,23794487,23812618') -knitr::kable(df) +if (exists('df')){ + if (!is.null(df)){ + knitr::kable(df) + } +} else print('the service appears to be down currently') ``` ## Get data for county In this example we access a couple variables at the watershed scale for the area of interest of a county (Benton County in this case) using the `sc_get_data` function. ```{r countydata} df <- lc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') -knitr::kable(head(df)) +if (exists('df')){ + if (!is.null(df)){ + knitr::kable(head(df)) + } +} else print('the service appears to be down currently') ``` ## Get NLCD data @@ -112,5 +139,9 @@ In this example we access National Land Cover Dataset (NLCD) data for 2019, just ```{r get_nlcd} df <- lc_nlcd(comid='23783629,23794487,23812618', year='2019', aoi='ws') -knitr::kable(df) +if (exists('df')){ + if (!is.null(df)){ + knitr::kable(df) + } +} else print('the service appears to be down currently') ``` From f2110c1fd0c9cc116a7d2ea601c90a4b72d58614 Mon Sep 17 00:00:00 2001 From: Weber Date: Mon, 20 Oct 2025 15:12:59 -0700 Subject: [PATCH 18/22] updated CRAN comments --- cran-comments.md | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index 499faf5..80d5149 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,10 +1,9 @@ -This is a minor update that: +This is a patch update that: -- Addresses CRAN error noted by Dr. Brian Ripley generated by tests that is - required to be fixed by 10/25/25 -- Adds tryCatch handling for functions calling web services in order to fail - gracefully and not produce errors -- Adds documentation to vignettes for two new functions added to the package +- Handles a web service being down in testing using `testthat::skip_on_cran()` +- Handles a web service being down in vignettes +- Due to the lapse in government funding in federal agencies in the US, + the web service StreamCatTools is built around may be donw for some time ------- From 62798267cec69c1082819d03be151f740147e738 Mon Sep 17 00:00:00 2001 From: Weber Date: Mon, 20 Oct 2025 15:15:17 -0700 Subject: [PATCH 19/22] Updated NEWS and DESCRIPTION --- DESCRIPTION | 2 +- NEWS.md | 7 ++++++- cran-comments.md | 2 +- 3 files changed, 8 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d84b6a3..60c2107 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: StreamCatTools Type: Package Title: 'StreamCatTools' -Version: 0.9.0.9000 +Version: 0.9.1 Authors@R: c(person(given = "Marc", family = "Weber", role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index ef3cdcb..8c6cd42 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,10 @@ -# StreamCatTools (development version) +# StreamCatTools 0.9.1 +- Handles a web service being down in testing using `testthat::skip_on_cran()` +- Handles a web service being down in vignettes +- Due to the lapse in government funding in federal agencies in the US, + the web service StreamCatTools is built around may be down for some time + # StreamCatTools 0.9.0 - Addresses CRAN error generated by tests that is diff --git a/cran-comments.md b/cran-comments.md index 80d5149..86f72e0 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -3,7 +3,7 @@ This is a patch update that: - Handles a web service being down in testing using `testthat::skip_on_cran()` - Handles a web service being down in vignettes - Due to the lapse in government funding in federal agencies in the US, - the web service StreamCatTools is built around may be donw for some time + the web service StreamCatTools is built around may be down for some time ------- From e83eada993b2f06aa2bb364e27cd9265db96ce74 Mon Sep 17 00:00:00 2001 From: Weber Date: Mon, 20 Oct 2025 15:19:45 -0700 Subject: [PATCH 20/22] updated CRAN comments --- cran-comments.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/cran-comments.md b/cran-comments.md index 86f72e0..b18cf49 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -4,6 +4,10 @@ This is a patch update that: - Handles a web service being down in vignettes - Due to the lapse in government funding in federal agencies in the US, the web service StreamCatTools is built around may be down for some time +- Because of the lapse in government funding in federal agencies in the US, I + may not be able to respond readily to any CRAN emails to my government + email account weber.marc@epa.gov but my personal email is mweber36@gmail.com + ------- From 60e4c31a6300344f26adba7226ccc923eabd6368 Mon Sep 17 00:00:00 2001 From: mhweber Date: Fri, 24 Oct 2025 16:16:35 -0700 Subject: [PATCH 21/22] Switched most vignettes to articles --- vignettes/{ => Articles}/Applications.Rmd | 31 +++---- vignettes/{ => Articles}/Introduction.Rmd | 105 ++++------------------ vignettes/{ => Articles}/LakeCat.Rmd | 55 +++--------- vignettes/StartHere.Rmd | 67 ++++++++++++++ 4 files changed, 106 insertions(+), 152 deletions(-) rename vignettes/{ => Articles}/Applications.Rmd (77%) rename vignettes/{ => Articles}/Introduction.Rmd (65%) rename vignettes/{ => Articles}/LakeCat.Rmd (78%) create mode 100644 vignettes/StartHere.Rmd diff --git a/vignettes/Applications.Rmd b/vignettes/Articles/Applications.Rmd similarity index 77% rename from vignettes/Applications.Rmd rename to vignettes/Articles/Applications.Rmd index 3fcfab2..9e497bc 100644 --- a/vignettes/Applications.Rmd +++ b/vignettes/Articles/Applications.Rmd @@ -12,7 +12,7 @@ output: smooth_scroll: no toc_depth: 2 vignette: > - %\VignetteIndexEntry{Applications withs StreamCatTools} + %\VignetteIndexEntry{Applications with StreamCatTools} %\VignetteEncoding{UTF-8}{inputenc} %\VignetteEngine{knitr::rmarkdown} --- @@ -37,28 +37,21 @@ flowline_nldi <- nhdplusTools::navigate_nldi(nldi_feature, mode = "UT", data_sou # get StreamCat metrics df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=flowline_nldi$UT_flowlines$nhdplus_comid) -if (exists('flowline_nldi')){ - if (!is.null(flowline_nldi)){ - # We can also pull out comids the following way: - # comids <- paste(as.integer(flowline_nldi$UT_flowlines$nhdplus_comid), collapse=",",sep="") - # df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=comids) - - flowline_nldi <- flowline_nldi$UT_flowlines - flowline_nldi$PCTIMP2011CAT <- df$pctimp2011cat[match(flowline_nldi$nhdplus_comid, df$comid)] - - basin <- nhdplusTools::get_nldi_basin(nldi_feature = nldi_feature) - } -} else print('the service appears to be down currently') + +# We can also pull out comids the following way: +# comids <- paste(as.integer(flowline_nldi$UT_flowlines$nhdplus_comid), collapse=",",sep="") +# df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=comids) + +flowline_nldi <- flowline_nldi$UT_flowlines +flowline_nldi$PCTIMP2011CAT <- df$pctimp2011cat[match(flowline_nldi$nhdplus_comid, df$comid)] + +basin <- nhdplusTools::get_nldi_basin(nldi_feature = nldi_feature) ``` ```{r wshd pt2} library(mapview) -if (exists('flowline_nldi')){ - if (!is.null(flowline_nldi)){ - mapview::mapviewOptions(fgb=FALSE) - mapview::mapview(basin, alpha.regions=.08) + mapview::mapview(flowline_nldi, zcol = "PCTIMP2011CAT", legend = TRUE) - } -} else print('the service appears to be down currently') +mapview::mapviewOptions(fgb=FALSE) +mapview::mapview(basin, alpha.regions=.08) + mapview::mapview(flowline_nldi, zcol = "PCTIMP2011CAT", legend = TRUE) ``` ### Working with NARS data diff --git a/vignettes/Introduction.Rmd b/vignettes/Articles/Introduction.Rmd similarity index 65% rename from vignettes/Introduction.Rmd rename to vignettes/Articles/Introduction.Rmd index cf9fe88..bb0ca2b 100644 --- a/vignettes/Introduction.Rmd +++ b/vignettes/Articles/Introduction.Rmd @@ -26,21 +26,6 @@ knitr::opts_chunk$set( ) ``` -## Installing and loading StreamCatTools -To install, currently you need to install from GitHub using devtools -```{r, message=FALSE, eval=FALSE} -library(devtools) -install_github('USEPA/StreamCatTools') -``` - -After installing load the library -```{r, message=FALSE} -library(StreamCatTools) -``` - -## Background -The `StreamCatTools` package was designed to simplify the use of [StreamCat](https://www.epa.gov/national-aquatic-resource-surveys/streamcat-dataset) data in R, leveraging the new [API for StreamCat](https://api.epa.gov/StreamCat/streams/metrics). - ## StreamCat API We can pull data into R from the [StreamCat API](https://usepa.github.io/StreamCatWebServices_Public/#/) by simply passing a URL to extract from json. We have to hard-wire parameters though and are limited in the number of records returned through a `GET` request. ```{r , message=FALSE, eval=FALSE} @@ -55,110 +40,66 @@ region_params <- sc_get_params(param='aoi') name_params <- sc_get_params(param='metric_names') -if (exists('region_params')){ - if (!is.null(region_params)){ - print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) - } -} else print('the service appears to be down currently') -if (exists('name_params')){ - if (!is.null(name_params)){ -print(paste0('A selection of available LakrCat metrics include: ',paste(name_params[1:10],collapse = ', '))) - } -} else print('the service appears to be down currently') +print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) +print(paste0('A selection of available StreamCat metrics include: ',paste(name_params[1:10],collapse = ', '))) ``` We can also see what metrics are available for what areas of interest and what years using the `sc_get_params` function (which returns a tibble of information about StreamCat metrics): ```{r params2} var_info <- sc_get_params(param='variable_info') -if (exists('var_info')){ - if (!is.null(var_info)){ - head(var_info) - } -} else print('the service appears to be down currently') +head(var_info) ``` We can look up the display name or names for a metric using the `sc_fullname` function via the API ```{r fullnames} metric='pcthbwet2011' fullname <- sc_fullname(metric) -if (exists('fullname')){ - if (!is.null(fullname)){ fullname - } -} else print('the service appears to be down currently') ``` ```{r fullnames2} metric='pctdecid2019,fert' fullname <- sc_fullname(metric) -if (exists('fullname')){ - if (!is.null(fullname)){ fullname - } -} else print('the service appears to be down currently') ``` We can additionally get a data frame of state FIPS codes, abbreviations and names, and the same information for counties as well using `sc_get_params`: ```{r states} states <- sc_get_params(param='state') -if (exists('states')){ - if (!is.null(states)){ - knitr::kable(head(states)) - } -} else print('the service appears to be down currently') +head(states) ``` ```{r counties} counties <- sc_get_params(param='county') -if (exists('counties')){ - if (!is.null(counties)){ - knitr::kable(head(counties)) - } -} else print('the service appears to be down currently') +head(counties) ``` ## Filter metric information by criteria We can also filter metric names and information by the metric year(s), the indicator categories for metrics, the metric data set names, or the Areas of Interest the metrics are available for. ```{r get_metric_names} metrics <- sc_get_metric_names(category = c('Deposition','Climate'),aoi=c('Cat','Ws')) -if (exists('metrics')){ - if (!is.null(metrics)){ - head(metrics) - } -} else print('the service appears to be down currently') +head(metrics) ``` ## Get data for COMIDs In this example we access several variables, for several areas of interest, and for several COMIDs using the `sc_get_data` function. Loads data into a tibble we can view. ```{r get_data} df <- sc_get_data(metric='pcturbmd2006,damdens,tridens', aoi='rp100cat,cat,ws', comid='179,1337,1337420') -if (exists('df')){ - if (!is.null(df)){ - knitr::kable(df) - } -} else print('the service appears to be down currently') +knitr::kable(df) ``` ## Get data for county In this example we access a couple variables at the watershed scale for the area of interest of a county (Benton County in this case) using the `sc_get_data` function. ```{r countydata} df <- sc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') -if (exists('df')){ - if (!is.null(df)){ - knitr::kable(head(df)) - } -} else print('the service appears to be down currently') +knitr::kable(head(df)) ``` ## Get all metrics for COMIDs or an Area of Interest We can also get all StreamCat metrics for a set of COMIDs or an area of interest. **Please do not request metric='all' and aoi='conus' in order not to overload requests to the server. Requesting metric='all' for a state or multiple states or hydroregions will also take a long time to process**. ```{r all} df <- sc_get_data(comid='179', aoi='cat', metric='all') -if (exists('df')){ - if (!is.null(df)){ - knitr::kable(head(df)) - } -} else print('the service appears to be down currently') +knitr::kable(head(df)) ``` ## Get NLCD data @@ -166,22 +107,14 @@ In this example we access National Land Cover Dataset (NLCD) data for 2001, just ```{r get_nlcd} df <- sc_nlcd(year='2001', aoi='cat', comid='179,1337,1337420') -if (exists('df')){ - if (!is.null(df)){ - knitr::kable(df) - } -} else print('the service appears to be down currently') +knitr::kable(df) ``` We can also pass a couple years for a different area of interest for another region like a county. ```{r get_nlcd2} df <- sc_nlcd(year='2006, 2019', aoi='ws', county='41003') -if (exists('df')){ - if (!is.null(df)){ - knitr::kable(head(df)) - } -} else print('the service appears to be down currently') +knitr::kable(head(df)) ``` ## Get COMIDs @@ -195,24 +128,16 @@ gages_coms <- sc_get_comid(gages, xcoord='LON_SITE', ycoord='L # Add the COMID we found back to gages data frame gages$COMID <- strsplit(gages_coms, ",")[[1]] df <- sc_get_data(metric='huden2010', aoi='ws', comid=gages_coms) -if (exists('df')){ - if (!is.null(df)){ - df$COMID <- as.character(df$comid) - gages <- dplyr::left_join(gages, df, by='COMID') - knitr::kable(head(gages)) - } -} else print('the service appears to be down currently') +df$COMID <- as.character(df$comid) +gages <- dplyr::left_join(gages, df, by='COMID') +knitr::kable(head(gages)) ``` ## Get data for a hydroregion In this example we access a couple watershed-only metrics for a particular NHDPlus hydroregion using the `sc_get_data` function. ```{r hydroregion} df <- sc_get_data(metric='pctwdwet2006', aoi='ws', region='Region17') -if (exists('df')){ - if (!is.null(df)){ - knitr::kable(head(df)) - } -} else print('the service appears to be down currently') +knitr::kable(head(df)) ``` ## Get data for CONUS diff --git a/vignettes/LakeCat.Rmd b/vignettes/Articles/LakeCat.Rmd similarity index 78% rename from vignettes/LakeCat.Rmd rename to vignettes/Articles/LakeCat.Rmd index 23b8231..27bf513 100644 --- a/vignettes/LakeCat.Rmd +++ b/vignettes/Articles/LakeCat.Rmd @@ -44,59 +44,35 @@ library(StreamCatTools) region_params <- lc_get_params(param='aoi') name_params <- lc_get_params(param='metric_names') -if (exists('region_params')){ - if (!is.null(region_params)){ - print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) - } -} else print('the service appears to be down currently') - -if (exists('name_params')){ - if (!is.null(name_params)){ -print(paste0('A selection of available LakrCat metrics include: ',paste(name_params[1:10],collapse = ', '))) - } -} else print('the service appears to be down currently') + +print(paste0('region parameters are: ', paste(region_params,collapse = ', '))) +print(paste0('A selection of available LakrCat metrics include: ',paste(name_params[1:10],collapse = ', '))) ``` We can also see what metrics are available for what areas of interest and what years using the `sc_get_params` function (which returns a tibble of information about StreamCat metrics): ```{r params2} var_info <- lc_get_params(param='variable_info') -if (exists('var_info')){ - if (!is.null(var_info)){ - head(var_info) - } -} else print('the service appears to be down currently') +head(var_info) ``` Look up the display name or names for a metric using the `lc_fullname` function via the API ```{r fullnames} metric='pcthbwet2016' fullname <- lc_fullname(metric) -if (exists('fullname')){ - if (!is.null(fullname)){ fullname - } -} else print('the service appears to be down currently') ``` ```{r fullnames2} metric=c('pctdecid2019','fert') fullname <- lc_fullname(metric) -if (exists('fullname')){ - if (!is.null(fullname)){ fullname - } -} else print('the service appears to be down currently') ``` ## Filter metric information by criteria We can also filter metric names and information by the metric year(s), the indicator categories for metrics, the metric data set names, or the Areas of Interest the metrics are available for. ```{r get_metric_names} metrics <- lc_get_metric_names(category = c('Anthropogenic','Natural'), aoi=c('Cat','Ws')) -if (exists('metrics')){ - if (!is.null(metrics)){ head(metrics) - } -} else print('the service appears to be down currently') ``` ## Get Waterbody COMIDs @@ -115,22 +91,19 @@ In this example we access several variables, for several areas of interest, and ```{r get_data} df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid=comids) -if (exists('df')){ - if (!is.null(df)){ - knitr::kable(df) - } -} else print('the service appears to be down currently') +knitr::kable(df) +``` + +```{r get_data2} +df <- lc_get_data(metric='pcturbmd2006,damdens', aoi='cat,ws', comid='23783629,23794487,23812618') +knitr::kable(df) ``` ## Get data for county In this example we access a couple variables at the watershed scale for the area of interest of a county (Benton County in this case) using the `sc_get_data` function. ```{r countydata} df <- lc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') -if (exists('df')){ - if (!is.null(df)){ - knitr::kable(head(df)) - } -} else print('the service appears to be down currently') +knitr::kable(head(df)) ``` ## Get NLCD data @@ -139,9 +112,5 @@ In this example we access National Land Cover Dataset (NLCD) data for 2019, just ```{r get_nlcd} df <- lc_nlcd(comid='23783629,23794487,23812618', year='2019', aoi='ws') -if (exists('df')){ - if (!is.null(df)){ - knitr::kable(df) - } -} else print('the service appears to be down currently') +knitr::kable(df) ``` diff --git a/vignettes/StartHere.Rmd b/vignettes/StartHere.Rmd new file mode 100644 index 0000000..ec5ebd5 --- /dev/null +++ b/vignettes/StartHere.Rmd @@ -0,0 +1,67 @@ +--- +title: "Start Here" +output: + html_document: + theme: flatly + keep_md: yes + number_sections: true + highlighted: default + toc: yes + toc_float: + collapsed: no + smooth_scroll: no + toc_depth: 2 +vignette: > + %\VignetteIndexEntry{Start Here} + %\VignetteEncoding{UTF-8}{inputenc} + %\VignetteEngine{knitr::rmarkdown} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>", + warning = FALSE, + message = FALSE +) +``` + +## Installing and loading StreamCatTools +To install, you can install from CRAN: +```{r, message=FALSE, eval=FALSE} +install.packages("StreamCatTools") +``` + +Or you can install from GitHub: +```{r, message=FALSE, eval=FALSE} +library(devtools) +install_github('USEPA/StreamCatTools') +``` + +After installing load the library +```{r, message=FALSE} +library(StreamCatTools) +``` + +## Background +The `StreamCatTools` package was designed to simplify the use of [StreamCat](https://www.epa.gov/national-aquatic-resource-surveys/streamcat-dataset) data in R, leveraging the new [API for StreamCat](https://api.epa.gov/StreamCat/streams/metrics). + +# Vignettes in `StreamCatTools` + +There are three additional vignettes in `StreamCatTools` that are available on our website [here](https://usepa.github.io/StreamCatTools/) under the "Articles" tab: + +1. Introduction + * An overview of the basic fucntionality of the package +2. LakeCat + * An overview of accessing data for lakes within the package and functions to do so +3. Applications + * A more in depth walk through with specific use-case examples and demonstrations + +These vignettes cover some of the core functions (and arguments within those functions) in `StreamCatTools`. Help files for a particular function are viewable by running `?function_name` after loading `StreamCatTools`. For example, to learn more about the `sc_get_data()` function, run `?sc-get_data`. + +# Citation information + +If you use `StreamCatTools` in your work, please cite it. You can view the most recent citation by running +```{r} +citation("StreamCatTools") +``` From 8b9df9ef777c16bcb3e57d5aa8628f2696b4056b Mon Sep 17 00:00:00 2001 From: mhweber Date: Fri, 24 Oct 2025 16:46:57 -0700 Subject: [PATCH 22/22] updated CRAN comments and NEWS --- NEWS.md | 4 +--- cran-comments.md | 19 +++++-------------- tests/testthat/test-sc_getdata.R | 3 +++ 3 files changed, 9 insertions(+), 17 deletions(-) diff --git a/NEWS.md b/NEWS.md index 8c6cd42..dfbce09 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,9 +1,7 @@ # StreamCatTools 0.9.1 - Handles a web service being down in testing using `testthat::skip_on_cran()` -- Handles a web service being down in vignettes -- Due to the lapse in government funding in federal agencies in the US, - the web service StreamCatTools is built around may be down for some time +- Converts most vignettes to articles and adds one new `Start Here` vignette # StreamCatTools 0.9.0 diff --git a/cran-comments.md b/cran-comments.md index b18cf49..a7fb6bb 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,7 +1,8 @@ This is a patch update that: - Handles a web service being down in testing using `testthat::skip_on_cran()` -- Handles a web service being down in vignettes +- Handles a web service being down in vignettes by converting most vignettes to + articles and leaving just one `Start Here` vignette - Due to the lapse in government funding in federal agencies in the US, the web service StreamCatTools is built around may be down for some time - Because of the lapse in government funding in federal agencies in the US, I @@ -17,19 +18,9 @@ This is a resubmission. ## R CMD check results -Here is the output from `devtools::check()` on R Version 4.4.1, +Here is the output from `devtools::check()` on R Version R version 4.5.0, devtools version 2.4.6, and Windows 11 x64 operating system -0 errors ✔ | 0 warnings ✔ | 2 notes ✖ +Duration: 2m 20.4s -R CMD check succeeded - -NOTES: - -checking installed package size ... NOTE - installed size is 5.0Mb - sub-directories of 1Mb or more: - doc 4.4Mb - -checking for future file timestamps ... NOTE - unable to verify current time +0 errors ✔ | 0 warnings ✔ | 0 notes ✔ diff --git a/tests/testthat/test-sc_getdata.R b/tests/testthat/test-sc_getdata.R index b6f2436..c124d13 100644 --- a/tests/testthat/test-sc_getdata.R +++ b/tests/testthat/test-sc_getdata.R @@ -9,6 +9,7 @@ test_that("sc_get_data for a sample COMID returns a data frame", { }) test_that("sc_get_data for multiple COMIDs and areas and metrics returns a data frame", { + testthat::skip_on_cran() df <- sc_get_data(metric='pcturbmd2006,pctconif2008,rddens', aoi='cat,ws', comid='179,1337,1337420') @@ -27,6 +28,7 @@ test_that("sc_get_data for showAreaSqKm and showPctFull returns a data frame", { }) test_that("sc_get_data for a hydroregion and ws metrics returns a data frame", { + testthat::skip_on_cran() df <- sc_get_data(metric='pctwdwet2006', aoi='ws', region='Region01') expect_true(exists("df")) @@ -35,6 +37,7 @@ test_that("sc_get_data for a hydroregion and ws metrics returns a data frame", { }) test_that("sc_get_data for a county and ws metrics returns a data frame", { + testthat::skip_on_cran() df <- sc_get_data(metric='pctwdwet2006', aoi='ws', county='41003') expect_true(exists("df"))