diff --git a/R/create_nepexplorer_app.R b/R/create_nepexplorer_app.R
index aad3908..3429407 100644
--- a/R/create_nepexplorer_app.R
+++ b/R/create_nepexplorer_app.R
@@ -41,7 +41,7 @@ if (is.null(mapping)) {
"visit_col" = "VISIT",
"visitn_col" = "VISITN",
"baseline_flag" = "BLFL",
- "baseline_values" = "Y",
+ "baseline_values" = list("Y" = "Y"),
"normal_col_high" = "STNRHI",
"id_col" = "USUBJID",
"age_col" = "AGE",
diff --git a/R/creatinine_data_fcn.R b/R/creatinine_data_fcn.R
index 2d0b78a..2c96149 100644
--- a/R/creatinine_data_fcn.R
+++ b/R/creatinine_data_fcn.R
@@ -15,10 +15,9 @@ creatinine_data_fcn <- function(df, settings) {
.data[[settings$measure_col]],
.data[[settings$value_col]], .data[[settings$baseline_flag]])
-
#get baseline creatinine levels for each subject for hover text
baseline_creat <- creatinine_data %>%
- filter(.data[[settings$baseline_flag]] == settings$baseline_values) %>%
+ filter(.data[[settings$baseline_flag]] == settings$baseline_values$Y) %>%
select(.data[[settings$id_col]], BASELINE = .data[[settings$value_col]])
diff --git a/R/init_nepExplorer.R b/R/init_nepExplorer.R
index 8294744..b5a4ba8 100644
--- a/R/init_nepExplorer.R
+++ b/R/init_nepExplorer.R
@@ -11,6 +11,26 @@
#' @export
init_nepExplorer <- function(data, settings) {
+
+ # check for any missing required settings and warn user
+ missing_settings <- check_required_settings(expected_settings, settings)
+
+ if (length(missing_settings) > 0) {
+ warning(paste("The following required nepExplorer settings were not detected:",
+ paste(names(missing_settings), collapse = ", ")))
+ }
+
+ # check for any missing columns that are specified in settings
+ missing_cols_results <- lapply(c("labs", "vitals", "dm"),
+ function(domain) check_expected_cols(domain, settings, data))
+
+ missing_cols_msgs <- Filter(Negate(is.null), missing_cols_results)
+
+ if (length(missing_cols_msgs) > 0) {
+ warning(paste(missing_cols_msgs, collapse = "\n"))
+ }
+
+ # subset vital signs dataset to blood pressure tests
vs_sub <-
data$vitals %>%
filter(.data[[settings[["vitals"]]$measure_col]] %in%
@@ -18,20 +38,21 @@ init_nepExplorer <- function(data, settings) {
settings[["vitals"]]$measure_values$DIABP,
settings[["vitals"]]$measure_values$SYSBP
))
-
+
+ # stack labs and vitals
vs_labs <- data$labs %>% bind_rows(vs_sub)
-
+
+ #subset dm dataset to usable columns
dm_sub <- data$dm %>%
dplyr::select(any_of(c(settings[["dm"]][["id_col"]],
- settings[["dm"]][["treatment_col"]],
- settings[["dm"]][["race_col"]],
- settings[["dm"]][["age_col"]])))
-
- # left join to keep all rows in dm
+ settings[["dm"]][["treatment_col"]],
+ settings[["dm"]][["race_col"]],
+ settings[["dm"]][["age_col"]])))
+
+ # left join labs/vitals to keep all rows in dm
anly <- dm_sub %>%
dplyr::left_join(vs_labs,
- by = c(settings[["labs"]][["id_col"]],
- settings[["labs"]][["treatment_col"]]))
-
+ by = setNames(settings[["dm"]][["id_col"]], settings[["labs"]][["id_col"]]))
+
list(data = anly, settings = settings)
}
diff --git a/R/nepexplorerMod.R b/R/nepexplorerMod.R
index f7cef0f..4e15688 100644
--- a/R/nepexplorerMod.R
+++ b/R/nepexplorerMod.R
@@ -118,10 +118,9 @@ nepexplorer_server <- function(input, output, session, params) {
measure_values[grep("nepFC", names(measure_values))])
# update selectize to reflect what's specific in metadata
-
shinyWidgets::updatePickerInput(session,
"measures",
- choices = measures,
+ choices = measures[!is.na(measures)],
selected = fold_change_measures
)
})
diff --git a/R/validation_checks_util.R b/R/validation_checks_util.R
new file mode 100644
index 0000000..7e0359a
--- /dev/null
+++ b/R/validation_checks_util.R
@@ -0,0 +1,102 @@
+#' Expected Settings List
+#'
+#' This list defines the expected settings for different data domains.
+#' Each domain contains specific columns and values that are required for data processing.
+#'
+#' @format A list with the following structure:
+#' \describe{
+#' \item{labs}{A list containing the expected settings for laboratory data:
+#' \describe{
+#' \item{id_col}{Column name for the subject identifier (e.g., "USUBJID").}
+#' \item{measure_col}{Column name for the measure parameter (e.g., "PARAM").}
+#' \item{measure_values}{A list of measure values and their corresponding descriptions
+#' (e.g., list("CREAT" = "Creatinine")).}
+#' \item{value_col}{Column name for the measurement value (e.g., "STRESN").}
+#' \item{unit_col}{Column name for the measurement unit (e.g., "STRESU").}
+#' \item{studyday_col}{Column name for the study day (e.g., "DY").}
+#' \item{visit_col}{Column name for the visit description (e.g., "VISIT").}
+#' \item{visitn_col}{Column name for the visit number (e.g., "VISITN").}
+#' \item{baseline_flag}{Column name for the baseline flag (e.g., "BLFL").}
+#' \item{baseline_values}{Value indicating baseline (e.g., "Y").}
+#' \item{normal_col_high}{Column name for the upper limit of normal range
+#' (e.g., "STNRHI").}
+#' }
+#' }
+#' \item{dm}{A list containing the expected settings for demographic data:
+#' \describe{
+#' \item{id_col}{Column name for the subject identifier (e.g., "USUBJID").}
+#' }
+#' }
+#' \item{vitals}{A list containing the expected settings for vital signs data:
+#' \describe{
+#' \item{id_col}{Column name for the subject identifier (e.g., "USUBJID").}
+#' \item{measure_col}{Column name for the measure parameter (e.g., "PARAM").}
+#' }
+#' }
+#' }
+expected_settings <- list(labs = list("id_col" = "USUBJID", "measure_col" = "PARAM",
+ "measure_values" = list("CREAT" = "Creatinine"),
+ "value_col" = "STRESN",
+ "unit_col" = "STRESU",
+ "studyday_col" = "DY",
+ "visit_col" = "VISIT",
+ "visitn_col" = "VISITN",
+ "baseline_flag" = "BLFL",
+ "baseline_values" = list("Y" = "Y"),
+ "normal_col_high" = "STNRHI"),
+ dm = list("id_col" = "USUBJID"),
+ vitals = list("id_col" = "USUBJID", "measure_col" = "PARAM"))
+
+#' Check Required Settings in a List
+#'
+#' This function checks if a given list contains all the required elements specified in another list.
+#' It allows for additional elements at any nesting level and prints out a message listing the missing settings, if any.
+#'
+#' @param required_list A list specifying the required elements.
+#' @param actual_list A list to be checked against the required elements.
+#' @param parent_key (Optional) A string used internally to track the full key path during recursion.
+#' Default is an empty string.
+#' @return A list of missing elements, if any.
+check_required_settings <- function(required_list, actual_list, parent_key = "") {
+ missing_elements <- list()
+
+ for (name in names(required_list)) {
+ full_key <- if (parent_key == "") name else paste(parent_key, name, sep = "$")
+
+ if (!name %in% names(actual_list)) {
+ missing_elements[[full_key]] <- required_list[[name]]
+ } else if (is.list(required_list[[name]])) {
+ if (!is.list(actual_list[[name]])) {
+ missing_elements[[full_key]] <- required_list[[name]]
+ } else {
+ nested_missing <- check_required_settings(required_list[[name]], actual_list[[name]], full_key)
+ missing_elements <- c(missing_elements, nested_missing)
+ }
+ }
+ }
+
+ return(missing_elements)
+}
+
+#' Check for Missing Columns in Data
+#'
+#' This function checks for any columns specified in the settings object that are not present in the data.
+#' It returns a message listing the missing columns, if any.
+#'
+#' @param data_domain A string specifying the data domain to check (e.g., "labs", "vitals", "dm").
+#' @param settings_list A list containing the settings for each data domain.
+#' @param data_list A list containing the data for each domain.
+#' @return A string message listing the missing columns, or NULL if all expected columns are present.
+check_expected_cols <- function(data_domain, settings_list, data_list) {
+
+ expected_cols <- settings_list[[data_domain]][!grepl("_values$", names(settings_list[[data_domain]]))] %>% unlist()
+
+ missing_cols <- setdiff(expected_cols, colnames(data_list[[data_domain]]))
+
+ if (length(missing_cols) > 0) {
+ paste("The following columns were specified in", data_domain, "settings but not found in the",
+ data_domain, "dataset: ", paste(missing_cols, collapse = ", "))
+ } else {
+ NULL
+ }
+}
diff --git a/data-raw/meta_nepExplorer.csv b/data-raw/meta_nepExplorer.csv
index 08a6770..4dd7a52 100644
--- a/data-raw/meta_nepExplorer.csv
+++ b/data-raw/meta_nepExplorer.csv
@@ -1,28 +1,28 @@
-text_key,domain,col_key,field_key,type,label,description,multiple,standard_adam,standard_sdtm
-id_col,vitals,id_col,,column,ID column,Unique subject identifier variable name.,FALSE,USUBJID,USUBJID
-value_col,vitals,value_col,,column,Value column,Vitals result variable name.,FALSE,AVAL,VSSTRESN
-measure_col,vitals,measure_col,,column,Measure column,Vitals measure variable name,FALSE,PARAM,VSTEST
-studyday_col,vitals,studyday_col,,column,Study Day column,Visit day variable name,FALSE,ADY,VSDY
-visit_col,vitals,visit_col,,column,Visit column,Visit variable name,FALSE,AVISIT,VISIT
-visitn_col,vitals,visitn_col,,column,Visit Number column,Visit number variable name,FALSE,AVISITN,VISITNUM
-measure_values--SYSBP,vitals,measure_col,SYSBP,field,Systolic value,Value used for Systolic Blood Pressure in the specified measure column,FALSE,Systolic Blood Pressure (mmHg),Systolic Blood Pressure
-measure_values--DIABP,vitals,measure_col,DIABP,field,Diastolic value,Value used for Diastolic Blood Pressure in the specified measure column,FALSE,Diastolic Blood Pressure (mmHg),Diastolic Blood Pressure
-unit_col,vitals,unit_col,,column,Unit column,Unit of measure variable name,FALSE,,VSSTRESU
-vs_baseline_flag,vitals,vs_baseline_flag,,column,Vital Signs Baseline Flag,Column for assigning VS baseline visits,FALSE,ABLFL,
-vs_baseline_values--Y,vitals,vs_baseline_flag,Y,field,Vital Signs Baseline Flag value,Value used for VS Baseline in the specified baseline column,FALSE,Y,
-measure_values--ALB,labs,measure_col,ALB,field,Albumin value,Value used for Albumin in the specified measure column,FALSE,Albumin (mg/dL),Albumin
-measure_values--ALB/CREAT,labs,measure_col,ALB/CREAT,field,Albumin/Creatinine Ratio value,Value used for Albumin/Creatinine ratio in the specified measure column,FALSE,Albumin/Creatinine,
-measure_values--BUN/CREAT,labs,measure_col,BUN/CREAT,field,Blood Urea Nitrogen/Creatinine Ratio value,Value used for Blood Urea Nitrogen/Creatinine ratio in the specified measure column,FALSE,Blood Urea Nitrogen/Creatinine,
-measure_values--nepFC_BICARB,labs,measure_col,BICARB,field,Bicarbonate value,Value used for Bicarbonate in the specified measure column,FALSE,Bicarbonate (umol/L),Bicarbonate
-measure_values--nepFC_BUN,labs,measure_col,BUN,field,Blood Urea Nitrogen value,Value used for Blood Urea Nitrogen in the specified measure column,FALSE,Blood Urea Nitrogen (mmol/L),Blood Urea Nitrogen
-measure_values--nepFC_CA,labs,measure_col,CA,field,Calcium value,Value used for Calcium in the specified measure column,FALSE,Calcium (mmol/L),Calcium
-measure_values--nepFC_CL,labs,measure_col,CL,field,Chloride value,Value used for Chloride in the specified measure column,FALSE,Chloride (mmol/L),Chloride
-measure_values--CREAT,labs,measure_col,CREAT,field,Creatinine value,Value used for Creatinine in the specified measure column,FALSE,Creatinine (mg/dL),Creatinine
-measure_values--CYSTC,labs,measure_col,CYSTC,field,Cystatin C value,Value used for Cystatin C in the specified measure column,FALSE,Cystatin C (umol/L),Cystatin C
-measure_values--eGFR,labs,measure_col,eGFR,field,eGFR value,Value used for the Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFR (mL/min),eGFR
-measure_values--eGFRcys,labs,measure_col,eGFRcys,field,eGFRcys value,Value used for the Cystatic C-based Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFRcys (mL/min),eGFRcys
-measure_values--nepFC_PHOS,labs,measure_col,PHOS,field,Phosphate value,Value used for Phosphate in the specified measure column,FALSE,Phosphate (mmol/L),Phosphate
-measure_values--nepFC_K,labs,measure_col,K,field,Potassium value,Value used for Potassium in the specified measure column,FALSE,Potassium (mmol/L),Potassium
-measure_values--nepFC_SODIUM,labs,measure_col,SODIUM,field,Sodium value,Value used for Sodium in the specified measure column,FALSE,Sodium (mmol/L),Sodium
-baseline_flag,labs,baseline_flag,,column,Baseline Flag column,Column for assigning baseline visits,FALSE,ABLFL,LBBLFL
-baseline_values--Y,labs,baseline_flag,Y,field,Baseline Flag value,Value used for Baseline in the specified baseline column,FALSE,Y,Y
+text_key,domain,col_key,field_key,type,label,description,multiple,standard_adam,standard_sdtm
+id_col,vitals,id_col,,column,ID column,Unique subject identifier variable name.,FALSE,USUBJID,USUBJID
+value_col,vitals,value_col,,column,Value column,Vitals result variable name.,FALSE,AVAL,VSSTRESN
+measure_col,vitals,measure_col,,column,Measure column,Vitals measure variable name,FALSE,PARAM,VSTEST
+studyday_col,vitals,studyday_col,,column,Study Day column,Visit day variable name,FALSE,ADY,VSDY
+visit_col,vitals,visit_col,,column,Visit column,Visit variable name,FALSE,AVISIT,VISIT
+visitn_col,vitals,visitn_col,,column,Visit Number column,Visit number variable name,FALSE,AVISITN,VISITNUM
+measure_values--SYSBP,vitals,measure_col,SYSBP,field,Systolic value,Value used for Systolic Blood Pressure in the specified measure column,FALSE,Systolic Blood Pressure (mmHg),Systolic Blood Pressure
+measure_values--DIABP,vitals,measure_col,DIABP,field,Diastolic value,Value used for Diastolic Blood Pressure in the specified measure column,FALSE,Diastolic Blood Pressure (mmHg),Diastolic Blood Pressure
+unit_col,vitals,unit_col,,column,Unit column,Unit of measure variable name,FALSE,,VSSTRESU
+baseline_flag,vitals,vs_baseline_flag,,column,Vital Signs Baseline Flag,Column for assigning VS baseline visits,FALSE,ABLFL,
+baseline_values--Y,vitals,vs_baseline_flag,Y,field,Vital Signs Baseline Flag value,Value used for VS Baseline in the specified baseline column,FALSE,Y,
+measure_values--ALB,labs,measure_col,ALB,field,Albumin value,Value used for Albumin in the specified measure column,FALSE,Albumin (mg/dL),Albumin
+measure_values--ALB/CREAT,labs,measure_col,ALB/CREAT,field,Albumin/Creatinine Ratio value,Value used for Albumin/Creatinine ratio in the specified measure column,FALSE,Albumin/Creatinine,
+measure_values--BUN/CREAT,labs,measure_col,BUN/CREAT,field,Blood Urea Nitrogen/Creatinine Ratio value,Value used for Blood Urea Nitrogen/Creatinine ratio in the specified measure column,FALSE,Blood Urea Nitrogen/Creatinine,
+measure_values--nepFC_BICARB,labs,measure_col,BICARB,field,Bicarbonate value,Value used for Bicarbonate in the specified measure column,FALSE,Bicarbonate (umol/L),Bicarbonate
+measure_values--nepFC_BUN,labs,measure_col,BUN,field,Blood Urea Nitrogen value,Value used for Blood Urea Nitrogen in the specified measure column,FALSE,Blood Urea Nitrogen (mmol/L),Blood Urea Nitrogen
+measure_values--nepFC_CA,labs,measure_col,CA,field,Calcium value,Value used for Calcium in the specified measure column,FALSE,Calcium (mmol/L),Calcium
+measure_values--nepFC_CL,labs,measure_col,CL,field,Chloride value,Value used for Chloride in the specified measure column,FALSE,Chloride (mmol/L),Chloride
+measure_values--CREAT,labs,measure_col,CREAT,field,Creatinine value,Value used for Creatinine in the specified measure column,FALSE,Creatinine (mg/dL),Creatinine
+measure_values--CYSTC,labs,measure_col,CYSTC,field,Cystatin C value,Value used for Cystatin C in the specified measure column,FALSE,Cystatin C (umol/L),Cystatin C
+measure_values--eGFR,labs,measure_col,eGFR,field,eGFR value,Value used for the Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFR (mL/min),eGFR
+measure_values--eGFRcys,labs,measure_col,eGFRcys,field,eGFRcys value,Value used for the Cystatic C-based Estimated Glomerular Filtration Rate in the specified measure column,FALSE,eGFRcys (mL/min),eGFRcys
+measure_values--nepFC_PHOS,labs,measure_col,PHOS,field,Phosphate value,Value used for Phosphate in the specified measure column,FALSE,Phosphate (mmol/L),Phosphate
+measure_values--nepFC_K,labs,measure_col,K,field,Potassium value,Value used for Potassium in the specified measure column,FALSE,Potassium (mmol/L),Potassium
+measure_values--nepFC_SODIUM,labs,measure_col,SODIUM,field,Sodium value,Value used for Sodium in the specified measure column,FALSE,Sodium (mmol/L),Sodium
+baseline_flag,labs,baseline_flag,,column,Baseline Flag column,Column for assigning baseline visits,FALSE,ABLFL,LBBLFL
+baseline_values--Y,labs,baseline_flag,Y,field,Baseline Flag value,Value used for Baseline in the specified baseline column,FALSE,Y,Y
diff --git a/data-raw/meta_nepExplorer2.csv b/data-raw/meta_nepExplorer2.csv
index 2485c67..327bf51 100644
--- a/data-raw/meta_nepExplorer2.csv
+++ b/data-raw/meta_nepExplorer2.csv
@@ -8,8 +8,8 @@ visitn_col,vitals,visitn_col,,column,Visit Number column,Visit number variable n
measure_values--SYSBP,vitals,measure_col,SYSBP,field,Systolic value,Value used for Systolic Blood Pressure in the specified measure column,FALSE,Systolic Blood Pressure (mmHg),Systolic Blood Pressure
measure_values--DIABP,vitals,measure_col,DIABP,field,Diastolic value,Value used for Diastolic Blood Pressure in the specified measure column,FALSE,Diastolic Blood Pressure (mmHg),Diastolic Blood Pressure
unit_col,vitals,unit_col,,column,Unit column,Unit of measure variable name for Blood Pressure,FALSE,STRESU,VSSTRESU
-vs_baseline_flag_col,vitals,vs_baseline_flag,,column,VS Baseline Flag,Column for assigning baseline visits for Blood Pressure,FALSE,ABLFL,
-vs_baseline_values--POS,vitals,vs_baseline_flag_col,POS,field,VS Baseline Flag value,Value used for Baseline in the specified baseline column for Blood Pressure,FALSE,Y,Y
+baseline_flag_col,vitals,vs_baseline_flag,,column,VS Baseline Flag,Column for assigning baseline visits for Blood Pressure,FALSE,ABLFL,
+baseline_values--Y,vitals,vs_baseline_flag_col,Y,field,VS Baseline Flag value,Value used for Baseline in the specified baseline column for Blood Pressure,FALSE,Y,Y
lab_unit_col,labs,lab_unit_col,,column,Unit column,Unit of measure variable name,FALSE,STRESU,STRESU
measure_values--ALB,labs,measure_col,ALB,field,Albumin value,Value used for Albumin in the specified measure column,FALSE,Albumin (g/L),Albumin
measure_values--BICARB,labs,measure_col,BICARB,field,Bicarbonate value,Value used for Bicarbonate in the specified measure column,FALSE,Bicarbonate (umol/L),Bicarbonate
diff --git a/data/meta_nepExplorer.rda b/data/meta_nepExplorer.rda
index 48f8e16..a7c010a 100644
Binary files a/data/meta_nepExplorer.rda and b/data/meta_nepExplorer.rda differ
diff --git a/docs/articles/get_started.html b/docs/articles/get_started.html
index f314de5..c7f4847 100644
--- a/docs/articles/get_started.html
+++ b/docs/articles/get_started.html
@@ -5,61 +5,45 @@
-
Getting Started with nepExplorer • nepExplorer
-
-
-
-
-
+
Skip to contents
-
-