diff --git a/DESCRIPTION b/DESCRIPTION index cfa9d59..8cc8a2f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,10 +1,12 @@ Package: theseus Type: Package Title: Analysis and Visualization Tools for Microbial Community Data -Version: 0.1.0 +Version: 0.1.1 Authors@R: c( - person("Jacob", "Price", email = "jrp355@drexel.edu", role = c("aut")), - person("Stephen", "Woloszynek", email = "sw424@drexel.edu", role = c("cre","aut")) + person("Jacob", "Price", email = "jacobrpricephd@gmail.com", role = c("cre","aut")), + person("Stephen", "Woloszynek", email = "sw424@drexel.edu", role = c("aut")), + person("Gail", "Rosen", email = "glr26@drexel.edu", role = c("aut")), + person("Christopher", "Sales", email = "chris.sales@drexel.edu", role = c("aut")) ) Description: An approach to the visualization, analysis, and interpretation of (microbial) community composition data, especially those originating from @@ -29,7 +31,6 @@ Imports: phyloseq (>= 1.20.0), ShortRead (>= 1.34.0), splancs, - tidyverse (>= 1.1.1), tidyr, vegan (>= 2.3.5), viridis (>= 0.4.0) @@ -39,4 +40,4 @@ Suggests: rmarkdown, testthat VignetteBuilder: knitr -RoxygenNote: 6.0.1 +RoxygenNote: 6.0.1.9000 diff --git a/NAMESPACE b/NAMESPACE index 4ef1b5f..46c2aeb 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -9,7 +9,6 @@ export(constord) export(envtoverlay) export(prev) export(pstoveg_otu) -export(pstoveg_sample) export(pstoveg_sd) export(qualcontour) import(ggplot2) diff --git a/NEWS.md b/NEWS.md index 748d83e..b3ebf79 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,12 @@ -# theseus 0.1.0 +CHANGES IN VERSION 0.1.1 +------------------------- + - Updated CITATION and DESCRIPTION to reflect preprint information + - Improved README markup + - corrected citation in data_WWTP_Impact.R documentation + - minor clarifications/corrections made in documentation for several functions and vignette + + +# theseus VERSION 0.1.0 +------------------------- * First release. \ No newline at end of file diff --git a/R/data_WWTP_Impact.R b/R/data_WWTP_Impact.R index 58711c9..7755ad4 100644 --- a/R/data_WWTP_Impact.R +++ b/R/data_WWTP_Impact.R @@ -17,7 +17,7 @@ #' phy_tree slots. #' #' @references Price, J. R., Ledford, S. H., Ryan, M. O., Toran, L., Sales, -#' C. M. (2017). Wastewater treatment plant effluent introduces recoverable +#' C. M. (2018). Wastewater treatment plant effluent introduces recoverable #' shifts in microbial community composition in receiving streams. Sci. Total #' Environ. doi:10.1016/j.scitotenv.2017.09.162. #' diff --git a/R/pstoveg_sample.R b/R/pstoveg_sample.R deleted file mode 100644 index 6b35563..0000000 --- a/R/pstoveg_sample.R +++ /dev/null @@ -1,34 +0,0 @@ -#' Converts sample_data slot of a phyloseq object to vegan-compatible matrix -#' -#' physeq2veg_otu is a helper function intended to convert the species/taxa -#' count slot of a phyloseq object to a vegan-friendly matrix. -#' -#' @param PS (required) a phyloseq object -#' -#' @return A matrix containing a phyloseq object's otu_table slot. -#' -#' @seealso \code{\link[phyloseq]{phyloseq-class}} -#' \code{\link[phyloseq]{otu_table-class}} \code{\link[phyloseq]{otu_table}} -#' -#' @examples -#' \dontrun{ -#' library(phyloseq) -#' data("GlobalPatterns") -#' # inspect otu_table() -#' dim(otu_table(GlobalPatterns)) -#' str(otu_table(GlobalPatterns)) -#' taxa_are_rows(GlobalPatterns) -#' gp.otu <- physeq2veg_otu(GlobalPatterns) -#' dim(gp.otu) -#' str(gp.otu) -#' } -#' -#' @export - -pstoveg_sample <- function(PS) { - - SAMP <- phyloseq::sample_data(PS) - - return(as(SAMP,'data.frame')) - -} diff --git a/README.Rmd b/README.Rmd index 390d563..567dc0b 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,10 +17,11 @@ knitr::opts_chunk$set(collapse=TRUE,comment='#>',fig.path='README-') theseus provides functions to assist in the analysis, visualization, and interpretation of community composition data, especially those originating from amplicon sequencing. -## Relevant Software and Literature -Callahan, Sankaran, Fukuyama, McMurdie, and Holmes (2017) [Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses](http://dx.doi.org/10.12688/f1000research.8986.2) -McMurdie and Holmes (2013) [phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data](http://dx.plos.org/10.1371/journal.pone.0061217) -Oksanen,Blanchet, Friendly, Kindt, Legendre, McGlinn, Minchin, O'Hara, Simpson, Solymos, Stevens, Szoecs, and Wagner (2017) [vegan: Community Ecology Package](https://CRAN.R-project.org/package=vegan) +## Relevant Software and Literature +* Price, Woloszynek, Rosen, and Sales (2018) [theseus - An R package for the analysis and visualization of microbial community data](https://www.biorxiv.org/content/early/2018/04/05/295675) +* Callahan, Sankaran, Fukuyama, McMurdie, and Holmes (2017) [Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses](http://dx.doi.org/10.12688/f1000research.8986.2) +* McMurdie and Holmes (2013) [phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data](http://dx.plos.org/10.1371/journal.pone.0061217) +* Oksanen,Blanchet, Friendly, Kindt, Legendre, McGlinn, Minchin, O'Hara, Simpson, Solymos, Stevens, Szoecs, and Wagner (2017) [vegan: Community Ecology Package](https://CRAN.R-project.org/package=vegan) ## Installation @@ -31,11 +32,11 @@ install.packages('theseus') # To install the developmental version via Github: # install.packages('devtools') -devtools::install_github('sw1/theseus',build_vignettes=TRUE) +devtools::install_github('EESI/theseus',build_vignettes=TRUE) ``` ## Development For future feature requests or suggestions, request an issue: - https://github.com/sw1/theseus/issues \ No newline at end of file + https://github.com/EESI/theseus/issues \ No newline at end of file diff --git a/cran-comments.md b/cran-comments.md index 8ae4907..1918daf 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,50 +1,13 @@ -This is a submission (first release) - ---- - ## Test environments -* Mac (travis-ci): R-release 3.4.3 [12/18/17] -* Mac OS X El Capitan (local machine): R 3.4.0 [12/18/17] -* Linux (travis-ci): R-release 3.4.2 [12/18/17] -* ubuntu 17.10 (local machine): R 3.3.2 [12/18/17] -* win-builder: R-release 3.4.3, R-dev [12/18/17] +* Mac OS X El Capitan (local machine): R 3.4.3 [09/24/18] ## R CMD check results -Mac, Linux: - -0 errors | 0 warnings | 0 notes - -Win: +Mac: 0 errors | 0 warnings | 0 notes -Dev versions: - -* Seemingly have issues with igraph and phyloseq installations. Both of these - dependencies are well maintained and shouldn't be an issue when new R versions - release. - -## Responses to Previous Submission [12/18/17] - -* Removed Akima depends due to licensing issues; it's not longer used in the pkg -* Vignette takes ~15s to knit; tests take ~47s to complete - -## Responses to Previous Submission [12/20/17] - -* Link in description now works -* No code is now run in vignette builds -- to improve check time -* Removes set of tests that generate figures -- to improve check time -* Linux check time: 247s -* Travis: linux job time 396s, mac job time 1018s -* Win-builder: install time 25s, check time 387s - -## License - -* License components with restrictions and base license permitting such: - MIT + file LICENSE - ## Downstream dependencies -* None (first release) \ No newline at end of file +* None diff --git a/inst/CITATION b/inst/CITATION index 42432c3..736cb45 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -1,13 +1,14 @@ -citHeader('To cite theseus for publications, see https://github.com/sw1/theseus for most recent information; otherwise, please use:') +citHeader('To cite theseus for publications, see https://github.com/EESI/theseus for most recent information; otherwise, please use:') citEntry( - entry = 'Manual', - title = 'theseus', + entry = 'article', + title = 'theseus - An R package for the analysis and visualization of microbial community data', author = personList(as.person('Jacob R. Price'), as.person('Stephen Woloszynek'), as.person('Gail Rosen'), as.person('Christopher M. Sales')), - year = '2017', - url = 'https://github.com/sw1/theseus', - textVersion = paste('theseus. 2017. Price, J., Woloszynek, S., Rosen, G., and C. Sales') + year = '2018', + journal = 'bioRxiv', + url = 'https://doi.org/10.1101/295675', + textVersion = paste('theseus - An R package for the analysis and visualization of microbial community data. 2017. Price, J., Woloszynek, S., Rosen, G., and C. Sales') ) \ No newline at end of file diff --git a/man/WWTP_Impact.Rd b/man/WWTP_Impact.Rd index 7614eb8..b2a4af4 100644 --- a/man/WWTP_Impact.Rd +++ b/man/WWTP_Impact.Rd @@ -23,7 +23,7 @@ obtained from the author's GitHub repository (see url below). } \references{ Price, J. R., Ledford, S. H., Ryan, M. O., Toran, L., Sales, - C. M. (2017). Wastewater treatment plant effluent introduces recoverable + C. M. (2018). Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in receiving streams. Sci. Total Environ. doi:10.1016/j.scitotenv.2017.09.162. } diff --git a/man/pstoveg_sample.Rd b/man/pstoveg_sample.Rd deleted file mode 100644 index f799c86..0000000 --- a/man/pstoveg_sample.Rd +++ /dev/null @@ -1,36 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/pstoveg_sample.R -\name{pstoveg_sample} -\alias{pstoveg_sample} -\title{Converts sample_data slot of a phyloseq object to vegan-compatible matrix} -\usage{ -pstoveg_sample(PS) -} -\arguments{ -\item{PS}{(required) a phyloseq object} -} -\value{ -A matrix containing a phyloseq object's otu_table slot. -} -\description{ -physeq2veg_otu is a helper function intended to convert the species/taxa -count slot of a phyloseq object to a vegan-friendly matrix. -} -\examples{ -\dontrun{ -library(phyloseq) -data("GlobalPatterns") -# inspect otu_table() -dim(otu_table(GlobalPatterns)) -str(otu_table(GlobalPatterns)) -taxa_are_rows(GlobalPatterns) -gp.otu <- physeq2veg_otu(GlobalPatterns) -dim(gp.otu) -str(gp.otu) -} - -} -\seealso{ -\code{\link[phyloseq]{phyloseq-class}} - \code{\link[phyloseq]{otu_table-class}} \code{\link[phyloseq]{otu_table}} -} diff --git a/vignettes/general_usage.Rmd b/vignettes/general_usage.Rmd index eef1929..895a0e9 100644 --- a/vignettes/general_usage.Rmd +++ b/vignettes/general_usage.Rmd @@ -109,7 +109,7 @@ sample_data(wwtp) <- as.data.frame(sampdat.altered) ## envtoverlay - Fitting environmental vectors and surfaces into ordination space -The calculations for unconstrained ordination does not take environmental or sample metadata into account. The *vegan* functions **envfit** and **ordisurf** attempt to fit environmental descriptors into ordination space and display them as vectors and surfaces respectively. Gavin Simpson, one of vegan's authors, has a great [blog](http://www.fromthebottomoftheheap.net/2011/06/10/what-is-ordisurf-doing/) explaining how these functions work and are interpreted. Jari Oksanen has provided several vignettes on [vegan's homepage ](https://cran.r-project.org/package=vegan) that also discuss the application of these functions. +The calculations for unconstrained ordination do not take environmental or sample metadata into account. The *vegan* functions **envfit** and **ordisurf** attempt to fit environmental descriptors into ordination space and display them as vectors and surfaces respectively. Gavin Simpson, one of vegan's authors, has a great [blog](http://www.fromthebottomoftheheap.net/2011/06/10/what-is-ordisurf-doing/) explaining how these functions work and are interpreted. Jari Oksanen has provided several vignettes on [vegan's homepage ](https://cran.r-project.org/package=vegan) that also discuss the application of these functions. Function **envtoverlay** (environmental variable overlay) takes advantage of ggplot2 to make these plots (usually generated in base::plot) a little prettier and user friendly, particularly when the user would like to present the results as a faceted plot. @@ -136,7 +136,7 @@ There are several differences between **constord** and **phyloseq::plot_ordinati Note: * The numbering approach is consistent with *vegan* (*theseus* and *phyloseq* rely on vegan::scores to get the scores themselves). -* The options for this function and it's plot are evolving and we may include additional ordination methods and plotting features later on. +* The options for this function and its plot are evolving and we may include additional ordination methods and plotting features later on. ## cohort_relabund - Cohort Relative Abundance Plots