EESI · JacobRPrice · Jul 16, 2018 · Jul 16, 2018 · Jul 16, 2018 · Jul 16, 2018
diff --git 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
@@ -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
@@ -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.
diff --git 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
diff --git a/README.Rmd b/README.Rmd
@@ -17,10 +17,11 @@ knitr::opts_chunk$set(collapse=TRUE,comment='#>',fig.path='README-')
 <!-- same text as "description" in DESCRIPTION, just as a (temporary) placeholder. once it's up and running we can flesh some of this out. -->
 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
+  https://github.com/EESI/theseus/issues
diff --git 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)
+* None 
diff --git 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')
 )
diff --git a/man/WWTP_Impact.Rd b/man/WWTP_Impact.Rd
diff --git a/man/pstoveg_sample.Rd b/man/pstoveg_sample.Rd
diff --git 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