Update README.md

Author: jedick

DESCRIPTION

@@ -1,6 +1,6 @@
-Date: 2020-02-04
+Date: 2020-02-20
 Package: canprot
-Version: 0.1.4-61
+Version: 0.1.5
 Title: Compositional Analysis of Differentially Expressed Proteins in Cancer and Cell Culture
 Authors@R: c(
     person("Jeffrey", "Dick", email = "j3ffdick@gmail.com", role = c("aut", "cre"),

README.md

@@ -2,12 +2,19 @@
 
 # canprot
 
-Datasets are collected here for differentially (up- and down-)
-expressed proteins identified in proteomic studies of cancer and in cell
-culture experiments. Tables of amino acid compositions of proteins are
-used for calculations of chemical composition, projected into selected
-basis species. Plotting functions are used to visualize the compositional
-differences and thermodynamic potentials for proteomic transformations.
+Compositional analysis of differentially expressed proteins in cancer and cell
+culture proteomics experiments. The data include lists of up- and
+down-regulated proteins in different types of cancer (colorectal, pancreatic,
+breast, lung, prostate) and laboratory conditions (hypoxia, hyperosmotic
+stress, 3D cell culture, and proteins secreted in hypoxia), together with amino
+acid compositions calculated for protein sequences from UniProt. Functions are
+provided to compute compositional metrics including protein length, carbon
+oxidation state, and stoichiometric hydration state. In addition, phylostrata
+(evolutionary ages) of protein-coding genes are available using data from
+[Liebeskind et al. (2016)](https://doi.org/10.1093/gbe/evw113) or [Trigos et
+al. (2017)](https://doi.org/10.1073/pnas.1617743114). The vignettes show
+references and plots of differences of chemical composition and phylostrata for
+all datasets.
 
 For more information, see two papers in *PeerJ* ([2016](http://doi.org/10.7717/peerj.2238)
 and [2017](http://doi.org/10.7717/peerj.3421)).
@@ -23,26 +30,27 @@ install.packages("canprot")
 
 ## Installation from Github
 
-First install the **devtools** package from CRAN:
+First install the **remotes** package from CRAN:
 
 ```R
-install.packages("devtools")
+install.packages("remotes")
 ```
 
 Then install **canprot** from Github:
 
 ```R
-devtools::install_github("jedick/canprot")
+remotes::install_github("jedick/canprot")
 ```
 
-## Building vignettes
+This also installs the **CHNOSZ** and **xtable** packages.
 
-To install the package including the vignettes:
+### Building vignettes
+
+Building the vignettes requires [pandoc](http://pandoc.org/installing.html) on the system.
+To install the package with the vignettes:
 
 ```R
-devtools::install_github("jedick/canprot", build_vignettes = TRUE)
+remotes::install_github("jedick/canprot", dependencies = TRUE, build_vignettes = TRUE)
 ```
 
-You may need to re-run this command one or more times. Note that this pulls in
-more R packages as dependencies, and [pandoc](http://pandoc.org/installing.html)
-is also required.
+This installs more R packages as dependencies (particularly **knitr** and **rmarkdown**).

inst/NEWS

@@ -1,7 +1,5 @@
-CHANGES IN canprot 0.1.4-54 (2020-01-17)
-----------------------------------------
-
-- Change license from GPL-3 to MIT.
+CHANGES IN canprot 0.1.5 (2020-02-20)
+-------------------------------------
 
 - Rename check_ID() to check_IDs() and add 'IDcol' argument. The
   function now uses a data frame for input and output.