diff --git a/README.md b/README.md index a8c5187c037e634d9e8482f5a11f5a24da7dd0a9..fcdc7357d312c9bfe57d66cae90107c1b016b3ba 100644 --- a/README.md +++ b/README.md @@ -1,70 +1,3 @@ -# MORSE: MOdelling tools for Reproduction and Survival data in Ecotoxicology - -Companion R package for MOSAIC website - - need `Rtools 3.3` and last `R` version. - -## Versions - -### CRAN release version - -[](https://cran.r-project.org/package=morse) [](https://cran.r-project.org/package=morse) - -### Build status for development version - -[](https://api.travis-ci.org/pveber/morse.svg) - -## Report a problem - -Use the [issue tracker](https://github.com/pveber/morse/issues) -to report a problem. - - -## Compilation (for command-line users) - -- `cd` to source directory -- Build from sources (creates vignette and archive) - `R CMD build .` -- Build and install `R CMD INSTALL --build .` -- Check the package - `R CMD check --as-cran morse_X.X.X.tar.gz` -- Update package description/NAMESPACE - - under the R interpreter: `roxygen2::roxygenise(".")` -- Generate documentation - - reference manual: `R CMD Rd2pdf --output=documentation .` - - vignettes (using the R interpreter): - `devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette'))` -- Run unit tests - - under the R interpreter: `devtools::test()` - -## Compilation (with RStudio) - -- need `devtools`, `ROxygen2 v5.0.1 or higgher` -- RStudio builder configuration: - - Project Options : - enable `Use devtools package...` - enable `Generate documentation...` - ROxygen options...`: - all enable exept `Vignettes` and `Source and binary package build` - - vignettes folder must contain only 3 files: - biblio.bib - modelling.Snw - tutorial.Rmd - - update Documentation (no vignette, only NAMESPACE and Rd) - `Document` or Ctrl + Shift + D - - check if the two folder inst and build were created. - - build the source file : - `More : Build Source Package` - -## Install the package from source -R: remove.packages("morse", lib="~/Documents/R/R-X.X.X/library") -R: install.packages("~/Documents/morse_X.X.X.tar.gz", repos = NULL, type = "source") -R: library("morse") -R: ?morse - -## Tests -- Build from sources: `Build & Reload` -- Test: `Build > More > Test package` (Ctrl + Shift + T). Note that you must activate the option "Use devtools package functions if available" in `Project Options > Build Tools`. -- Generate the documentation: `Build & Reload or Build > More > Document` (Ctrl + Shift + D) -- Check the package with the stable and the devel version of R: - - in `Build > More > Configure Build Tools`, add `--as-cran` in `Check Package -- R CMD check additional` options - - `Build > Check` (Ctrl + Shift + E) +# morse_paper +the R-package 'morse' paper for publication in JOSS +[](https://doi.org/10.21105/joss.03200) \ No newline at end of file