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Unverified Commit 7724c285 authored by CHARLES SANDRINE's avatar CHARLES SANDRINE :butterfly: Committed by GitHub
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readme.md updated

addition of the link towards the published paper online
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# 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
[![CRAN version](http://www.r-pkg.org/badges/version/morse)](https://cran.r-project.org/package=morse) [![](http://cranlogs.r-pkg.org/badges/grand-total/morse)](https://cran.r-project.org/package=morse)
### Build status for development version
[![Build Status](https://api.travis-ci.org/pveber/morse.svg?branch=master)](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
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03200/status.svg)](https://doi.org/10.21105/joss.03200)
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