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

Build status for development version

Report a problem

Use the issue tracker 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 .
  • 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 VignettesandSource 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)