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Install JAGS and the R Packages Needed by CMSY++

Source: R/cmsy_system.R
cmsy_setup.Rd

This function prepares the computer for cmsy_run(): it installs the missing R packages from CRAN, downloads the JAGS installer that matches this system and R version (see cmsy_jags_versions(); with cmsy_download_jags(), which checks its size and checksums) and opens it, and checks the bundled CMSY++ files. It asks before installing anything when R is used interactively.

Usage

cmsy_setup(
  jags = "recommended",
  os = "auto",
  ask = TRUE,
  data_dir = fao_data_dir(),
  silent = fao_setting("silent")
)

Arguments

jags

The JAGS version to recommend: "recommended" (default; the newest JAGS 4 release built for this R version, which works with rjags from CRAN), "latest" (JAGS 5.0.0, which needs rjags 5-x from SourceForge) or a version number such as "4.3.2".

os

The operating system whose settings are used: "auto" (default, detect it), "windows", "macos" or "linux".

ask

A logical value. If TRUE (default), ask before installing anything. In a non-interactive session nothing is installed when ask is TRUE.

data_dir

The directory where downloads are kept. Default is fao_data_dir().

silent

A logical value. If TRUE, no summary is printed. Default is FALSE, or the value set with fao_settings(silent = ).

Value

Invisibly, the result of cmsy_system() after the installation. With silent = TRUE no summary or download messages are printed (questions are still asked when ask is TRUE).

Details

JAGS is a separate program, so it cannot be installed from R. On Windows and macOS the installer is opened and you click through it; on Linux the commands to install it are shown. Restart R after installing JAGS and run cmsy_setup() again to check.

The JAGS installer must match the R version (see cmsy_jags_versions()): on Windows JAGS 4.3.2 for R 4.5 and 4.6 and JAGS 4.3.1 for R 4.2 to 4.4; on macOS JAGS 4.3.2 for R 4.3 and later and 4.3.1 for R 4.2; on Linux the JAGS of the package manager. JAGS 4 is used by default because rjags on CRAN (4-17) needs JAGS 4. JAGS 5.0.0 (jags = "latest") also installs rjags 5-3 from SourceForge.

References

Plummer, M. (2003). JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003), Vienna. https://mcmc-jags.sourceforge.io/

Examples

if (FALSE) { # \dontrun{
# Check the computer and install what is missing (asks first)
cmsy_setup()

# Install without asking, e.g. on a server or in a script
cmsy_setup(ask = FALSE)

# JAGS 5.0.0 with rjags 5-3 (from SourceForge) instead of JAGS 4.3.2
cmsy_setup(jags = "latest")
} # }