CMSY++ runs its MCMC in JAGS through the rjags package, and the JAGS installer must match the operating system and the R version: on Windows and macOS each JAGS binary is built for a range of R versions, and rjags from CRAN (4-17) works only with JAGS 4. This function lists, for each system, the R versions, the JAGS installer, the rjags version it needs, whether it is the default, and the evidence (the README of the JAGS downloads, and the runs on Windows, macOS and Linux of the package's GitHub Actions workflow), and marks the row for this computer.
Usage
cmsy_jags_versions(
os = "all",
r_version = getRversion(),
silent = fao_setting("silent")
)Details
In short (JAGS 4, the default):
| System | R version | JAGS installer |
| Windows | 4.5 or 4.6 | JAGS-4.3.2.exe |
| Windows | 4.2 to 4.4 | JAGS-4.3.1.exe |
| macOS | 4.3 or later | JAGS-4.3.2.pkg |
| macOS | 4.2 | JAGS-4.3.1.pkg |
| Linux | any | package manager (e.g. apt-get install jags) or JAGS-4.3.2.tar.gz |
All of them work with rjags 4 from CRAN (4-17; the CRAN binary for R 4.2 on macOS is 4-15). JAGS 5.0.0 (version = "latest" in
cmsy_download_jags() and jags = "latest" in cmsy_setup()) needs rjags 5-3, which is not
yet on CRAN and is downloaded from SourceForge.
cmsy_download_jags() downloads the matching installer automatically, and cmsy_setup()
downloads and opens it.
References
Plummer, M. (2003). JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. Proceedings of DSC 2003, Vienna. https://mcmc-jags.sourceforge.io/
Examples
# The whole table, with the row for this computer marked
cmsy_jags_versions()
#> This computer (Linux, R 4.6.1): JAGS 4.3.2 (JAGS-4.3.2.tar.gz) with rjags 4-17 (CRAN, built from source).
#> system r_versions jags installer
#> 1 Windows 4.5 to 4.6.x 4.3.2 JAGS-4.3.2.exe
#> 2 Windows 4.2 to 4.4.x 4.3.1 JAGS-4.3.1.exe
#> 3 macOS >= 4.3 4.3.2 JAGS-4.3.2.pkg
#> 4 macOS 4.0 to 4.2.x 4.3.1 JAGS-4.3.1.pkg
#> 5 Linux >= 4.2 4.3.2 JAGS-4.3.2.tar.gz
#> 6 Windows 4.5 to 4.6.x 5.0.0 JAGS-5.0.0.exe
#> 7 macOS >= 4.3 5.0.0 JAGS-5.0.0-universal.pkg
#> 8 Linux >= 4.2 5.0.0 JAGS-5.0.0.tar.gz
#> rjags default this_computer
#> 1 4-17 (CRAN) TRUE FALSE
#> 2 4-17 (CRAN) TRUE FALSE
#> 3 4-17 (CRAN) TRUE FALSE
#> 4 4-15 or later (CRAN; its binary for R 4.2 is 4-15) TRUE FALSE
#> 5 4-17 (CRAN, built from source) TRUE TRUE
#> 6 5-3 (SourceForge, Windows binary) FALSE FALSE
#> 7 5-3 (SourceForge: binary for R 4.6, else source) FALSE FALSE
#> 8 5-3 (SourceForge, source) FALSE FALSE
#> evidence
#> 1 JAGS README: the Windows binary of 4.3.2 "was built with Rtools45 and is suitable for interfacing with R 4.5.x"; Rtools45 builds serve R 4.5.0 to 4.6.x (JAGS 5 README); run on R 4.6 by the package's CI
#> 2 JAGS README: earlier releases "are built with earlier versions of the Rtools tool chain"; 4.3.1 (April 2022) is the build for R before 4.5; run on R 4.2, 4.3 and 4.4 by the package's CI
#> 3 JAGS README: "JAGS-4.3.2.pkg for compatibility with R version 4.3.0 and later"; run on R 4.6 (Apple silicon) by the package's CI
#> 4 JAGS README: "JAGS-4.3.1.pkg for compatibility with R versions 4.0.x to 4.2.x"; run on R 4.2 (Apple silicon, with rjags 4-15) by the package's CI
#> 5 Install JAGS with the package manager (e.g. Debian/Ubuntu: sudo apt-get install jags) or from source; rjags is then built for the installed JAGS and any R version; run on Ubuntu by the package's CI
#> 6 JAGS 5 README: "For compatibility with R 4.5.0 to R 4.6.x, use binaries in the Rtools45 subfolder"; needs rjags 5-x, not yet on CRAN; run on R 4.6 by the package's CI
#> 7 JAGS 5 README: universal installer built for R for macOS 4.3.0 and later (it also contains JAGS 4.3.2); needs rjags 5-x: SourceForge has binaries for R 4.6, other R versions build it from source; run on R 4.6 (Apple silicon) by the package's CI
#> 8 JAGS 5 source code; needs rjags 5-x from source
#> readme
#> 1 https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/
#> 2 https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/
#> 3 https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/
#> 4 https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Mac%20OS%20X/
#> 5 https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/
#> 6 https://sourceforge.net/projects/mcmc-jags/files/JAGS/5.x/Windows/
#> 7 https://sourceforge.net/projects/mcmc-jags/files/JAGS/5.x/macOS/
#> 8 https://sourceforge.net/projects/mcmc-jags/files/JAGS/5.x/Source/
# One system, e.g. to tell a colleague on Windows with R 4.4 which installer to use
cmsy_jags_versions("windows", r_version = "4.4.1")
#> No JAGS build is listed for R 4.4.1 on this system; see https://sourceforge.net/projects/mcmc-jags/files/JAGS/
#> system r_versions jags installer rjags
#> 1 Windows 4.5 to 4.6.x 4.3.2 JAGS-4.3.2.exe 4-17 (CRAN)
#> 2 Windows 4.2 to 4.4.x 4.3.1 JAGS-4.3.1.exe 4-17 (CRAN)
#> 3 Windows 4.5 to 4.6.x 5.0.0 JAGS-5.0.0.exe 5-3 (SourceForge, Windows binary)
#> default this_computer
#> 1 TRUE FALSE
#> 2 TRUE FALSE
#> 3 FALSE FALSE
#> evidence
#> 1 JAGS README: the Windows binary of 4.3.2 "was built with Rtools45 and is suitable for interfacing with R 4.5.x"; Rtools45 builds serve R 4.5.0 to 4.6.x (JAGS 5 README); run on R 4.6 by the package's CI
#> 2 JAGS README: earlier releases "are built with earlier versions of the Rtools tool chain"; 4.3.1 (April 2022) is the build for R before 4.5; run on R 4.2, 4.3 and 4.4 by the package's CI
#> 3 JAGS 5 README: "For compatibility with R 4.5.0 to R 4.6.x, use binaries in the Rtools45 subfolder"; needs rjags 5-x, not yet on CRAN; run on R 4.6 by the package's CI
#> readme
#> 1 https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/
#> 2 https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/
#> 3 https://sourceforge.net/projects/mcmc-jags/files/JAGS/5.x/Windows/