This function finds the operating system, R version and processor of the computer, checks
whether JAGS and the R packages that CMSY++ needs are installed, and shows the settings that
cmsy_run() will use on this system.
Usage
cmsy_system(
os = "auto",
device = c("file", "screen"),
jags = "recommended",
silent = fao_setting("silent")
)Arguments
- os
The operating system whose settings are used: "auto" (default, detect it), "windows", "macos" or "linux".
- device
Where CMSY++ draws its charts before saving them as JPEG files: "file" (default), an off-screen device that works on every system and in batch runs, or "screen", the system's own window (
windows(),quartz()orx11()).- 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".
- silent
A logical value. If TRUE, no summary is printed. Default is FALSE, or the value set with
fao_settings(silent = ).
Value
Invisibly, a list with the system (os, os_detected, arch, r_version), the
installed jags and rjags versions, the packages table, the recommended jags_installer
and rjags_source, the chart device and antialias settings, and the changes
made to the CMSY++ code.
Details
The CMSY++ code (CMSY++16.R) was written on Windows. Its user guide (step 12) tells Mac users
to change every windows() call to quartz() and antialias = "cleartype" to
antialias = "default", and to comment out windows() on other systems. The code tests for
Windows with grepl("win", sysname), which is also true for macOS ("Darwin"), so on a Mac it
calls windows() and stops. cmsy_run() makes these changes automatically for the system
found here, in a copy of the code; the bundled original is never changed. The other changes,
made on every system, are listed in the changes element.
The system is detected automatically. To use the settings of another system (e.g. when the
detection is wrong), set os, or set it for the session with
options(faofishingreport.cmsy_os = "macos").
References
Froese, R., Demirel, N., Coro, G. and Winker, H. (2021). User Guide for CMSY++. GEOMAR, Germany, 17 pp. https://oceanrep.geomar.de/id/eprint/52147/
See also
cmsy_setup() to install what is missing, cmsy_sources() for versions and links.
Examples
# \donttest{
# What this computer has, and the settings cmsy_run() will use on it
sys <- cmsy_system()
#> CMSY++ on this computer
#> System: Linux (detected), x86_64, R 4.6.1
#> JAGS: 4.3.2, rjags 4.17
#> Installer for this system: JAGS 4.3.2 (JAGS-4.3.2.tar.gz) https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/
#> R packages: all installed
#> Charts: grDevices::pdf(NULL, width, height) (off-screen); JPEG antialias = "default"
#> Ready to run cmsy_run().
sys$changes # the changes made to a copy of the CMSY++ code
#> change applies_to
#> 1 Package installation all
#> 2 snpar all
#> 3 Working directory all
#> 4 Settings all
#> 5 Chart windows linux
#> 6 JPEG antialias linux
#> 7 Results for charts all
#> what
#> 1 Lines that install missing packages on every run are removed (cmsy_setup() installs them).
#> 2 library(snpar) is removed and snpar::runs.test() is replaced by the same approximate runs test, reproduced from snpar 1.0 (Debin Qiu, GPL >= 2; archived on CRAN on 2022-05-10: https://cran.r-project.org/src/contrib/Archive/snpar/; source mirror: https://github.com/cran/snpar).
#> 3 setwd(rstudioapi::getActiveDocumentContext()$path) is removed, so RStudio is not needed; each stock runs in its own folder.
#> 4 File names, the stock, the chart switches and the general settings (CMSY++ defaults unless changed with cmsy_run(settings = ), including the MCMC iterations of the JAGS call) are set by cmsy_run() after the original settings section.
#> 5 The test grepl("win", sysname), which is also true on macOS ("Darwin"), is replaced; windows(): changed to an off-screen device, so charts are drawn and saved without opening windows.
#> 6 antialias = "cleartype" (Windows only) is changed to "default" (user guide, step 12).
#> 7 After the main analysis of a stock, its priors, the posterior draws of r, k and B/k, the yearly estimates with 95% limits and the last-year Kobe draws are saved to cmsy_extra.rds (retrospective runs to cmsy_retro.rds) for cmsy_plot(); no calculation is changed.
# The settings that would be used on Windows or macOS, e.g. to check them for a colleague
cmsy_system(os = "windows", silent = TRUE)$changes
#> change applies_to
#> 1 Package installation all
#> 2 snpar all
#> 3 Working directory all
#> 4 Settings all
#> 5 Chart windows windows
#> 6 JPEG antialias windows
#> 7 Results for charts all
#> what
#> 1 Lines that install missing packages on every run are removed (cmsy_setup() installs them).
#> 2 library(snpar) is removed and snpar::runs.test() is replaced by the same approximate runs test, reproduced from snpar 1.0 (Debin Qiu, GPL >= 2; archived on CRAN on 2022-05-10: https://cran.r-project.org/src/contrib/Archive/snpar/; source mirror: https://github.com/cran/snpar).
#> 3 setwd(rstudioapi::getActiveDocumentContext()$path) is removed, so RStudio is not needed; each stock runs in its own folder.
#> 4 File names, the stock, the chart switches and the general settings (CMSY++ defaults unless changed with cmsy_run(settings = ), including the MCMC iterations of the JAGS call) are set by cmsy_run() after the original settings section.
#> 5 The test grepl("win", sysname), which is also true on macOS ("Darwin"), is replaced; windows(): changed to an off-screen device, so charts are drawn and saved without opening windows.
#> 6 antialias = "cleartype" is kept (Windows).
#> 7 After the main analysis of a stock, its priors, the posterior draws of r, k and B/k, the yearly estimates with 95% limits and the last-year Kobe draws are saved to cmsy_extra.rds (retrospective runs to cmsy_retro.rds) for cmsy_plot(); no calculation is changed.
cmsy_system(os = "macos", silent = TRUE)$device_call
#> [1] "grDevices::pdf(NULL, width, height) (off-screen)"
# The JAGS installer recommended here, and the newest JAGS
cmsy_system(silent = TRUE)$jags_installer[, c("version", "file", "url")]
#> version file
#> 10 4.3.2 JAGS-4.3.2.tar.gz
#> url
#> 10 https://downloads.sourceforge.net/project/mcmc-jags/JAGS/4.x/Source/JAGS-4.3.2.tar.gz
cmsy_system(jags = "latest", silent = TRUE)$jags_installer[, c("version", "file", "requires")]
#> version file requires
#> 13 5.0.0 JAGS-5.0.0.tar.gz C++ compiler, BLAS and LAPACK; rjags 5-x
# }