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cmsy_setup(): 安装JAGS和CMSY++所需的R包

Source: vignettes/articles/zh/reference/cmsy_setup.Rmd
cmsy_setup.Rmd

英文原页：cmsy_setup()

说明

本函数为cmsy_run()做好准备：从CRAN安装缺少的R包，下载与本系统和R版本匹配的JAGS安装程序（见cmsy_jags_versions()；通过cmsy_download_jags()下载，并核对文件大小和校验值）并打开它，同时检查包内置的CMSY++文件。以交互方式使用R时，安装任何内容之前都会先询问。

English

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.

用法 

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

参数

jags
推荐的JAGS版本：“recommended”（默认；针对当前R版本编译的最新JAGS 4版本，可与CRAN上的rjags配合使用）、“latest”（JAGS 5.0.0，需要SourceForge上的rjags 5-x）或版本号，例如”4.3.2”。
English 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
采用哪个操作系统的设置：“auto”（默认，自动检测）、“windows”、“macos”或”linux”。
English The operating system whose settings are used: “auto” (default, detect it), “windows”, “macos” or “linux”.
ask
逻辑值。为TRUE（默认）时，安装任何内容之前先询问。在非交互式会话中，ask为TRUE时不会安装任何内容。
English A logical value. If TRUE (default), ask before installing anything. In a non-interactive session nothing is installed when ask is TRUE.
data_dir
下载文件的保存目录。默认为fao_data_dir()。
English The directory where downloads are kept. Default is fao_data_dir().
silent
逻辑值。为TRUE时不输出汇总信息。默认为FALSE，或fao_settings(silent = )设置的值。
English A logical value. If TRUE, no summary is printed. Default is FALSE, or the value set with fao_settings(silent = ).

返回值

以不可见方式返回安装后cmsy_system()的结果。silent = TRUE时不输出汇总信息和下载信息（ask为TRUE时仍会询问）。

English

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).

详细说明

JAGS是一个独立的程序，无法在R中安装。在Windows和macOS上会打开安装程序，按其步骤点击完成安装即可；在Linux上则显示安装命令。安装JAGS后请重启R，并再次运行cmsy_setup()进行检查。

JAGS安装程序必须与R版本匹配（见cmsy_jags_versions()）：Windows上，R 4.5和4.6用JAGS 4.3.2，R 4.2至4.4用JAGS 4.3.1；macOS上，R 4.3及以后用JAGS 4.3.2，R 4.2用4.3.1；Linux上用包管理器提供的JAGS。默认使用JAGS 4，因为CRAN上的rjags（4-17）需要JAGS 4。选择JAGS 5.0.0（jags = "latest"）时，还会从SourceForge安装rjags 5-3。

English

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.

参考文献

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/

示例 

# 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")