AFNI program: @afni_R_package_install
Output of -help
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@afni_R_package_install ~1~
Helper script to install R packages for various afni-ish purposes.
You must have R installed, and permissions for its package library.
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options: ~1~
-afni : Current list of packages for afni.
Similar to rPkgsInstall.
Installs:
afex phia snow nlme lme4 paran brms
-shiny : Current list of packages for afni based shiny apps.
May have trouble with openssl on some linux OS's.
Make sure the openssl OS package is installed with a
package manager (apt-get, yum, etc.).
Installs:
shiny shinydashboard plotly colourpicker data.table
gplots RColorBrewer psych
-bayes_view : Packages the program bayes_view.
Lots of shiny and ggplots packages.
Only needed if you want to run bayes_view.
-circos : Packages for FATCAT_matplot.
Installs OmicCircos via biocLite.
Actually runs OmicCircos_pkg_install.R.
-custom : Install whatever R packages you desire.
Requires a space separated list of packages.
Must start and end with double quotes.
e.g. "earth wind fire"
-mirror : Set the cran mirror to something besides the default of
https://cloud.r-project.org
-help : Show this help.
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examples: ~1~
@afni_R_package_install -afni
@afni_R_package_install -afni -shiny -custom "earth wind fire"
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Justin Rajendra 11/2017
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Mon Sep 29 10:44:18 PM EDT 2025