@afni_R_package_install

@afni_R_package_install

Helper script to install R packages for various afni-ish purposes.
You must have R installed, and permissions for its package library.

options:

-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.

examples:

   @afni_R_package_install -afni

   @afni_R_package_install -afni -shiny -custom "earth wind fire"

Justin Rajendra 11/2017