:orphan:

.. _ahelp_@afni_R_package_install:

***********************
@afni_R_package_install
***********************

.. contents:: :local:


| 

    

@afni_R_package_install
=======================

.. code-block:: none

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

options:
========

.. code-block:: none

    
          -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:
=========

.. code-block:: none

    
          @afni_R_package_install -afni
    
          @afni_R_package_install -afni -shiny -custom "earth wind fire"
    
       Justin Rajendra 11/2017