Network Inductive Reasoning Model
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nirm.Rcheck
nirm.tags
nirm
README
compile.nirm.R
compile.nirm.Rout
nirm.master.R
nirm.master.Rout

README

#This file to be kept in /repos/Tools/nirm/
#Created on 12 January 12
#Last modified on 07 May 12

Note: 
    Use the most current binary version of nirm is located in nirm.tags/
    Do not compile the nirm package "natively" 
    To compile, use R CMD BATCH compile.nirm.R
    The original sources of the nirm package are located in: ../Flu_R21/Flu model on the network/
    In this document, reference is made to "/path/to/", which simply means "the path to your SVN repository."

Updating Code and Package:
    A) Changes to internal functionality (i.e., EVOLVE dynamics, adding/modifying/removing functions, behavioral models, etc) 
          should be made and committed to the appropriate source files in ../Flu_R21/Flu model on the network/ . Changes to
          model arguments or order-of-operations should be made to nirm.master.R. However modifying nirm.master.R should be 
          limited to rare cases as errors in this file will break the package. Assuming that nirm.master.R is not to be changed,
          the following list can be used as working-model of updating the package:
             1) Add a new function to ../Flu_R21/Flu model on the network/Library/ called foo.R and commit file to SVN
             2) Manually increment the "Version" number in /path/to/RiskPerceptionNetworks/Tools/nirm/nirm/DESCRIPTION by +0.0.1
             3) Manually document the change following GNU ChangeLog rules in /path/to/RiskPerceptionNetworks/Tools/nirm/nirm/ChangeLog
             4) Set working directory to /path/to/RiskPerceptionNetworks/Tools/nirm/
             5) Compile (see below)
             6) Commit changes to SVN.
    B) Changes to package documentation should be done using the Rd typsetting format and only committed to 
       /path/to/RiskPerceptionNetworks/Tools/nirm/nirm/man/nirm.Rd
    C) It is important to increment the Version number and document changes in the ChangeLog. Failing to increment the Version
       number will result in previous package overwriting upon compilation.

To Compile:
    Compilation can only be done from a Linux or Mac terminal. Windows compilation is currently not supported.
    1) Working directory must be: /path/to/RiskPerceptionNetworks/Tools/nirm/
       where "/path/to" is your SVN repository path.
    2) If changes were made to the files, be sure that you incremented the Version number in /nirm/DESCRIPTION and documented
       these changes in the /nirm/ChangeLog
    3) Compilation is done in on easy step from the terminal command-line:
       $> R CMD BATCH compile.nirm.R
    4) The newly compiled package will be located in /nirm.tags/nirm.v.tar.gz where "v" is the version number.

To Install (MAC and Linux):
    From a command line terminal run: R CMD INSTALL /path/to/RiskPerceptionNetworks/Tools/nirm/nirm.tags/nirm.v.tar.gz
       where "/path/to" is your SVN repository path and "nirm.v.tar.gz" is the version of the package you want to install (i.e., nirm.0.5.7.tar.gz)
To Install (Windows):
    Please reference the online R Windows documentation for how to install downloaded packages. :)

WARNING:
    Remember to manually update all R documentation files in /nirm/man/, failing to do so will cause compilation to fail.
    Remember to manually increment the R package version in /nirm/DESCRIPTION, failing to do so will OVERWRITE your old package in nirm.tags/