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README for 'infer' R package
============================

This is the README file for the 'infer' R package.  If you are reading this
document, you have already found the location of this package in the infer project git repository.  Congratulations!

Files
=====

infer -- directory containing the R package files.
test.pop -- ids, x/y coordinates (OSGB1936), number of cattle, pigs, and sheep for farms in the test population.
test.epi -- CSV file containing ids, infection, notification (i.e. detection), and removal times of infected farms in the test epidemic.
testscript.r -- example of how to run the inference algorithm on a Spatial Point Population model (e.g. for UKFMD2001).

Building
========

1. > cd infer
2. > autoremake -i # Creates configure script and Makefiles
3. > cd ..
4. Ensure CUDA, CUDPP >= 2.1, Boost >= 1_51_0, GSL >= 1.15, HDF5 >= 1.8.12 are installed.  Set CUDA_HOME, CUDPP_HOME, BOOST_HOME, GSL_HOME if CUDA, CUDPP, Boost and GSL are in non-standard locations.  Set CPPFLAGS and LDFLAGS appropriately for HDF5 if non installed in standard locations (needs a HDF5_HOME implementing).
5. > R CMD INSTALL infer

Usage
=====

See example 'testscript.r'.