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Readme
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D.J. Schad, November 2012
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PLOTTING:
To generate the figures from the manuscript, extract the archive Figures.zip. Then, go to the directory Figures/scripts. The file plotAll.R contains instructions about how to generate the Figures in the R System for Statistical Computing.


SWIFT 3:
- C-code for the model is in the archive swift3pg.zip
- Compile the code for your machine. In Mac OS X: open the Terminal, go to the extracted directory "cd swift3pg/", and run  "./cga" (also, precompiled code for Mac OS X is contained in swift3pg/)
- To start the SWIFT-simulations: in the Terminal go to folder 'swift3pg' and enter "./swiftstat". The console should then display details on the simulations and its progress.

To make changes to the simulations edit the following files in a text editor:
- swiftstat.inp  indicates which experiment to simulate ("shuf" or "psc") and the total number of model runs (simulated subjects)
- sd.shuf.par  and  sd.psc.par  indicate parameter values for the simulated model. To generate predictions based on different model parameters, change these entries manually.

To plot simulation results, copy the following files from the folder 'swift3pg'  to the folders 'Figures/data/01_PSC275', 'Figures/data/01_SHUF', or 'Figures/data/01_SHUFb_reducedDelta1':
- fit.dat
- newgoffunc.fit.dat
- seq.dat
Then, run the R-script Figures/scripts/plotAll.R