PlosCompBio_2013

This repository contains code for generating Figures 2-5 and Table 1 from the following paper.

Perkins TA, Scott TW, Le Menach A, Smith DL (2013) Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission. PLoS Computational Biology 9(12): e1003327. doi:10.1371/journal.pcbi.1003327

All code contained within this repository is released under the CRAPL v0.1 License.

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Figure 2

Within the folder ./fig2/, execute source('figKernels.R') in R to produce ./fig2/output/fig2.pdf.

Figures 3 & 4

Within the folder ./fig34/, first execute source('runPhylogram.R') in R and then source('figMix.R') and source('figHet.R') to produce ./fig34/output/mixing.pdf and ./fig34/output/heterogeneity.pdf, respectively.

Figure 5

Within the folder ./fig5/, first execture source('runInfectionsOverTime.R') in R and then source('figInfectionsOverTime.R') to produce ./fig5/output/fig5.pdf.

Table 1

Within the folder ./tab1/, execute source('makeTable.R') in R to produce a matrix called tab that resides within ./tab1/output/table.RData.