Analysis code and raw data for Mollentze et al. (2020), Virulence mismatches in index hosts shape the outcomes of cross-species transmission, PNAS.
The main dataset is available in Data/Internal/
. See Data/Internal/Metadata.html
for details.
Analyses were performed in R version 3.5.1. To install the packages used in this analysis, start R and run packrat::restore()
.
To re-run analyses, see ModelFitting_Durations.R
and ExcretedVirus_JointModels.R
. For data pre-processing steps, see PrepareData.R
.
├──Data/
│ ├──External/ Data from external sources
│ └──Internal/ Data generated in this study
│
├──Scripts/
│ ├──Main/
│ │ ├──PrepareData.R Performs data cleaning steps and consolidates data
│ │ │ (called by other scripts)
│ │ ├──ModelFitting_Durations.R Fits incubation and clinical period models
│ │ ├──ExcretedVirus_JointModels.R Fits joint salivary gland titre - incubation period
│ │ │ duration models
│ │ ├──GenerateReleaseData.R Generates the cleaned dataset for release
│ │ └──Metadata.Rmd Combines column descriptions and references into a
│ │ human-readable metadata file (Metadata.html)
│ │
│ ├──Plotting/
│ │ ├──DataSummaryStats.R Calculates summary statistics about dataset size,
│ │ │ as reported in text
│ │ ├──Plot_Raw_Data_As_Network.R Generates figure 1B
│ │ ├──ResultPlotting_Durations.R Generates all panels of figure 2, as well as
│ │ │ supplementary figures S1 & S2
│ │ ├──ResultPlotting_ExcretedVirus.R Generates all panels of figure 3
│ │ ├──Plot_BodytempDiffVsPhyloDist.R Generates supplementary figure S3
│ │ └──Plot_InoculationDistance.R Generates supplementary figure S4
│ │
│ └──Utils/ Utility functions loaded by other scripts
└──packrat/ Cache of R packages used in this project