Evolutionary analysis of USVI Zika epidemic

Predictor data for phylogeographic GLM.

Currently planned predictors

  • Great circle distances between population-weighted country centroids. Generating code in Mathematica notebook and file here.

  • Origin country population size. Source: CIA World Factbook and UNdata. Reformatted World Factbook data available in this file

  • Fraction of population living in an urban center: Source: Data downloaded as CSV from The World Bank | Data.

  • Destination country population size. Source: CIA World Factbook and UNdata, same as above.

  • Degree of air traffic between countries. Source: Bluedot. Please note that due to licensing agreements with IATA, this predictor cannot be made publicly available on Github.

  • Vector abundance of country. Possible source: Messina et al paper.

  • Latitudinal direction of ZIKV migration. This pairwise predictor has a 1 value for the cell if the origin's population-weighted centroid is north of the destination's, and a -1 if origin is south of the destination.

Possible other predictors

  • Country population size that is native-born or foreign-born (available from UNdata) as a possible measure of population-level migrancy?

Workflow for data standardization and making predictor matrices in BEAST format.

1) Standardize country names. See indexed-countries-50.tsv for canonical project names. Cleaned up data are written to tsv.

Importantly, at this point there are two types of tsv files, those that contain data that is not pairwise (e.g. country population size) or data that is inherently pairwise (e.g. amount of air traffic passengers flowing between countries). Pairwise predictor tsv files are written to the following format:

origin \t destination \t predictor_value

Non-pairwise tsv files are written as:

country \t value

2) All tsv files that are not pairwise, are collated within a single dataframe by left-joining on indexed-countries-45.tsv. This allows filtering out of countries that are not included in the analysis.

3) Make pairwise-format tsv files from the non-pairwise data by assigning either the origin value to the destination value to all origin-destination pairs. These tsv files are the input files for making the predictor matrices. They are stored in the origin-destin-tsv directory.

4) Import all origin-destination pair data from each of the tsv files, then make flattened matrices. Note that matrix indexing for GLM predictor matrices is unique. We've accounted for this in our code.

5) Take ln of all values in the matrix, then standardize the log transformed values by doing the following for each value in the matrix. Note that the predictor for latitudinal direction of ZIKV migration is not ln-transformed, but is still standardized.

(value - mean)/(standard deviation)

6) Export log-transformed and standardized flattened matrices to tsv. These tsv files can be directly copied and pasted into the BEAST xml file for the phylogeographic analysis. These tsv files are stored in the transformed-linearized-matrices directory .