Code for: Phylogenetic and biogeographical traits predict unrecognized hosts of zoonotic leishmaniasis 2023. Caroline K Glidden, Aisling R. Murran, Rafaella Albuquerque Silva, Adrian A. Castellanos, Barbara A. Han, Erin A. Mordecai. PLoS NTD: https://doi.org/10.1371/journal.pntd.0010879 Code written by Caroline K. Glidden & Aisling R. Murran
This github contains the following R files (for each Leishmania genus):
- timetree_phylo_distance.R: code to get phylogenetic distance PCoA axes
- pubmed_data_collection.R: code to build variable importance plots and tables for each model in the manuscript
- clean_merge_data_4.1.R : code to clean and merge host status data and trait data included in the raw_data folder
- xgboost_model_performance.R : codel to evaluate model performance using nested cross-validation
- variableImp_pdp.R: code to bootstrap variable importance and partial dependence plot analysis
- figures.R : code to generate figures for final model
The folder study_effort_supp includes the same analyses but for the supplemental study effort analysis
The final data included in the analysis (cleaned_data/analysis_data/trait_data_small.rds) includes data from the following sources:
- Host status data: data sources can be found in raw_data/reservoir_host_status_using_rank_final.csv
- Species life-history traits: Pantheria https://doi.org/10.1890/08-1494.1
- Foraging data: EltonTraits https://doi.org/10.1890/13-1917.1
- Climate data: CHELSA https://chelsa-climate.org/
- Main habitat (categorical variables): IUCN https://www.iucnredlist.org/
- Phylogenetic distances: TimeTree http://timetree.org/
- Landcover data: Copernicus Global Land Cover Layers: CGLS-LC100 Collection 3 https://developers.google.com/earth-engine/datasets/catalog/COPERNICUS_Landcover_100m_Proba-V-C3_Global
- Global human modification index: CSP gHM: Global Human Modification https://developers.google.com/earth-engine/datasets/catalog/CSP_HM_GlobalHumanModification
- Zoonotic host status: GIDEON https://www.gideononline.com/
Species range shapefiles for cleaning data, building figures, and aggregating habitat traits for species ranges can be found here: https://www.iucnredlist.org/
Occurrence points to generate polygons for invasive species in the Americas were downloaded from da Rosa et al. 2020: https://doi.org/10.1002/ecy.3115
Occurrence points to generate polygons for zoonotic Leishmania occurrence were downloaded from Herrera et al. 2020: https://doi.org/10.1038/s41597-020-0451-5