Package for "Amphibian Collapses Increased Malaria Incidence in Central America"

by Michael R. Springborn, Joakim A. Weill, Karen R. Lips, Roberto Ibanez, and Aniruddha Ghosh

General ploting options

Scripts/general_options.R provides basic plotting options,

Code/draw_crosshatch.R (adding crosshatch on the maps)

Main text

Fig 1: aggregated malaria, lines

Scripts/plot_lines_number_malaria_cases_paper.R

Fig2: Map,Bd-driven amphibian declines timing

Scripts/plot_spread_optimal_model_years_decline_paper.R

Fig 3: Event study

Scripts/model_main_specification_paper.R

Table 1: Main reg table

Scripts/models_main_robustness_checks_paper.R

Appendix

Table S1: Summary Table and Table S2: Balance Table

Scripts/summary_table.R

Table S3 (temperatures robustness checks), S4 (Land use + weather), S5 (county exclusion)

#Same script as Table 1

Fig S1: Map of elevation and road network

Scripts/code_plotSM1.R

Fig S2: Map raster Thinplate Spline

Scripts/plot_spline_interpolation_raster_paper.R

Fig S3: Event studies with alternative models for elevation-dependent spread

Scripts/models_event_study_many_spreads.R

Fig S4: Thinplate Spline Event Studies

Scripts/models_splines_paper.R

Fig S5: Bacon-Goodman decomposition

Scripts/lardon.R, script to make the decomposition faster

Scripts/model_bacondecomp.R

Fig S6:

Scripts/plot_lines_mitigExpend_country_paper.R

Data files

sp object Costa Rica and Panama

Data/cr_pan_agg_sp.rds

Spread model in raster format for fig 2

Data/optimal_spread_model_extracted_dataframe_rho_linear_0.rds

Observed dates of amphibian declines

Data/sites_declines_sp.rds

Thinplate splines models used in appendix

Data/preBigdf_to_merge.rds

Mitigation efforts at the country level

Data/MalariaExpendSprayDataCRPan_cleaned.csv

Merged datasets (contains most variables)

Data/spread_bd_df_*.rds, where * is the choice of elevation model for the spatial spread (linear or tabletop) as well as the strength of elevation (varies between 0 and 1)

Elevation raster

Data/alt_cri_pan.tif

Roads network

gROADS-v1_cri_pan.rds