Data and R code to support Lee S.A. et al., (2021). The impact of climate suitability, urbanisation, and connectivity on the expansion of dengue in 21st century Brazil. _PLOS Neglected Tropical Diseases 15(12): e0009773 (https://doi.org/10.1371/journal.pntd.0009773).
To cite this repo:
Lee S.A. et al (2021). Data and R code to accompany 'The impact of climate suitability, urbanisation, and connectivity on the expansion of dengue in 21st century Brazil' (version 1.0.0) (V1.0.0). Zenodo.
Dengue is hyperendemic in Brazil, with outbreaks affecting all regions. Previous studies identified geographical barriers to dengue transmission in Brazil, beyond which certain areas, such as South Brazil and the Amazon rainforest, were relatively protected from outbreaks. Recent data shows these barriers are being eroded. In this study, we explore the drivers of this expansion and identify the current limits to the dengue transmission zone.
A description of each file and folder is provided below:
01_exploratory_plots.R: R script to explore and visualise dengue, socioeconomic, climate, and connectivity data.
02_model_fitting.R: R script to fit spatio-temporal models.
03_model_output.R: R script to explore and visualise model output.
data: a folder containing databases necessary to create the visualisations provided in the manuscript and fit the spatio-temporal models.
output: a folder to save the output generated by the R scripts.
The analysis was performed using R version 4.0.3 (2020-10-10).
For any issues with the code please contact Sophie Lee.