Data and code from: Integrating microclimate to understand vector development and disease patterns: Challenges and lessons from plague in Madagascar's Central Highlands

Abstract

This dataset contains code and data supporting the generation of microclimate-driven estimates of plague vector development across the Central Highlands of Madagascar. It comprises three zipped archives. The first archive includes scripts, spatial input datasets, and intermediate outputs required to construct a mechanistic microclimate model of below-ground temperature at 0.15 m depth for summer 2023 using the microclimf modelling framework. Input data include categorical soil class rasters, a digital elevation model, MODIS-derived land-cover rasters, and hourly ERA5 climate data, and the archive produces hourly microclimate temperature rasters. The second archive contains scripts and microclimate outputs used to convert hourly below-ground temperatures into annual Vector Development Index (VDI) rasters for two flea species (Synopsyllus fonquerniei and Xenopsylla cheopis). The third archive contains scripts and data for calculating temporal slopes of VDI, plotting VDI gradients, and conducting null analyses that compare observed pre-case VDI gradients with temporally permuted null case series. Dummy human plague case datasets (RDS and CSV formats) are provided to enable execution of the workflow without releasing sensitive surveillance records. All analyses are implemented in the R programming environment, with package dependencies specified within scripts and installed automatically via the pacman package. No personally identifiable information is included. Original human plague surveillance data are curated by the Plague Unit of the Institut Pasteur de Madagascar and may be requested separately. The dataset supports reproduction of the full analytical workflow, adaptation of the modelling framework to other regions or vector systems, and reuse of scripts for microclimate modelling, vector development estimation, and null-model based gradient testing. Data are released under a public domain waiver.