Aedes albopictus is rapidly invading its climatic niche in France: wider implications for biting nuisance and arbovirus control in Western Europe (Radici et al., 2025)

WHAT THIS REPOSITORY CONTAINS The R scripts here enables simulations that generate the results of the publication "Aedes albopictus is rapidly invading its climatic niche in France: wider implications for biting nuisance and arbovirus control in Western Europe" (https://www.biorxiv.org/content/10.1101/2025.02.14.638223v2) Radici et al (2019). In this article, we use the dynamic model laid out in Metelmann et al., (2019) - a shortened version of which can be found here: https://zenodo.org/records/14731815 - to estimate the increase in vector risk in Europe over the past two decades due to the impact of climate change. DISCLAIMER To generate the figures, the scripts must be run in sequence from 01 to 17. The figure produced is in the file name. Scripts whose name starts with a letter should not be run; they are called by other scripts. Warning: most of the scripts need a computer cluster to run, and the computing capabilities of a regular laptop may not be sufficient. THE SCRIPTS IN DETAIL · 01_Read_EOBS_cycle.R: reads EOBS files for weather (0.1 or 0.25° resolution of choice) and transforms them into dataframes, associating each cell (attached ESRI shapefile) and each date with values of environmental variables (including human population from Global Population of the World, ver 4.0) · 02_MM_EOBS_cycle_E0.R: runs the Metelmann model on the previous dataframes, for the given years, resetting the population at the beginning of the year for suitability calculation (R0) · 03_MM_EOBS_cycle_consec.R: Same as the previous one, but without reset, for calculation of adult abundance, from which weekly egg hatching rate and epidemic risk indicators for dengue are derived · 04_Extract_Presence_Absence.R: Extracts the presence (GBIF) and absence (ECDC) data of tiger mosquitoes that are provided · 05_MM_EOBS_cycle_E0_Fig2a.R: To compare the spatial data of presence/absence with the estimated suitability · 06_MM_EOBS_cycle_consec_Fig2b.R: To compare spatial data of autochthonous transmission with the estimated epidemic risk · 07_MM_EOBS_cycle_E0_Fig3abcde.R: To compare spatiotemporal data of colonization of French municipalities with model predictions · 08_MM_EOBS_cycle_E0_Fig3f.R: To estimate the rapidity of mosquito spread (according to observations and according to the model) · 09_MM_EOBS_cycle_E0_Fig5abc.R: To show the evolution over time of suitability · 10_MM_EOBS_cycle_consec_Fig5defghi.R: To show the evolution over time of adult mosquito density and epidemic risk · 11_Extract_fromEOBS_Exposure_Space.R: To extract the environmental data of the sites for which you want to do the sensitivity analysis · 12_MM_EOBS_cycle_Exposure_Space_Fig6.R: To run the sensitivity analysis (“exposure space”) · 13_Extract_VectAbundance.R: To carry out the pre-processing of the VectAbundance data · 14_Plot_VectAbundance_Trajectories_Fig4abc.R: To compare estimated and observed oviposition at VectAbundance sites · 15_Read_MeteoFrance_cycle.R: To download and pre-process MeteoFrance data for Altopictus and EID surveillance sites · 16_MM_MeteoFrance_cycle_consec.R: launches the Metelmann model on these weather data · 17_MM_Altopictus_EID_Fig4e.R: estimated and observed oviposition at Altopictus and EID surveillance sites are compared Scripts A_MM_integration_functions_runAsSource.R, B_MM_integration_functions_runAsSource.R, C_MM_parameters_extraction_runAsSource.R are for support. THE DATA IN DETAIL · GBIF data (presence of tiger mosquitoes), ECDC (absence of tiger mosquitoes, native dengue transmissions until 2022), already published and cited in Radici et al. 2025 publication, are provided · VectAbundance data are provided (Da Re et al.), already published and cited in the publication of Radici et al. 2025 · Colonized municipalities are provided in a csv with the year of colonization · Ovitrap data are provided as median data per week in an RData with the week and site of reading · If you have any questions, please refer to the main publication and if necessary contact the corresponding author.