Repository containing all the code and data to simulate different microclimates for Reyes-Puig et al. 2026 Physiology-microhabitat matching may help organisms cope with the thermal and hydric challenges under climate change: a tale of two lizards (Ecography)

This repository contains all the code and data to simulate different microclimates. We simulate different microclimates in Castro São Paio using NicheMapR. The weather data comes from Modivas (https://www.wunderground.com/dashboard/pws/IMODIV1). Repository structure /code/ aux_functions.R: helpful functions to handle data readLoggers: reads and cleans datalogger data given the logger name and timeperiod. read.logger: reads the data from iButton csv files. Internal of readLoggers. clean.logger: cleans datalogger data, and formats dates. Internal of readLoggers. clean.logger2: same as clean.logger but for a different time format. Internal of readLoggers. prepare.weather: adds logger data to the weather station data. Internal of run.microclimate. retrieve.output: retrieves output of the microclimate model. Internal of run.microclimate. run.microclimate: runs the model, if needed it prepares the weather data, and finally retrieves the data from the model. plot.predictions: plot simulation predictions and datalogger observations. site.info: get coordinates, elevation, slope and aspect for each site from the datalogger table. micro_custom.R: Function to prepare the input for NicheMapR microclimate model and run the model. microclimate_hourly_Castro.R: example script that shows how to use hourly data from weather stations as input for the NicheMapR microclimate model. prepare_rasters.R: script used to compute the slope and aspect in the study area, and save the files in the terrain folder. prepare_weather.R: script used to download and prepare the weather data from Modivas station, which is then saved in the weather folder. The script can download data from any station, if you supply its code in wunderground. read_dataLoggers.R: example script to read and plot datalogger data (Old). /dataloggers_Castro/ datalogger data on temperature and humidity. /terrain/ marrisk-2019-02-20-dsm.tif: digital elevation model of Castro Saõ Paio. marrisk-2019-02-20-dsmshd.tif: digital elevation model (shade). marrisk-2019-02-20-orto.tif: ortophoto. slope.tif: slope for the area where dataloggers where placed. aspect.tif: aspect for the area where dataloggers where placed. /weather/ weather data from Modiva station, downloaded from wunderground. microclimates_CastroSampaio.Rmd: Run simulations for different microhabitats and compare to the data recorded by iButtons placed in those microclimates.