Neotropical mammal responses to forest fires in Serra do Amolar, Brazil

# Neotropical mammal responses to forest fires in Serra do Amolar, Brazil [https://doi.org/10.5061/dryad.p5hqbzkwt](https://doi.org/10.5061/dryad.p5hqbzkwt) The data and scripts contained in this folder are from data collected by Instituto Homen Pantaneiro and Panthera collected between 2019-2021 in the Serra do Amolar, Mato Grosso do Sul, Brazil. The purpose of the study was to evaluate occupancy and density of mammal species before and after forest fires in 2020. These data and the attached scripts are from the article Bardales et al. (2024): DOI : 10.1111/gcb.17278. ## Description of the data and file structure The data are detections (presence and absence) of eight mammal species in the Serra do Amolar for occupancy analysis and recaptures of jaguars and ocelots for density analysis.. The scripts attached are for dynamic occupancy models for three years of data and multi-year density for jaguars and ocelots. List of files: **Dynamic occupancy (19 files total)** * MS_Occupancy_allsppSA.R is the R script for all eight species. * SA_TE1 is the file with the trapping effort and start and end date for each camera. * SiteCov_St has all the site covariates for all the cameras. Trail (Y/N), normalized data vegetation index (NDVI), normalized burn ratio (NBR), Area burned (AB), Distance from water in meters (Dwater), and percent area burned (BP). Details for sources and how to derive covariates is included in the methodology with links to Google Earth Engine code. * There is a .csv file for each species (*Dasyprocta azarae, Dicotyles tajacu, Leopardus pardalis, Mazama americana, Panthera onca, Priodontes maximus, Puma concolor, Tapirus terrestris*) that has a detection history for the species. The numbers in the title, ex. "Tapirus_14d" indicate the length of the secondary sampling period, adjusted per the goodness-of-fit test for each species capture history. The columns in the csv files represent the secondary sampling occasion, and ex. "o1" and they repeat for each year. 1s represent detection and 0s represent non-detection. * There is an accompanying .csv for each species with the trapping effort for the species adjusted for sampling occasion length. The numbers in the title indicate the length of the secondary sampling period, adjusted per the goodness-of-fit test for each species capture history. **SECR Density (7 files total)** * MS Density Jag & Oc.R is the R script for jaguar and ocelot density for the three years. * Capture histories for years 1, 2, and 3 for jaguars and ocelots. ID: Jaguar ID, OCC: Occasion number, Det: Detector number, Site: camera on road, Prey: number of prey species recorded. * Masks and effort files for years 1, 2, and 3 have been removed for security purposes of camera locations. These files can be made available via request to the authors. ## Code/Software All code is run in R software. Information on necessary packages are in the scripts. Scripts can be downloaded or forked via Github: [https://github.com/matt-hyde-s/Amolar](https://github.com/matt-hyde-s/Amolar)