Data from: Environmental variation is related to morphotype differentiation in a Brunfelsia (Solanaceae) complex

Description This repository contains the data, spatial layers, intermediate outputs, and R scripts required to reproduce the analyses presented in the associated manuscript on environmental and morphological variation in Brunfelsia hydrangeiformis. The repository is organized into the following components: R scripts and input data Script_Brunfelsia_DataManagment_DataAnalyses_DataVisualization.R — main R script containing the complete analytical workflow, including preparation of environmental predictors, ecological niche modelling, model evaluation, variable importance, partial dependence analyses, spatial projections, niche analyses, and classification analyses. data_pdp_adjusted.R — custom R function used to calculate adjusted partial dependence data. morpho_latlong.csv — morphological measurements and geographic coordinates of the specimens used in the analyses. Rasters (Rasters.zip) This archive contains the environmental raster layers used as predictors in the analyses, including: Rasters/current/ — current climatic raster layers used to construct the climatic predictor dataset. Rasters/soilgrids/ — edaphic raster layers derived from SoilGrids and used to construct the soil predictor dataset. The raster layers are used throughout the workflow for environmental characterization, ecological niche modelling, extraction of environmental values at occurrence locations, niche-space analyses, and classification analyses. Spatial layers (Shapefiles.zip) This archive contains the spatial layers required for defining the study area and for producing the spatial figures, including: WWF biogeographical realms used to delimit the Neotropical background; Natural Earth country boundaries used for mapping; Natural Earth graticules used for map visualization. The archive contains the complete shapefile components required to read these spatial datasets in R. Results and intermediate files (Results.zip) This archive contains intermediate datasets, fitted models, derived spatial predictions, and other objects generated during the analytical workflow. These files are provided both to facilitate verification of the analyses and to allow users to inspect or reuse intermediate outputs without rerunning the entire workflow. Results/Datasets/ contains: VIF_table.csv — results of predictor selection based on variance inflation factors. CleannedOcc.txt — cleaned occurrence records used in subsequent analyses. OccData.csv — occurrence data and associated environmental information. VarImpData.csv — variable importance estimates from the fitted ecological niche models. PartialPlotData.csv — partial dependence data describing the relationships between environmental predictors and predicted habitat suitability. ENM_ModelPerformance.csv — performance metrics for the individual ecological niche models and ensemble models. Results/RData/ contains R objects required for reproducing or inspecting intermediate analyses: OccDataPart.RData — partitioned occurrence datasets used for model calibration and evaluation. SppModels.RData — fitted species distribution models. PCA_plots.RData — intermediate PCA-based environmental space plots. eq.test.clim.RData — climatic niche equivalency test results. sim.test.clim.RData — climatic niche similarity test results. eq.test.soil.RData — edaphic niche equivalency test results. sim.test.soil.RData — edaphic niche similarity test results. leg.RData — intermediate graphical object used in figure construction. Results/Ensemble/ contains the final ensemble habitat suitability rasters for the focal taxa: bahia.tif capitata.tif hydrangeiformis.tif Together, these files provide the input data, environmental layers, spatial layers, analytical scripts, fitted models, intermediate datasets, and derived outputs necessary to reproduce and evaluate the analyses reported in the associated manuscript. Software and reproducibility The analyses were conducted in R using the packages specified in the accompanying R script. The main workflow is designed to be executed sequentially, with intermediate files generated during earlier steps subsequently used by later steps. The Results archive is therefore provided as a complete set of intermediate and derived outputs for users who wish to inspect the analyses without rerunning every computational step. Folder and file structure WorkingDirectory/├── Script_Brunfelsia_DataManagment_DataAnalyses_DataVisualization.R├── data_pdp_adjusted.R├── morpho_latlong.csv├── Rasters.zip├── Shapefiles.zip└── Results.zip