Translocation effects on regional and local population viability and connectivity

Abstract Data and R-scripts necessary to perform demographic and connectivity analysis. The files include raw output files for scenarios 1 and 2 from the spatially-explicit individual-based model of lynx, and datasets to perform linear model analysis. Dataset Datasets, auxiliary spatial data and r-scripts for the demographic and connectivity analysis of this project. scen1_patches_All_Felids.txt; scen2_patches_All_Felids.txt File Description: output file from the model for simulation scenario 1 (scen1_patches_All_Felids.txt) and scenario 2 (scen2_patches_All_Felids.txt) where the fate of all individuals is recorded throughout the simulation.Columns Description: columns are the same for files scen1_patches_All_Felids.txt and scen2_patches_All_Felids.txt . repetition: simulation id. PMortDisp: daily baseline mortality probabilitiy parameter of dispersing lynx. PMortRes: yearly baseline mortality probability parameter of resident lynx. birthprob: probability of lynx to reproduce when a female and a male overlap territories. timestep: time unit defining a lynx year in the simulation. felid_ID: identifier of an individual. birthX: x-cell where the lynx was born. birthY: y-cell where the lynx was born. sex: sex of the individual. MortReason: fate of the individual at a specific timestep. status: social status of the individual at a specific timestep. When status = 1, the individual has a territory ("resident"), when status = 0 the individual has no territory ("disperser"). ActualX: x-cell location of an individual at the end of the timestep. ActualY: y-cell location of an individual at the end of the timestep. BirthPatchNo: patch number, which represents a spatial area (i.e. population), where the individual is born. FromPatchNo: patch number, which represents a spatial area (i.e. population), where the individual was located at the beginning of the timestep. LastPatchNo: patch number, which represents a spatial area (i.e. population), where the individual was located at the end of the timestep. Age: age of the individual scen1_population_FelidsPerPatch_ESA.txt ; scen2_population_FelidsPerPatch_ESA.txt Files Description: output file from the model containing, for every timestep of the simulation of scenario 1 (scen1_population_FelidsPerPatch_ESA.txt) and scenario 2 (scen2_population_FelidsPerPatch_ESA.txt), the number of resident and dispersing individuals recorded in different areas.Columns Description: columns are the same for files scen1_population_FelidsPerPatch_ESA.txt and scen2_population_FelidsPerPatch_ESA.txt. birthprob: probability of lynx to reproduce when a female and a male overlap territories. mortprobD: daily baseline mortality probabilitiy parameter of dispersing lynx. mort_probres: yearly baseline mortality probability parameter of resident lynx. repetition: simulation id. timestep: time unit defining a lynx year in the simulation. year: timestep in real time. patchno: representation of the spatial area (i.e. lynx population). NResFem: number of resident females at a patchno and timestep in a repetition. NResMal: number of resident males at a patchno for a timestep for a repetition. NRes: number of residents at a patchno for a timestep in a repetition. NDisp: number of dispersers at a patchno for a timestep in a repetition. conn_patch_area.csv File Description: area (km2) of the local connectivity patches (1 to 26). This file is used in the "08_analysis_linear_models.Rmd" script.Columns: id_conn: identifier of the local connectivity patch. PatchName: name of the local connectivity patch. area: total area, in km2, of the local connectivity patch. Lynx_reintrod_in_raster10km.csv File Description: locations, within a 10km2 area, of lynx reintroductions carried out in Central Europe since 1970's.Columns:Date: year of reintroduction.Population: associated lynx population of the reintroduction.Site: area of the reintroduction.nMal: number of males reintroduced.nFem: number of females reintroduced.nUnknown: number of animals of unknown sex reintroduced.Remark: additional information to the reintroduction.lon: longitude coordinate of a 10km2 where the reintroducion took place.lat: latcoordinate of a 10km2 where the reintroducion took place. lm_imm_data File Description: Dataset for the analysis of the contribution of immigrants to the population size of residents in target patches using linear models.Columns: Scenario: simulation scenario (1 or 2). LastPatchNo: PathID where an individual is found at the end of the simulation. year: year. timestep: simulation timestep. meanNewImm: average number of immigrants at a patch (LastPatchNo) and a specific year. area: area of the patch (km2). year_num: year. meanRes: average number of residents at a patch (LastPatchNo) and a specific year. meanRes_lead: number of immigrants in a patch (LastPatchNo) in the previous year. Spatial data Auxialiary data for the demography and connectivity analysis. lynx_habitat_3035.tif Description: habitat suitability map of lynx.Values: 0: unsuitable habitat. 2: matrix (occasional dispersal habitat). 3: dispersal habitat. 4: breeding habitat (habitat suitables for dispersal and territory settlement). Type: rasterPixel size: 1000, 1000width: 1382height: 931Coordinate Reference System:Name : EPSG:3035 - ETRS89-extended / LAEA EuropeUnits: metersMethod: Lamber Azimuthal Equal Area patches_3035.tif Description: distribution of local connectivity patches (1 to 26) and regional connectivity patches (30 to 160) used for the connectivity analysis in the model. Local patches include the core areas of lynx populations and areas of importance for the expansion and connectivity of lanx populations. Regional patches include the mountain regions around the target patches.Type: rasterPixel size: 1000, 1000width: 1382height: 931Coordinate Reference System:Name : EPSG:3035 - ETRS89-extended / LAEA EuropeUnits: metersMethod: Lamber Azimuthal Equal Area Code/Software Coords_reintrod_to_xyCell_10km2.R Description: r-script to transform xy coordinates (EPSG:4326) of lynx reintroductions in Central Europe into xy cells of a raster (EPSG:3035).Input files: Lynx_reintrod_in_raster10km.csv lynx_habitat_3035.tif analysis_demo.R Description: r-script analysing, for scenarios 1 and 2 of our simulation, the demography of lynx populations within our simulation model. Analysis of demography includes the calculation for every lynx popualtion, population size, diffusion parameters (growth and variation) and extinction probability throughout the simulation. Extinction probability is calculated based on a population threshold of 50 resident lynx and an extinction threshold of 0.05.Code for plotting the results is also provided at the end of the script.Input files: scen1_population_FelidsPerPatch_ESA.txt scen2_population_FelidsPerPatch_ESAtxt analysis_conn_Scen1.R ; analysis_conn_Scen2.R Description: r-scripts (07a_analysis_connectivity_Scen1_data-prep.Rmd - for scenario 1 - ; 07b_analysis_connectivity_Scen2_data-prep.Rmd - for scenario 2 -)or the analysis of connectivity probabilities between connectivity patches. Connectivity probabilities are analysed annually and average for two different periods.In the script 07b_analysis_connectivity_Scen2_data-prp.Rmd there is additionally, the calculation of immigrations per patch per timestep. The output of this section is used as input file for the r-script 08_analysis_linear_models.Rmd.Input files: scen1_patches_All_Felids.txt (for analysis_conn_scen1.R) scen2_patches_All_Felids.txt (for analysis_conn_scen2.R) patches_3035.tif (both files) analysis_lms.R Description: r-script for tha analyses of the influence of immigration load on the population size of residents in the local connectivity patches using linear mixed effects models. Code for the diagnostics, and model plotting is also provided.Input patches: lm_imm_data.csv