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摘要 本数据集包含开展种群统计与连通性分析所需的全部数据及R脚本。文件涵盖基于空间显式个体基模型（spatially-explicit individual-based model）生成的情景1与情景2的原始输出文件，以及用于线性模型分析的数据集。 ### 数据集 本项目种群统计与连通性分析所用的数据集、辅助空间数据及R脚本。 `scen1_patches_All_Felids.txt`；`scen2_patches_All_Felids.txt` #### 文件说明 该文件为模型针对模拟情景1（`scen1_patches_All_Felids.txt`）与情景2（`scen2_patches_All_Felids.txt`）生成的输出文件，全程记录了模拟过程中所有个体的生存结局。两文件的列字段完全一致。 ##### 列字段说明 - `repetition`：模拟ID。 - `PMortDisp`：扩散猞猁的日基准死亡率参数。 - `PMortRes`：定居猞猁的年基准死亡率参数。 - `birthprob`：当雌雄猞猁领地重叠时的繁殖概率。 - `timestep`：模拟中定义猞猁年的时间单位。 - `felid_ID`：个体标识符。 - `birthX`：猞猁出生所在的x单元格。 - `birthY`：猞猁出生所在的y单元格。 - `sex`：个体性别。 - `MortReason`：特定时间步下个体的生存结局。 - `status`：特定时间步下个体的社会地位。当`status=1`时，个体拥有领地，即为“定居者”；当`status=0`时，个体无领地，即为“扩散者”。 - `ActualX`：时间步结束时个体所在的x单元格位置。 - `ActualY`：时间步结束时个体所在的y单元格位置。 - `BirthPatchNo`：出生斑块编号，代表个体出生所在的空间区域（即种群）。 - `FromPatchNo`：起始斑块编号，代表时间步开始时个体所在的空间区域。 - `LastPatchNo`：结束斑块编号，代表时间步结束时个体所在的空间区域。 - `Age`：个体年龄。 `scen1_population_FelidsPerPatch_ESA.txt`；`scen2_population_FelidsPerPatch_ESA.txt` #### 文件说明 该文件为模型输出文件，涵盖情景1（`scen1_population_FelidsPerPatch_ESA.txt`）与情景2（`scen2_population_FelidsPerPatch_ESA.txt`）的每个模拟时间步内，不同空间区域内记录的定居与扩散个体数量。两文件的列字段完全一致。 ##### 列字段说明 - `birthprob`：当雌雄猞猁领地重叠时的繁殖概率。 - `mortprobD`：扩散猞猁的日基准死亡率参数。 - `mort_probres`：定居猞猁的年基准死亡率参数。 - `repetition`：模拟ID。 - `timestep`：模拟中定义猞猁年的时间单位。 - `year`：实时时间步。 - `patchno`：空间区域（即猞猁种群）的标识。 - `NResFem`：特定重复模拟中，某patchno与时间步下的定居雌性个体数量。 - `NResMal`：特定重复模拟中，某patchno与时间步下的定居雄性个体数量。 - `NRes`：特定重复模拟中，某patchno与时间步下的定居个体总数量。 - `NDisp`：特定重复模拟中，某patchno与时间步下的扩散个体总数量。 `conn_patch_area.csv` #### 文件说明 记录了1至26号本地连通性斑块的面积（单位：km²），该文件将在`08_analysis_linear_models.Rmd`脚本中使用。 ##### 列字段说明 - `id_conn`：本地连通性斑块的标识符。 - `PatchName`：本地连通性斑块的名称。 - `area`：本地连通性斑块的总面积，单位为km²。 `Lynx_reintrod_in_raster10km.csv` #### 文件说明 记录了1970年代以来中欧地区开展的猞猁再引入项目的位置（位于10km²网格内）。 ##### 列字段说明 - `Date`：再引入年份。 - `Population`：该次再引入对应的猞猁种群。 - `Site`：再引入区域。 - `nMal`：再引入的雄性个体数量。 - `nFem`：再引入的雌性个体数量。 - `nUnknown`：再引入的性别未知个体数量。 - `Remark`：该次再引入的补充说明信息。 - `lon`：再引入所在10km²网格的经度坐标。 - `lat`：再引入所在10km²网格的纬度坐标。 `lm_imm_data` #### 文件说明 用于通过线性模型分析迁入个体对目标斑块定居种群规模的贡献的数据集。 ##### 列字段说明 - `Scenario`：模拟情景（1或2）。 - `LastPatchNo`：模拟结束时个体所在的斑块ID。 - `year`：年份。 - `timestep`：模拟时间步。 - `meanNewImm`：特定斑块（LastPatchNo）与特定年份下的平均迁入个体数量。 - `area`：斑块面积（单位：km²）。 - `year_num`：年份数值。 - `meanRes`：特定斑块（LastPatchNo）与特定年份下的平均定居个体数量。 - `meanRes_lead`：前一年某斑块（LastPatchNo）的迁入个体数量。 ### 空间数据 用于种群统计与连通性分析的辅助数据。 `lynx_habitat_3035.tif` #### 说明 猞猁栖息地适宜性地图。像素值含义如下： - 0：不适宜栖息地。 - 2：基质（偶发性扩散栖息地）。 - 3：扩散栖息地。 - 4：繁殖栖息地（兼具扩散与领地定居适宜性的栖息地）。 #### 格式参数 - 类型：栅格（raster） - 像素尺寸：1000×1000 - 宽度：1382 - 高度：931 - 坐标参考系统： - 名称：EPSG:3035 - ETRS89-extended / LAEA Europe - 单位：米 - 投影方法：兰伯特方位等面积投影（Lambert Azimuthal Equal Area） `patches_3035.tif` #### 说明 模型连通性分析所用的本地连通性斑块（1至26号）与区域连通性斑块（30至160号）的分布。本地斑块涵盖猞猁种群核心区域以及对猞猁种群扩张与连通性至关重要的区域；区域斑块涵盖目标斑块周边的山地区域。 #### 格式参数 - 类型：栅格（raster） - 像素尺寸：1000×1000 - 宽度：1382 - 高度：931 - 坐标参考系统： - 名称：EPSG:3035 - ETRS89-extended / LAEA Europe - 单位：米 - 投影方法：兰伯特方位等面积投影（Lambert Azimuthal Equal Area） ### 代码与软件 `Coords_reintrod_to_xyCell_10km2.R` #### 说明 用于将中欧地区猞猁再引入项目的xy坐标（EPSG:4326）转换为栅格（EPSG:3035）的xy单元格的R脚本。 ##### 输入文件： 1. `Lynx_reintrod_in_raster10km.csv` 2. `lynx_habitat_3035.tif` `analysis_demo.R` #### 说明 用于针对本模拟的情景1与情景2，分析模拟模型内猞猁种群的种群统计特征的R脚本。种群统计分析包括针对每个猞猁种群计算种群规模、扩散参数（增长与变异）以及模拟全程的灭绝概率。灭绝概率基于50只定居猞猁的种群阈值与0.05的灭绝阈值计算。脚本末尾附带结果可视化代码。 ##### 输入文件： 1. `scen1_population_FelidsPerPatch_ESA.txt` 2. `scen2_population_FelidsPerPatch_ESA.txt` `analysis_conn_Scen1.R`；`analysis_conn_Scen2.R` #### 说明 用于分析连通性斑块间连通概率的R脚本（情景1对应`07a_analysis_connectivity_Scen1_data-prep.Rmd`，情景2对应`07b_analysis_connectivity_Scen2_data-prep.Rmd`）。连通概率按年度分析，并针对两个不同周期取平均值。其中`07b_analysis_connectivity_Scen2_data-prep.Rmd`脚本额外计算了每个时间步各斑块的迁入个体数量，该部分输出将作为`08_analysis_linear_models.Rmd`脚本的输入文件。 ##### 输入文件： 1. 针对`analysis_conn_scen1.R`：`scen1_patches_All_Felids.txt` 2. 针对`analysis_conn_scen2.R`：`scen2_patches_All_Felids.txt` 3. 两个脚本均需`patches_3035.tif` `analysis_lms.R` #### 说明 用于通过线性混合效应模型分析迁入负荷对本地连通性斑块定居种群规模的影响的R脚本，同时附带模型诊断与可视化代码。 ##### 输入文件： `lm_imm_data.csv`