Data and code for 'Age structure of amphibian populations with endemic chytridiomycosis, across climatic regions with markedly different infection risk'

This repository provides all data and R code from the analysis presented in the following paper: Turner, A., Heard, G., Hall, A., Wassens, S. (in review). Age structure of amphibian populations with endemic chytridiomycosis, across climatic regions with markedly different infection risk. The data are provided as a series of .csv files, R script and two zip folders of R packages (Surv_mod and VB_mod) 1. Skeleto_dat_ready_Jan2021.csv Data from frog surveys conducted by Anna Turner 2. Geoffs_data.csv Data from frog surveys conducted by Geoff Heard 3. Environmental_variables_skeleto.csv Environmental data collected during surveys 4. sk.dat_July21.csv Collated data from Anna and Geoff - created by 'Data_collation_for_analysis_2.R' ready for analysis 5. Variables_that_are_highly_correlated_with_each_other_season_wide.csv Testing for correlation 6. Model_structure_skeleto_2.csv creates model structure for analysis 7. Model_selection_statistics_June_21.csv Output from model R code is provided seperately for each of the following components: 1. Data_collation_for_analysis_2.R Collating data from Anna and Geoffs datasets 2. Skeleto_analysis_5.R - First uses regression modelling to explore factors correlated with variation in age - Following Scheele et al. (2016) regression models with a poisson distribution - Use bayesian non-linear regression to fit the Von Bertalanffy growth model to size-at-age data - Plots male and female growth curves - Uses catch curve approach to estimate survival from best fitting regression model following Scroggie (2012) but with bayesian implementation

本仓库提供了下述审稿中论文的分析所用全部数据与R代码：Turner, A., Heard, G., Hall, A., Wassens, S.，论文题为《具有地方性壶菌病的两栖动物种群年龄结构——跨感染风险差异显著的气候区域》。
本次公开的数据以一系列.csv文件、R脚本以及两个R软件包压缩文件夹（Surv_mod与VB_mod）的形式提供，具体文件如下：
1. Skeleto_dat_ready_Jan2021.csv：Anna Turner开展的蛙类调查数据
2. Geoffs_data.csv：Geoff Heard开展的蛙类调查数据
3. Environmental_variables_skeleto.csv：调查期间采集的环境变量数据
4. sk.dat_July21.csv：整合自Anna与Geoff的数据集——由`Data_collation_for_analysis_2.R`生成，用于后续分析
5. Variables_that_are_highly_correlated_with_each_other_season_wide.csv：用于相关性检验的数据集
6. Model_structure_skeleto_2.csv：用于构建分析所需模型结构的文件
7. Model_selection_statistics_June_21.csv：模型选择统计结果文件

配套的R代码按以下组件分别提供：
1. Data_collation_for_analysis_2.R：用于整合Anna与Geoff的两份数据集
2. Skeleto_analysis_5.R：
- 首先通过回归建模探究与年龄变异相关的影响因子
- 参照Scheele等（2016）的研究，使用泊松分布构建回归模型
- 采用贝叶斯非线性回归，将冯·贝塔朗菲生长模型（Von Bertalanffy growth model）拟合至年龄-体型数据
- 绘制雄性与雌性个体的生长曲线
- 采用捕获曲线法（catch curve approach），参照Scroggie（2012）的研究方法，结合贝叶斯实现方式，基于最优拟合回归模型估算种群存活率