A spatial phase transition between neutral and niche communities: R code and model output

R source code for the determination of critical points in the phase transition, the analysis of richness and Shannon diversity of the model, early warnings and the application to Barro Colorado Island fores plot (BCI) . 

The neutral-niche model C++ program is available at: 
https://dx.doi.org/10.6084/m9.figshare.969692

R Markdown files:
I usually run Rmd files chunk by chunk because there are long simulations, and save ".RData" to keep the results.  Neutral_steadyState.Rmd: Simulations to determine the time to reach steady state
Neutral_simulCT.Rmd: Simulations to find critical values, and plots H vs Rho vs Migration
Neutral_EarlyWarnings_Smax.Rmd: Early warnings of the critical transition based on Maximun Patch 
BCIpatchAnalysis.Rmd: Barro Colorado Island analysis  you have to obtain the BCI data from http://ctfs.si.edu/webatlas/datasets/bci/Terms%20and%20conditions.htm
R Files
Neutral_fun.r:  functions used for the analysis and simulations
BCI_fun.r:  functions used for the analysis of BCI data
powerlaw.zip: code to fit powerlaws from http://tuvalu.santafe.edu/~aaronc/powerlaws/ (by Cosma Shalizi)
Data files
.RData  are the results of simulations in data.frame format

Simul.zip Output of all simulations.

用于确定相变临界点、分析模型的物种丰富度（richness）与香农多样性（Shannon diversity）、生成临界转变早期预警信号，并应用于巴罗科罗拉多岛森林样地（Barro Colorado Island forest plot, BCI）的R语言源代码。

本数据集配套的中性-生态位模型（neutral-niche model）C++程序获取地址为：
https://dx.doi.org/10.6084/m9.figshare.969692

R Markdown（R Markdown）脚本文件：
由于涉及长时模拟运算，通常会分块运行Rmd脚本，并保存".RData"格式文件以留存运算结果。各脚本功能说明如下：
- Neutral_steadyState.Rmd：用于确定模型达到稳态所需时间的模拟实验脚本
- Neutral_simulCT.Rmd：用于搜寻临界值，并绘制H、Rho与迁移率关系图的模拟实验脚本
- Neutral_EarlyWarnings_Smax.Rmd：基于最大斑块的临界转变早期预警分析脚本
- BCIpatchAnalysis.Rmd：巴罗科罗拉多岛数据分析脚本，需从http://ctfs.si.edu/webatlas/datasets/bci/Terms%20and%20conditions.htm自行获取BCI数据集

R工具脚本：
- Neutral_fun.r：用于分析与模拟运算的自定义函数集
- BCI_fun.r：用于巴罗科罗拉多岛数据分析的自定义函数集
- powerlaw.zip：用于拟合幂律（powerlaws）分布的代码，源自http://tuvalu.santafe.edu/~aaronc/powerlaws/（作者为Cosma Shalizi）

数据文件：
- .RData（.RData）：以数据框（data.frame）格式存储的模拟运算结果
- Simul.zip：全部模拟实验的输出结果压缩包