Extinction risk and evolution of a quantitative trait in a variable environment with increasing frequency of extreme events

Data and code for "Extinction risk and evolution of a quantitative trait in a variable environment with increasing frequency of extreme events"

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The simulation model in in the file Monte.Carlo.topub.r. Within the file, all input and output are described in detail.

You can simply source the file: source("Monte.Carlo.topub.r")

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the file ext.RDS can be loaded in R by typing

ext.df = readRDS("ext.RDS")

after having moved the file to you current directory

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In the data set ext.RDS, I included the following variables and outcomes of simulations:

sel - strength of selection

cat.freq - probability of occurrence of point extremes

pop.ext10.rand - mean population size in the "sampling window"

addvar.mean.10.rand. - mean additive genetic variance in the "sampling window"

meanopt - directional trend

mut - mutation amplitude

mean.pheno - mean phenotype at the end of simulation time (interesting for replicates in which ext = 1)

cat.bef - number of point extremes in the five years before extinction (interesting for replicates in which ext = 1)

ext_year - extinction time (299 for replicates that persisted up to the end of simulation time)

ext - extinct (1) or not (0)

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For some of the analyses and plots in Vincenzi Point Extremes.r, the full dataset is required

Please download sum.ris1.RDS and sum.ris2.RDS and move them to the current directory of R

Then:

sum.ris1 = readRDS("sum.ris1.RDS")

sum.ris2 = readRDS("sum.ris2.RDS")

sum.ris = c(sum.ris1,sum.ris2)

rm(list=c("sum.ris1","sum.ris2"))

The list sum.ris contains some of the measured variables for all the 25 600 replicates.

In particular:

extinct - pop going extinct or not
addvar - additive genetic variance at each time step
phenvar - phenotypic variance at each time step
yearextinct - year of extinction (299 if not extinct)
phenomean - phenotypic mean at each time step
sdopt - increase in variability of the optimum
meanopt - directional trend
selstrength - strength of selection
mutalfa - mutation amplitude
fitness.mean - mean fitness at each time step
optimum - optimum at each time step
popsize.post - population size after mortality at each time step

Please write to [e-mail] in the case help or clarifications are needed

本数据集与代码配套于论文《极端事件频率升高的可变环境中数量性状的灭绝风险与演化》（Extinction risk and evolution of a quantitative trait in a variable environment with increasing frequency of extreme events）。

模拟模型存储于Monte.Carlo.topub.r文件中，该文件内对所有输入、输出项均有详细说明。您可直接运行该文件：source("Monte.Carlo.topub.r")

ext.RDS文件可通过R语言加载，操作步骤为：将文件移动至当前工作目录后，在R控制台输入ext.df = readRDS("ext.RDS")

在ext.RDS数据集中，收录了以下模拟变量与结果：
- sel：选择强度（strength of selection）
- cat.freq：极端单点事件发生概率
- pop.ext10.rand：“采样窗口”内的平均种群规模
- addvar.mean.10.rand.：“采样窗口”内的平均加性遗传方差（additive genetic variance）
- meanopt：定向演化趋势
- mut：突变幅度
- mean.pheno：模拟结束时的平均表型值（针对ext=1的重复实验具有研究价值）
- cat.bef：灭绝前五年内发生的极端单点事件总数（针对ext=1的重复实验具有研究价值）
- ext_year：灭绝时间（若种群存活至模拟结束，则取值为299）
- ext：灭绝状态，1表示已灭绝，0表示未灭绝

针对Vincenzi Point Extremes.r中的部分分析与绘图任务，需使用完整数据集。请下载sum.ris1.RDS与sum.ris2.RDS，并将其移动至R的当前工作目录，随后执行以下代码：
sum.ris1 = readRDS("sum.ris1.RDS")
sum.ris2 = readRDS("sum.ris2.RDS")
sum.ris = c(sum.ris1,sum.ris2)
rm(list=c("sum.ris1","sum.ris2"))

sum.ris列表包含全部25600次重复实验的部分测量变量，具体如下：
- extinct：种群是否灭绝
- addvar：每个时间步的加性遗传方差（additive genetic variance）
- phenvar：每个时间步的表型方差（phenotypic variance）
- yearextinct：灭绝年份（若未灭绝则取值为299）
- phenomean：每个时间步的表型均值（phenotypic mean）
- sdopt：最适表型的变异程度增量
- meanopt：定向演化趋势
- selstrength：选择强度
- mutalfa：突变幅度
- fitness.mean：每个时间步的平均适应度（fitness）
- optimum：每个时间步的最适表型值
- popsize.post：每个时间步死亡率后的种群规模

如需协助或相关说明，请发送邮件至[e-mail]。