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 simon.vincenz@gmail.com in the case help or clarifications are needed