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# R script for simulating heterozygosity in a hypothetical population by drawing from values in real populations
# preplague3 are the real heterozygosity values in 3 populations
# Ho = average observed heterozygosity across loci for each individual
pdogavg <- rep(NA,10000) #empty vector for populating with simulated mean Ho of all individuals present in colonies where survivors were sampled
surv <- mean(survivors, na.rm=TRUE) #survivors is a vector of Ho in 6 surviving prairie dogs
count <- 0
for (i in 1:10000) {
pdogavg[i] <- mean(sample(preplague3, 6, replace=FALSE)) #sample without replacement from preplague3, a vector of Ho in all 3 pre-plague colonies where survivors were sampled. There were 6 survivors, so we sample 6 individuals at a time
if (pdogavg[i] > surv)
count <- count + 1 #count the number of times mean Ho pre-plague is greater than mean survivor Ho
}
p <- count/10000 #proportion of times Ho(pre) > Ho(survivor)
p