# short script to run the simulations assessing the MCMC method for
# detecting contaminated samples.
# Must be run in the directory that contains the directories "simulations", "supplements",
# and "manuscript"
if(!all(file.exists("simulations", "manuscript", "supplements"))) {
stop("You must run 01_simulation_1.R in directory that includes: \"simulations\", \"manuscript\", \"supplements\"")
}
library(SNPcontam)
library(parallel)
source("simulations/simulation_functions.R")
#### Get data set and choose Feather H Spring as an example collection of allele freqs ####
tmp_data <- swfsc_chinook_baseline
data <- tmp_data[tmp_data$Pop == "Feather_H_sp", ]
#### Run the MCMC simulations and put output in a big Rda file
set.seed(10) # Set Seed For reproducibility
out_list_01 <- MCMC_sims(
sample_data = data,
N = 200,
Lvals = c(20,60,100,200),
rhovals = c(0,.025,0.075,0.2,0.5),
n = 100
)
save(out_list_01, file = "simulations/out_list_01.rda", compress = "xz")
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