Archive/test.code/testRunFastsimcoal.R

In christianparobek/skeleSim: Genetic Simulation Engine

rm(list = ls())
library(skeleSim)
set.seed(1)

# ---- Load parameters ---

# create new skeleSim parameters object
test.params <- new("skeleSim.params")
test.params@title <- "testRun"
test.params@date <- Sys.time()
test.params@quiet <- FALSE
test.params@question <- "n"
test.params@simulator.type <- "c"
test.params@simulator <- "fsc"
test.params@num.reps <- 4
test.params@num.perm.reps <- 5
test.params@sim.func <- fsc.run
test.params@wd <- "testRun.wd"

# create and load scenarios
test.params@scenarios <- list(
  fsc.loadScenario(
    num.pops = 3,
    pop.size = c(20000, 5000, 10000),
    sample.size = c(20, 20, 6),
    sample.times = c(0, 0, 1500),
    locus.type = "dna",
    sequence.length = 1000,
    mut.rate = runif(3, 1e-6, 1e-3),
    chromosome = 1:3,
    migration = matrix(
      c(0, 0.5, 0.05, 0.025, 0, 0.025, 0.05, 0.5, 0), nrow = 3
    ),
    num.gen = c(2000, 2980, 3000, 15000),
    source.deme = c(1, 1, 1, 0),
    sink.deme = c(2, 1, 0, 2),
    prop.migrants = c(0.05, 0, 1, 1),
    new.sink.size = c(1, 0.04, 1, 3)
  )
)

# set fastsimcoal check
test.params@sim.check.func <- fsc.scenarioCheck

# ---- Set analysis function ----
test.params@rep.analysis.func <- skeleSim::analysisFunc

# ---- Run replicates ----
result <- runSim(test.params)

save(result, file = paste(result$params@title, "result.rdata"))