runMacs2 {AlphaSimR} | R Documentation |
A wrapper function for runMacs
. This wrapper is designed
to be easier to use than supply custom comands to manualCommand in
runMacs
. It effectively automates the creation of an
appropriate manualCommand using user supplied variables, but only deals
with a subset of the possibilities. The defaults were chosen to match
species="GENERIC" in runMacs
.
runMacs2(nInd, nChr = 1, segSites = NULL, Ne = 100, bp = 1e+08, genLen = 1, mutRate = 2.5e-08, histNe = c(500, 1500, 6000, 12000, 1e+05), histGen = c(100, 1000, 10000, 1e+05, 1e+06), inbred = FALSE, split = NULL, ploidy = 2L, returnCommand = FALSE, nThreads = NULL)
nInd |
number of individuals to simulate |
nChr |
number of chromosomes to simulate |
segSites |
number of segregating sites to keep per chromosome |
Ne |
effective population size |
bp |
base pair length of chromosome |
genLen |
genetic length of chromosome in Morgans |
mutRate |
per base pair mutation rate |
histNe |
effective population size in previous generations |
histGen |
number of generations ago for effective population sizes given in histNe |
inbred |
should founder individuals be inbred |
split |
an optional historic population split in terms of generations ago |
ploidy |
ploidy level of organism |
returnCommand |
should the command passed to manualCommand in
|
nThreads |
if OpenMP is available, this will allow for simulating chromosomes in parallel. If the value is NULL, the number of threads is automatically detected. |
an object of MapPop-class
or if
returnCommand is true a string giving the MaCS command passed to
the manualCommand argument of runMacs
.
# Creates a populations of 10 outbred individuals # Their genome consists of 1 chromosome and 100 segregating sites # The command is equivalent to using species="GENERIC" in runMacs founderPop = runMacs2(nInd=10,nChr=1,segSites=100)