Description Usage Arguments Examples
This is a wrapper around ms2geno that should make it much easier to use
1 2 3 |
refsizes |
integer vector of sample sizes for the reference samples from each collection (population) |
mixsizes |
integer vector of samples sizes of individuals that go into the mixture data set. |
num_loci |
the number of loci to simulate |
num_sets |
desired number of data sets. |
variability_string |
the command to pass to ms to influence the number of segregating sites. Either something like "-s 20" for fixed number of segsites, or "-t 8" to set the value of theta to 8. |
marker_pars |
a string that gives all the command line arguments needed for either microsatellites or SNPs (but not both!) to be simulated. See the documentation for ms2geno. |
M_num |
a number for 4Nem to be passed to ms to make a symmetrical island model. Gets overridden by M_matrix if M_matrix is present (i.e. non-NULL). Set this to NA if you want to simulate a single panmictic population that is masquerading as multiple populations using ms2geno's –ms-pop-override option. |
M_matrix |
a full migration matrix if you want to pass one in. Will override M_num if present. By default it will be NULL. |
repunits |
optional vector that must be the same length as refsizes and which gives the reporting units to which each collection belongs (NOT IMPLEMENTED) |
ploidy |
the ploidy of the organisms to be simulated. |
write_012 |
logical. If TRUE, writes Basefile and Mixfile as sets of 012 files to be read by, for example, genoscapeRtools::read_012. Default is FALSE |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | # microsatellites
GSImulate(
refsizes = c(200, 200, 150, 100),
mixsizes = c(25, 25, 10, 30),
num_loci = 20,
num_sets = 5,
variability_string = "-t 2.4",
marker_pars = "-u .15 3",
M_num = 5)
# microsatellites using --ms-pop-override
GSImulate(
refsizes = c(200, 200, 150, 100),
mixsizes = c(25, 25, 10, 30),
num_loci = 20,
num_sets = 5,
variability_string = "-t 2.4",
marker_pars = "-u .15 3",
M_num = NA)
# SNPs ascertained from 8 individuals from each population
# and taken if all three genotypes are seen
GSImulate(
refsizes = c(200, 200, 150, 100),
mixsizes = c(25, 25, 10, 30),
num_loci = 20,
num_sets = 5,
variability_string = "-t 2.4",
marker_pars = "-s 1 8 -2 -s 2 8 -2 -s 3 8 -2 -s 4 8 -2 --all-pops-geno-asc",
M_num = 5)
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