strataG (version 2.4.905)

fsc.input: Input functions for fastsimcoal parameters

Description

These functions specify and format simulation parameters used to write fastsimcoal2 parameter or template files, parameter estimation files, parameter definition files, and site frequency spectrum files.

Usage

fscDeme(deme.size, sample.size, sample.time = 0, inbreeding = 0, growth = 0)
fscSettingsDemes(..., ploidy = 2)
fscEvent(
  event.time = 0,
  source = 0,
  sink = 0,
  prop.migrants = 1,
  new.size = 1,
  new.growth = 0,
  migr.mat = 0
)
fscSettingsEvents(...)
fscSettingsMigration(...)
fscBlock_dna(
  sequence.length,
  mut.rate,
  recomb.rate = 0,
  transition.rate = 1/3,
  chromosome = 1
)
fscBlock_microsat(
  num.loci,
  mut.rate,
  recomb.rate = 0,
  gsm.param = 0,
  range.constraint = 0,
  chromosome = 1
)
fscBlock_snp(sequence.length, mut.rate, recomb.rate = 0, chromosome = 1)
fscBlock_standard(num.loci, mut.rate, recomb.rate = 0, chromosome = 1)
fscBlock_freq(mut.rate, outexp = TRUE)
fscSettingsGenetics(..., num.chrom = NULL)
fscEstParam(
  name,
  is.int = TRUE,
  distr = c("unif", "logunif"),
  min = NA,
  max = NA,
  value = NA,
  output = TRUE,
  bounded = FALSE,
  reference = FALSE
)
fscSettingsEst(..., obs.sfs, rules = NULL, sfs.type = c("maf", "daf"))
fscSettingsDef(mat)

Arguments

deme.size

the number of individuals in the deme.

sample.size

the number of samples to take.

sample.time

the number of generations in the past at which samples are taken.

inbreeding

the inbreeding coefficient for the deme [0:1].

growth

the growth rate of the deme.

...

a set of comma-separated values for settings. See Notes for more information.

ploidy

the desired ploidy of the final data. deme.size and sample.size will be multiplied by this value in the parameter or template file as fastsimcoal2 generates haploid data.

event.time

the number of generations before present at which the historical event happened.

source

the source deme (the first listed deme has index 0).

sink

the sink deme.

prop.migrants

the expected proportion of migrants to move from the source to the sink deme.

new.size

the new size for the sink deme, relative to its size in the previous (later in time) generation.

new.growth

the new growth rate for the sink deme.

migr.mat

the number of the new migration matrix to be used further back in time. The matrices are those supplied to the fscSettingsMigration function. The first matrix has index 0.

sequence.length

number of base pairs to use for each block.

mut.rate

per base pair or locus mutation rate.

recomb.rate

recombination rate between adjacent markers. No effect for SNPs.

transition.rate

dna: fraction of substitutions that are transitions.

chromosome

number or character identifying which chromosome the marker is on.

num.loci

number of loci to simulate.

gsm.param

value of the geometric parameter for a Generalized Stepwise Mutation (GSM) model. This value represents the proportion of mutations that will change the allele size by more than one step. Values between 0 and 1 are required. A value of 0 is for a strict Stepwise Mutation Model (SMM).

range.constraint

msat: Range constraint (number of different alleles allowed). A value of 0 means no range constraint.

outexp

logical describing if the expected site frequency spectrum given the estimated parameters should be output?

num.chrom

the number of chromosomes to be simulated. If this is specified and not the same as the number of linkage blocks specified by the fscBlock_ functions, then this many chromosomes with duplicated structures will be simulated. If num.chrom = NULL, then the chromosome specification for each block will be used.

name

name of the parameter being specified. Must match a name used in one of the simulation settings functions.

is.int

logical specifying whether or not the parameter is an integer.

distr

a character string giving the distribution to use to select initial values for parameter estimation. Can be "unif" or "logunif".

min, max

minimum and maximum values for the distribution specified in distr.

value

character string giving the value that the complex parameter is to take.

output

logical indicating if estimates for the parameter should be output.

bounded

logical indicating whether to treat the parameter as a bounded estimate.

reference

logical indicating whether the parameter is to be used as a reference.

obs.sfs

vector, matrix, or list containing observed SFS to use for parameter estimation.

rules

character vector giving rules for the parameter estimation.

sfs.type

type of SFS to write. Can be maf or daf.

mat

numeric matrix or data frame with values of parameters to use in place of parameter names in simulation.

References

Excoffier, L. and Foll, M (2011) fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios Bioinformatics 27: 1332-1334. Excoffier, L., Dupanloup, I., Huerta-S<U+00E1>nchez, E., Sousa, V.C., and M. Foll (2013) Robust demographic inference from genomic and SNP data. PLOS Genetics, 9(10):e1003905. http://cmpg.unibe.ch/software/fastsimcoal2/

See Also

fscWrite, fscRun, fscRead

Examples

# NOT RUN {
# three demes with optional names
demes <- fscSettingsDemes(
  Large = fscDeme(10000, 10), 
  Small = fscDeme(2500, 10),
  Medium = fscDeme(5000, 3, 1500)
)

# four historic events
events <- fscSettingsEvents(
  fscEvent(event.time = 2000, source = 1, sink = 2, prop.migrants = 0.05),
  fscEvent(2980, 1, 1, 0, 0.04),
  fscEvent(3000, 1, 0),
  fscEvent(15000, 0, 2, new.size = 3)
 )
 
# four genetic blocks of different types on three chromosomes.  
genetics <- fscSettingsGenetics(
  fscBlock_snp(10, 1e-6, chromosome = 1),
  fscBlock_dna(10, 1e-5, chromosome = 1),
  fscBlock_microsat(3, 1e-4, chromosome = 2),
  fscBlock_standard(5, 1e-3, chromosome = 3)
)

#' same four genetic blocks of different types with same structure repeated three times.  
genetics <- fscSettingsGenetics(
  fscBlock_snp(10, 1e-6),
  fscBlock_dna(10, 1e-5),
  fscBlock_microsat(3, 1e-4),
  fscBlock_standard(5, 1e-3),
  num.chrom = 3
)

# }