Sim.HatchExp: Simulate genotypes over many generations

In patbarry6/PseudoBabies: Assess power of genetic markers for parentage through simulation

Description

This function allows you to simulate multilocus genotypes through time

Usage

Sim.HatchExp(
  AnalysisName,
  Founders,
  AOMfile,
  Markerfile = "MarkerPanels.csv",
  NumuSats,
  NumSNPs,
  NB = 600,
  NumYears = 19,
  StartYear = format(Sys.Date(), "%Y"),
  nSim = 10,
  Geno_Error = FALSE,
  Miss_data = FALSE,
  MissingVec = c(0, 2.5),
  ErrorVals = 1,
  Programs = c("FRANz", "Colony"),
  SexInf = FALSE,
  perl.dir,
  GPHomogeneity = FALSE,
  OffspringDist = "Poisson",
  SexInfo = FALSE,
  MatingStr = "Polygamy",
  lambda = 2,
  Umin,
  Umax,
  nBprob,
  HatchYear,
  SireHatch,
  DamHatch,
  Hatch_Dist,
  lambda_h = 2,
  Umin_h,
  Umax_h,
  nBprob_h,
  BreedDesign = "1:2"
)

Arguments

AnalysisName	name of the analysis
Founders	.csv file containing the genotypes to use for initiating the simulation. Use function CompleteGenotypes to remove missing data before performing simulations.
AOMfile	.csv of Age of maturity estimates.
Markerfile	.csv for marker panels that will be evaluated.
NumuSats	number of microsatellite markers.
NumSNPs	number of SNP markers.
NB	number of crosses to perform each year. Defaults to 100.
NumYears	How many years should the simulation last? Defaults to 50.
StartYear	What year should the simulation start? Defaults to current year.
Geno_Error	Would you like to add genotyping error to the simualated data? Defaults to FALSE
Miss_data	Would you like to add missing data to the simulations? Defaults to FALSE
MissingVec	A vector of values for the percent of missing data in the input file. Required if Miss_data=TRUE. Defaults to 0 and 2.5 percent.
Programs	Which programs would you like to create input files for? Defaults to c('FRANz','Colony')
SexInf	Use the sex of individuals in the parentage inference program
perl.dir	File path for the perl directory for FRANz utility for formating.
OffspringDist	What distribution should we use for the number of offspring produced for each cross. Options are Uniform (specify a min and a max), NegativeBinomial (specify a prob for the scale parameter see NegBinomial options), and Poisson (specify lambda).
SexInfo	Does your dataset have information on sex?
MatingStr	Should the simulation allow for polygamy, polygyny, polandry, or monogomy?
SireHatch	How many individuals to collect for the sires
DamHatch	How many individuals to collect for the dams
BreedDesign	What is the breeding design for the experiment? Defaults to 2:1.
nSim=10	How many replicate simulations would you like to do? Defaults to 10.
ErrorVec	A vector of error values for genotyping error. Required if Geno_Error=TRUE. Defaults to 0 and 2 percent.
HatchYr	In what year do we want to implement a hatchery experiment
HatchDist	What distrbution do we want to use for the hatchery offspring?

Examples

Sim.HatchExp()

patbarry6/PseudoBabies documentation built on Dec. 22, 2021, 6:41 a.m.