Genotype and Genotyping Error Simulation
Description
Simulates genotypes given a pedigree and allele frequencies. Option exists to simulate observed genotypes given Wangs's (2004) or CERVUS's model (Marshall 1998) of genotyping error for codominat markers or an asymmetric allele based model for dominant markers (Hadfield, 2009).
Usage
1  simgenotypes(A, E1 = 0, E2 = 0, ped, no_dup = 1, prop.missing=0, marker.type="MSW")

Arguments
A 
list of allele frequencies at each locus 
E1 
if Wang's (2004) model of genotyping error for codominant markers is used this is the probability of an allele dropping out. If CERVUS's (Kalinowski, 2006; Marshall, 1998) model of genotyping error for codominant markers is used this parameter is not used. If Hadfield's (2009) model of genotyping error for dominant markers is used this is the probability of a dominant allele being scored as a recessive allele. 
E2 
if Wang's (2004) or CERVUS's (Kalinowski, 2006; Marshall, 1998) model of genotyping error for codominant markers are used this is the probability of an allele being missscored. In the CERVUS model errors are not independent for the two alleles within a genotype and so if a genotyping error has occurred at one allele then a genotyping error occurs at the other allele with probability one. Accordingly, 
ped 
pedigree in 3 columns: id, dam, sire. Base individuals have NA as parents. All parents must be in id. 
no_dup 
integer: number of times genotypes are to be observed 
prop.missing 
proportion of observed genotypes that are missing 
marker.type 

Value
G 
list of genotype objects; true genotypes for each locus 
Gid 
vector of id names indexing 
Gobs 
list of genotype objects; observed genotypes for each locus 
id 
vector of 
Author(s)
Jarrod Hadfield j.hadfield@ed.ac.uk
References
Marshall, T. C. et al (1998) Molecular Ecology 7 5 639655 Kalinowski S.T. et al (2007) Molecular Ecology 16 5 10991106 Hadfield J. D. et al (2009) in prep
See Also
genotype
Examples
1 2 3 4 5 6 7 