Check the genotype and life history data for duplicate IDs (not permitted) and duplicated genotypes (not advised), and count how many individuals in the genotype data are not included in the life history data (permitted). The order of IDs in the genotype and life history data is not required to be identical.
DuplicateCheck(
GenoM = NULL,
Specs = NULL,
ErrM = NULL,
LhIN = NULL,
quiet = FALSE
)matrix with genotype data, size nInd x nSnp
The 1-row dataframe with parameter values
3x3 matrix with genotyping error probabilities; rows=actual, columns=observed
life history data
suppress messages
A list with one or more of the following elements:
Dataframe, row numbers of duplicated IDs in genotype data. Please do remove or relabel these to avoid downstream confusion.
Dataframe, duplicated genotypes (with or without identical IDs). The specified number of maximum mismatches is allowed, and this dataframe may include pairs of closely related individuals. Mismatch = number of SNPs at which genotypes differ, LLR = likelihood ratio between 'self' and most likely non-self.
Dataframe, row numbers of duplicated IDs in life history data
Vector, IDs (in genotype data) for which no life history data is provided