Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/allele.sharing.R
Internal function of Demerelate to calculate different allele sharing indices or estimators for any pair of population.
1 2 3 | allele.sharing(pop1, pop2, allele.column, data,
value = NA, ref.pop)
|
pop1 |
Specific dataframe of type inputformat. Population one used for calculations. Inputformat needs to be standard three digits mode for Demerelate. |
pop2 |
Specific dataframe of type inputformat. Population two used for calculations. Inputformat needs to be standard three digits mode for Demerelate. |
allele.column |
Numeric value - It equals the number of the first column in the dataframe containing allele information. Order of loci in both populations needs to be exactly equal. |
data |
If set as TRUE allele sharing is only calculated for each pairwise comparison of individuals in the same position in pop1 with this position in pop2 - i.e. the diagonal of a distance matrix. If set as data.frame each pairwise comparison of column 1 with column 2 is calculated - i.e. the lower triangle of a distance matrix. |
value |
Character defining method to calculate allele sharing or similarity estimates. Can be set as "Bxy", "Sxy", "Mxy", "Li", "rxy", "lxy", "loiselle", "wang.fin", "wang", "ritland", "morans.fin" or "morans". |
ref.pop |
Reference population used for relatedness calculations. |
The function uses each population to build a dataframe with row positions for pairwise comparisons according to their position in pop1
and pop2
. Similarity indices are calculated for each pair in one locus defined by the number indicated in allele.column
. If allele.column
is set as 1
allele information will be taken from the two columns of the first locus.
Function returns the object simil.vector as vector of similarities according to value
.
Philipp Kraemer, <philipp.kraemer@uni-oldenburg.de>
inputformat
Demerelate
Emp.calc
Bxy
Sxy
Mxy
Li
rxy
lxy
loiselle
wang.fin
wang
ritland
morans.fin
1 2 3 | ## internal function not intended for direct use
|
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