Fis.calc: Calculation of Fis empirical and bootstrapped values

In Demerelate: Functions to Calculate Relatedness on Diploid Genetic Data

Description

Internal function of Demerelate and F.stat to calculate F_{is} values from empirical datasets. Performing randomization statistics and preparing output.

Usage

     Fis.calc(tab.pop, iteration, number.loci, object, 
              directory.name, out.name)
     

Arguments

tab.pop	Data.frame following format of inputformat only column three and four are used for calculations.
iteration	Number of replicates for bootstrap statistics.
number.loci	Number of loci in tab.pop.
object	Whether tab.pop is an object or file.
directory.name	Name of the directory results should be send to.
out.name	Filename of the output.

Value

Function returns a list containing the following information:

output.fis[[1]]	Empirical F_{is} values according to Nei 1983.
output.fis[[2]]	Empirical F_{is} values according to Weir and Cockerham 1984.
output.fis[[3]]	p values for significance for F_{is} values according to Nei 1983.
output.fis[[4]]	p values for significance for F_{is} values according to Weir and Cockerham 1984.

Additionally, a file will be generated containing all these information if file.output is set as TRUE or alternatively when directory.name and out.name are given.

SummaryPopulationout.name.txt

Combined output with different F_{is} metrices and allele\genotype frequencies

Author(s)

Philipp Kraemer, <[e-mail]>

References

Weir, B.S. and Cockerham, C.C. (1984) Estimating F-Statistics for the analysis of population structure. Evolution, 38, 1358-1370.
Nei, M. (1977) F-statistics and analysis of gene diversity in subdivided populations. Annals of Human Genetics, 41, 225-233.
Nei, M. and Chesser R.K. (1983) Estimation of fixation indices and gene diversities. Annals of Human Genetics, 47, 253-259.

See Also

weir F.stat Fis

Examples

     ## internal function of F.stat not intended for direct usage
     
     

Demerelate documentation built on May 2, 2019, 4:01 p.m.