Fis.calc: Calculation of Fis empirical and bootstrapped values

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/Fis.calc.R

Description

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

Usage

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     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, <[email protected]>

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

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

Demerelate documentation built on May 30, 2017, 8:14 a.m.