boot.vc | R Documentation |
Provides a bootstrap confidence interval (over loci) for sums of the different variance components (equivalent to gene diversity estimates at the different levels), and the derived F-statistics, as suggested by Weir and Cockerham (1984). Will not run with less than 5 loci. Raymond and Rousset (199X) points out shortcomings of this method.
boot.vc(levels=levels,loci=loci,diploid=TRUE,nboot=1000,quant=c(0.025,0.5,0.975))
levels |
a data frame containing the different levels (factors) from the outermost (e.g. region) to the innermost before the individual |
loci |
a data frame containing the different loci |
diploid |
Specify whether the data are coming from diploid or haploid organisms (diploid is the default) |
nboot |
Specify the number of bootstrap to carry out. Default is 1000 |
quant |
Specify which quantile to produce. Default is c(0.025,0.5,0.975) giving the percentile 95% CI and the median |
boot |
a data frame with the bootstrapped variance components. Could be used for obtaining bootstrap ci of statistics not listed here. |
res |
a data frame with the bootstrap derived statistics. H stands for gene diversity, F for F-statistics |
ci |
Confidence interval for each statistic. |
Raymond M and Rousset F, 1995. An exact test for population differentiation. Evolution. 49:1280-1283
Weir, B.S. (1996) Genetic Data Analysis II. Sinauer Associates.
Weir BS and Cockerham CC, 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
varcomp.glob
.
#load data set data(gtrunchier) boot.vc(gtrunchier[,c(1:2)],gtrunchier[,-c(1:2)],nboot=100)
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