Nothing
allelefreq <- function(tab){
#Variables
#------------------------------------------------------------------------------------------------------------------------------
# Input:
# tab <- Dest.Chao(), all.pops.Dest(), all.pops.Gst();
# Output:
# sample.sizes, allelefrequency, List -> Workspace;
#------------------------------------------------------------------------------------------------------------------------------
# A function that calculates the allelefrequencies and sample sizes per
# locus from a table of the following format:
# individual population fragment.length locus
# 1 B1.1 Borkum 323 L12
# 2 B1.1 Borkum 266 L12
# 3 B1.2 Borkum 325 L12
# 4 B1.2 Borkum 274 L12
# 5 B1.3 Borkum 266 L12
# 6 B1.3 Borkum 323 L12
# 7 B1.4 Borkum 325 L12
# The column names must be equal to those in this example.
# Certain tables of another format can be converted to this format
# by the function 'inputformat()' that is included in this package.
y <- tab
# the argument, a table, is assigned to the object 'y'.
y2 <- split(y,y$locus)
# The data are splitted according to the loci that have been
# examined.
sample.sizes1 <- lapply(y2,sample.size.calc)
sample.sizes <- do.call(rbind,sample.sizes1)
colnames(sample.sizes)=c("population","sample.size","locus")
allelefrequency1 <- lapply(y2,allelefreq.calcs)
allelefrequency <- do.call(rbind,allelefrequency1)
colnames(allelefrequency)= c("allele","number","population","locus","proportion")
rownames(allelefrequency)=seq(1:length(allelefrequency[,1]))
List<-list(allelefrequency,sample.sizes)
names(List)=c("Table","Sample sizes")
invisible(List)
# The matrix 'allelefrequency' is combined with the matrix 'sample.sizes'
# in a list.
assign("sample.sizes",sample.sizes,pos = DEMEtics.env)
assign("allelefrequency",allelefrequency,pos = DEMEtics.env)
assign("List",List,pos = DEMEtics.env)
# The objects 'sample.sizes' and 'allelefrequency'are ascribed to the
# workspace in order to be available for further calculations.
}
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