Nothing
Gst.Nei <- function(filename, bias="correct", object=FALSE, format.table=TRUE, pm="pairwise",statistics="CI",bt=1000){
# pm = pairwise/overall
# statistics = p,CI,none (for "all" warn, that it will take long)
# bt = 1000 (number of bootstrapping steps)
filename <- filename
if (bias=="correct"){x="Gst.est"
}else{x="Gst"}
if (object==TRUE){
tab <- get(filename)
# The data table can be either an object in the R Workspace (a data table
# that is already loaded in the Workspace)...
}else{
tab <- read.table(filename, header=TRUE, sep="")}
# Or a data table that is saved in a .txt-file and that has to be
# assigned to the workspace.
if (format.table==TRUE){
inputformat(filename,object)
tab <- read.table("Output-Inputformat.txt", header=TRUE, sep="")
}
# If the argument 'format.table is set as true, the format of the
# table is changed in that format, that is needed for further
# calculations.
# This function will calculate the D values for every locus and
# the mean D value over all loci for all the populations that
# have been sampled.
# The table 'tab' has to be 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.
allelefreq(tab)
# From the table that contains the empirical data, the allelefrequencies
# as well as the sample.sizes are calculated for each locus.
# The table that contains the allelefrequencies and the table that
# lists the sample sizes are assigned to the R workspace in the
# object List, but also separately in the object allelefrequency
# and the object sample.sizes.
actual.date <- as.Date(Sys.time())
filename.for.sample.sizes <- paste("sample.sizes.",actual.date,sep="")
filename.for.sample.sizes <- paste(filename.for.sample.sizes,".txt",sep="")
filename.for.sample.sizes <- paste(filename,".",filename.for.sample.sizes,sep="")
# The filename under which the table that contains the sample sizes
# for the several loci, is created. It will encompass the actual
# date at the end.
filename.for.allelefrequencies <- paste("allelefreq.",actual.date,sep="")
filename.for.allelefrequencies <- paste(filename.for.allelefrequencies,".txt",sep="")
filename.for.allelefrequencies <- paste(filename,".",filename.for.allelefrequencies,sep="")
# The filename under which the table that contains the allelefrequencies
# for the several loci, is created. It will encompass the actual
# date at the end.
write.table(as.data.frame(as.matrix(DEMEtics.env$List[[1]])),file=filename.for.allelefrequencies, append = TRUE, quote = FALSE, sep = " ", na = "NA", dec = ".", row.names = FALSE, col.names = TRUE)
write.table(as.data.frame(as.matrix(DEMEtics.env$List[[2]])),file=filename.for.sample.sizes, append = TRUE, quote = FALSE, sep = " ", na = "NA", dec = ".", row.names = FALSE, col.names = TRUE)
# The tables are saved in the working directory. Two or more analysis
# that are carried under the same working directory, are saved in the
# under the same file name. The data are combined in the order as they
# have been analysed. No data is lost due to be overwritten.
cat("\n","====================================================================================================","\n",sep="")
cat("====================================================================================================","\n")
cat("======================================== Start of Analysis =========================================","\n")
cat("====================================================================================================","\n")
cat("====================================================================================================","\n")
cat("\n","Table with allelefrequencies is saved in ","'",filename.for.allelefrequencies,"'","\n",sep="")
cat("\n","Per locus calculated sample sizes are saved in ","'",filename.for.sample.sizes,"'","\n",sep="")
H.out(tab,data.name=FALSE,filename)
if (pm=="pairwise"){pair.pops(tab,statistics,bt,x,filename)
}else {over.all.pops(tab,statistics,bt,x,filename)}
}
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