Usage
stat.pops(Thresholds, tab.pop.pop, pairs, p.correct, directory.name, out.name, file.output, inputdata, object, value, iteration, pm, genotype.ref)
Arguments
Thresholds
Thresholds of relatedness to be used for statistics on empirical data.
tab.pop.pop
Dataframe following format of inputformat only column three and four are used for calculations. pairs
Number of randomized pairings used for reference populations.
p.correct
logical - should Yates correcture be used for $\chi^2$ statistics.
directory.name
Name of the directory results send to.
out.name
Filename of the output.
file.output
logical. Should a cluster dendogram, histograms and .txt files be sent as standard output in your working directory. In some cases (inflating NA values) it may be necessary that this value has to be set as FALSE due to problems in calculating clusters on pairwise NA values.
inputdata
R object or external file to be read internally with standard Demerelate inputformat. Dataframe will be split by population information and calculations will run separately. If no reference population information is specified (ref.pop = "NA") all information on loci are used as reference by omitting population information. object
Information whether inputdata are an object or should be read in as file.
value
String defining method to calculate allele sharing or similarity estimates.
iteration
Number of bootstrap iterations in $F_{is}$ calculations.
pm
R object or external file to be read internally. Custom reference populations will be loaded for the analysis. The object should be a list of allele frequencies. For each locus a vector with allele frequencies p and allele names as vector names needs to be combined to a list. The last list object is a vector of sample sizes for each locus.
genotype.ref
logical. If set as TRUE random non related populations are generated from genotypes of the reference population. If set as false allele frequencies are used for reference population generation.