divBasic: A function to calculate basic population parameters such as...

In kkeenan02/diveRsity-dev: Genetic diversity partition statistics and Informative locus selection using Fst, Gst, Dest(Jost Chao) G'st and In.

Description

divBasic allows the calculation of locus and overall basic population parameters. divBasic will write results to a .xlsx workbook. The function accepts co-dominant genetic data in both 2 and 3 digit genepop formats.

Usage

divBasic(infile = NULL, outfile = NULL, gp = 3)

Arguments

infile	Specifying the name of the ‘genepop’(Rousset, 2008) file from which the statistics are to be calculated. This file can be in either the 3 digit of 2 digit format, and must contain only one whitespace separator (e.g. “space” or “tab”) between each column including the individual names column. The number of columns must be equal to the number of loci + 1 (the individual names column). If this file is not in the working directory the file path must be given. The name must be a character string (i.e. enclosed in “” or '').
outfile	Allows users to specify a prefix for an output folder. Name must a character string enclosed in either “” or ''.
gp	Specifies the digit format of the infile. Either 3 (default) or 2.

Details

All results will be written to a user defined folder ("working_directory/outfile"), providing an argument is passed for 'outfile'. Results will be written to .xlsx files, and multiple R objects are also written to the current environment.

HWE tests are carried out as standard. These tests are known to be unreliable where classes are observed less that five times. This is often the case when using highly polymorphic loci. Caution is encouraged.

Value

locus_pop_size	A matrix containing the number of indivuduals typed per locus per population sample. Mean values across loci are also given.
Allele_number	A matrix containing the number of alleles observed per locus per population sample. Mean values across loci are also given.
proportion_Alleles	A matrix containing the percentage of total alleles observed per locus per population sample. Mean values across loci are also given.
Allelic_richness	A matrix containing the allelic richness per locus per population sample. Allelic richness is calculated using 1000 resamples (n = smallest sample in the input data file), with replacement per population sample locus per population sample. Mean values across loci are also given.
Ho	A matrix containing observed heterozygosity per locus per population sample. Mean values across loci are also given.
He	A matrix containing expected heterozygosity per locus per population sample. Mean values across loci are also given.
HWE	A matrix containing uncorrected p-values from chi-square test for goodness-of-fit to Hardy-Weinberg equilibrium. Overall p-values are also given per population sample.

Author(s)

Kevin Keenan <[e-mail]>

References

Rousset, F., “genepop'007: a complete re-implementation of the genepop software for Windows and Linux.,” Molecular ecology resources, vol. 8, no. 1, pp. 103-6, (2008).

Examples

# To run an example use the following format
#
# test_results <- divBasic(infile = Test_data, outfile = 'out', gp = 3)

kkeenan02/diveRsity-dev documentation built on May 20, 2019, 10:46 a.m.