Description Usage Arguments Details Value Author(s) References Examples
Diversity ratios derived from allelic richness and expected heterozygosity are calculated from either a genepop file containing raw data for all populations of interest, or from a genepop file containing raw data for only the reference population and a data frame containing relevant information for the populations of interest. See below for more details the structure of this data frame.
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infile |
A character string argument specifying the name of either a 3 digit or 2 digit genepop file containing the raw genotypes of at least the reference population sample. |
outfile |
A character string specifying a prefix name for an automatically generated results folder, to which results file will be written. |
gp |
Specifies the digit format of the |
pop_stats |
A character string indicating the name of the population statistics data frame file. This argument is required if only raw data for the reference population are give in |
refPos |
A numeric argument specifying the position of the reference population in |
boots |
Specifies the number of times the reference population should be resampled when calculating the sample size standardised allelic richness and expected heterozygosity for calculating the diversity ratios. The larger the number of bootstraps the longer the analysis will take to run. As an indication of runtime, running |
para |
A logical argument indicating whether the analysis should make use of all available cores on the users system. |
All results will be written to a user defined folder, providing an argument is passed for 'outfile'. Results will be written to .xlsx
files if the package xlsx
and its dependencies are installed, or a .txt
file otherwise.
A data frame containing the following columns:
pop |
The names of each population of interest, including the reference population |
n |
The sample size of each population |
alr |
Mean allelic richness across loci |
alrSE |
The standard error of the allelic richness across loci |
He |
Mean expected heterozygosity across loci |
HeSE |
Standard error of expected heterozygosity across loci |
alrRatio |
The ratio of the allelic richness of the subject population sample and the sample size standardised reference population allelic richness |
alrSEratio |
The standard error of divisions for the allelic richness ratio |
heRatio |
The ratio of expected heterozygosity between the standardised reference population sample and subject population samples |
heSEratio |
The standard error of divisions for the expected heterozygosity ratio |
Kevin Keenan <kkeenan02@qub.ac.uk>
Skrbinsek, T., Jelencic, M., Waits, L. P., Potocnik, H., Kos, I., & Trontelj, P. (2012). Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear. Heredity, 109(5), 299-305. doi:10.1038/hdy.2012.42
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