diversityMultilocus: Calculate diversity across a set of allele tables

In douglasgscofield/dispersalDiversity: Analyse individual and genetic diversity of dispersal processes in biological populations

Description

Calculate diversity for a set of loci encoded in an object of class 'allele_tables' as created with createAlleleTables, and diversity for each locus is calculated separately using diversitySingleLocus.

Usage

## S3 method for class 'allele_divtables'
diversityMultilocus(x, ploidy = 2,
  method = c("r", "q.nielsen", "q"), ...)

Arguments

x	Allele diversity data contained in an object of class allele_divtables
ploidy	Ploidy of underlying genotypes
method	Method to use for calculating diversity statistics. See diversity and Scofield et al. (2012), Sort et al. (in press).

Value

A list of class multilocus_diversity. Elements of the list are calculated from values returned by diversitySingleLocus and include:

• q.gg, matrix of allele.alpha.g values across sites (rows), for each locus (columns)

• alpha.gk, matrix of allele.alpha.g values across sites (rows), for each locus (columns) (are these simply reciprocals of q.gg?)

• q.k, vector of mean q.gg values across loci, the mean values of the rows of q.gg

• alpha.k, vector of mean allele.alpha.g values across loci, the mean values of the rows of alpha.gk

• q.bar.weighted.a, vector of allele.q.bar.weighted for each locus

• alpha.bar.weighted.a, vector of allele.alpha.bar.weighted for each locus ????

• overlap.a, vector of allele.overlap for each locus ????

• divergence.a, vector of allele.divergence for each locus ????

• Q.0.a, vector of allele.Q.0 values for each locus

• q.bar.weighted, mean of q.bar.weighted.a

• alpha.bar.weighted, reciprocal of q.bar.weighted

• Q.0, mean of Q.0.a ????

• gamma, reciprocal of mean of Q.0.a, Q.0 ????

• beta, gamma divided by alpha.bar.weighted

• G, number of loci

• N, allele count for in each locus

• K, number of sites

• alpha.scaled, alpha.bar.weighted scaled to fall in the interval [0, 1]

• gamma.scaled, gamma scaled to fall in the interval [0, 1]

• beta.scaled, beta scaled to fall in the interval [0, 1]

• q.gh, site-by-site matrix of mean of q.gh values across all loci

• overlap, sum of q.gh divided by K - 1 times the sum of q.k

• divergence, 1 - overlap

• overlap.mean, mean of allele.divergence values for each locus (overlap.a ???)

• divergence.mean, mean of allele.overlap values for each locus (divergence.a ???)

These items were left out for no apparent reason or are confusing:

• Q.0

• alpha.bar.weighted.a

• G

• N

• K

• overlap.a

• divergence.a

ans <- list(q.gg = q.gg, alpha.gk = alpha.gk, q.k = q.k, alpha.k = alpha.k, q.bar.weighted.a = q.bar.weighted.a, Q.0.a = Q.0.a, q.bar.weighted = q.bar.weighted, alpha.bar.weighted = alpha.bar.weighted, gamma = gamma, beta = beta, G = G, N = N, K = K, alpha.scaled = alpha.scaled, gamma.scaled = gamma.scaled, beta.scaled = beta.scaled, q.gh = q.gh, overlap = overlap, divergence = divergence, overlap.mean = overlap.mean, divergence.mean = divergence.mean)

References

Scofield, D. G., Smouse, P. E., Karubian, J. and Sork, V. L. (2012) Use of alpha, beta and gamma diversity measures to characterize seed dispersal by animals. American Naturalist 180:719-732.

Sork, V. L., Smouse, P. E., Grivet, D. and Scofield, D. G. (In press) Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata N\'ee). Evolutionary Ecology.

Examples

## Workflow to calculate basic allelic diversity statistics:
library(readGenalex)
data(Qagr_pericarp_genotypes)
gt <- createAlleleTables(Qagr_pericarp_genotypes)
div <- diversityMultilocus(gt)

douglasgscofield/dispersalDiversity documentation built on March 30, 2021, 9:50 a.m.