alphaDiversityTest: Test for differences in alpha diversity among sites within a...

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

Description

The null hypothesis for this tests is that there is no difference in alpha diversity between the sites represented in tab or adt. The initial (class divtable) version of this was described in Scofield et al. (2012), while the allelic (class link{allele_divtables} extension was described in Sort et al. (In press).

Usage

## S3 method for class 'divtable'
alphaDiversityTest(tab, zero.div.adjust = TRUE,
  n.resample = 10000, method = c("bootstrap", "permute"),
  test.quantiles = c(0.001, 0.01, 0.05, 0.1, 0.5, 0.9, 0.95, 0.99, 0.999),
  ...)

## Default S3 method:
alphaDiversityTest(tab, ...)

## S3 method for class 'allele_divtables'
alphaDiversityTest(adt, zero.div.adjust = TRUE,
  n.resample = 10000, method = c("bootstrap", "permute"),
  test.quantiles = c(0.001, 0.01, 0.05, 0.1, 0.5, 0.9, 0.95, 0.99, 0.999),
  ...)

Arguments

tab	Site-by-source table of class divtable
zero.div.adjust	Logical, if TRUE (the default), then groups with 0 within-group diversity are assigned a minimum diversity which is half the empirical diversity possible given the group size
n.resample	Number of iterations for creation of the null distribution
method	"bootstrap" or "permute", whether to create null distribution iterations with ("bootstrap") or without ("permute") replacement
adt	Allele diversity dataset of class allele_divtables
...	Additional parameters

Value

An diversity_test object with the result of the test

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.

See Also

alphaContrastTest, alphaContrastTest3, print.diversity_test

Examples

## Add example with class divtable
##
## Using allele diversity dataset of class allele_divtables.  Compare
## allele diversity between sites in the same sample:
##
## library(readGenalex)  # already loaded as a prerequisite
data(Qagr_pericarp_genotypes)  # from readGenalex
gt <- createAlleleTables(Qagr_pericarp_genotypes)
alpha.test <- alphaDiversityTest(gt)

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