test.dispRity {dispRity}R Documentation

Testing disparity hypotheses

Description

Applying statistical tests to dispRity objects

Usage

test.dispRity(
  data,
  test,
  comparisons = "pairwise",
  rarefaction = NULL,
  correction = "none",
  concatenate = TRUE,
  conc.quantiles = c(mean, c(95, 50)),
  details = FALSE,
  ...
)

Arguments

data

A dispRity object.

test

A test function to apply to the data.

comparisons

If data contains more than two subsets, the type of comparisons to apply: either "pairwise" (default), "referential", "sequential", "all" or a list of pairs of subset names/number to compare (see details).

rarefaction

A numeric value indicating whether to use a specific rarefaction level (default = NULL).

correction

Which p-value correction to apply to htest category test (see p.adjust; default = "none").

concatenate

Logical, whether to concatenate bootstrapped disparity values (TRUE; default) or to apply the test to each bootstrapped value individually (FALSE).

conc.quantiles

If concatenate = TRUE, must be a central tendency function and a vector of quantiles (default = c(mean, c(95, 50))).

details

Whether to output the details of each test (non-formatted; default = FALSE).

...

Additional options to pass to the test function.

Details

The comparison argument can be:

IMPORTANT: if you are performing multiple comparisons (e.g. when using "pairwise", "referential" or "sequential"), don't forget about the Type I error rate inflation. You might want to use a p-value correction (see p.adjust).

Author(s)

Thomas Guillerme

See Also

dispRity, null.test, bhatt.coeff, pair.plot, adonis.dispRity, randtest.dispRity, test.dispRity

Examples

## Load the Beck & Lee 2014 data
data(BeckLee_mat50)
data(BeckLee_tree)

## Calculating the disparity from customised subsets
## Generating the subsets
groups <- crown.stem(BeckLee_tree, inc.nodes = FALSE)
customised_subsets <- custom.subsets(BeckLee_mat50, groups)
## Bootstrapping the data
bootstrapped_data <- boot.matrix(customised_subsets, bootstraps = 100)
## Calculating the sum of variances
sum_of_variances <- dispRity(bootstrapped_data, metric = c(sum, variances))

## Measuring the subset overlap
test.dispRity(sum_of_variances, bhatt.coeff, "pairwise")

## Measuring differences from a reference subset
test.dispRity(sum_of_variances, wilcox.test, "referential")

## Measuring disparity as a distribution
disparity_var <- dispRity(bootstrapped_data, metric = variances)
## Differences between the concatenated bootstrapped values of the subsets
test.dispRity(disparity_var, test = t.test, comparisons = "pairwise",
     concatenate = TRUE, correction = "bonferroni")
## Differences between the subsets bootstrapped
test.dispRity(disparity_var, test = t.test, comparisons = "pairwise",
     concatenate = FALSE, correction = "bonferroni",
     conc.quantiles = c(mean, c(95, 5)))


[Package dispRity version 1.8 Index]