dispRity.through.time: Disparity through time.

In TGuillerme/dispRity: Measuring Disparity

Disparity through time.

Description

Performs a disparity through time analysis.

Usage

dispRity.through.time(data, tree, time, metric = c(median, centroids), ...)

Arguments

data	An ordinated matrix.
tree	A phylo object.
time	A numeric value for the number of subsets to create.
metric	A vector containing one to three functions (default = c(median, centroids)) (see dispRity for details).
...	Optional arguments to be passed to chrono.subsets, boot.matrix and dispRity.

Details

By default the time subsets use method = "discrete", the matrix is bootstrapped 100 times.

Note that this is a wrapper function that allows users to run a basic disparity-through-time analysis without too much effort. As such it has a lot of defaults described in the functions that make up the analysis. See chrono.subsets, boot.matrix, dispRity.metric, summary.dispRity, plot.dispRity for more details of the defaults used in each of these functions. Note that any of these defaults can be changed within the disparity.through.time function.

Value

A dispRity object that can be passed to summary or plot.

Author(s)

Thomas Guillerme

See Also

chrono.subsets, boot.matrix, dispRity.metric, summary.dispRity, plot.dispRity.

Examples

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

## Run a simple disparity through time analysis (with three time bins)
result <- dispRity.through.time(BeckLee_mat50, BeckLee_tree, 3)
summary(result) ; plot(result)

## This is equivalent to run the following decomposed code
dispRity(boot.matrix(chrono.subsets(BeckLee_mat50, BeckLee_tree, time = 3, method = "discrete"),
                     bootstraps = 100),
         metric = c(median, centroids))

TGuillerme/dispRity documentation built on Dec. 21, 2024, 4:05 a.m.