partitionR {comstab}

Partitioning of the temporal CV of ecological communities

Description

PartitionR() is a function used to partition the temporal coefficient of variation of a community into the variability of the average species and three stabilizing effects: the dominance, asynchrony and averaging effects (see Details).

Usage

partitionR(z, ny = 1)

Arguments

z

A matrix containing repeated measurements of species abundances. The matrix must contain numerical values only, with years in rows and species in columns. Remove any extra column.

ny

Only species appearing more than ny years (integer, defaults to 1) are used in the calculations.

Details

The analytic framework is described in details in Segrestin et al. (2024). In short, the partitioning relies on the following equation:

CV_{com} = CV_e \Delta \Psi \omega

where CV_{com} is the community coefficient of variation (reciprocal of community stability), CV_e is the expected community CV when controlling for the dominance structure and species temporal synchrony, \Delta is the dominance effect, \Psi is the asynchrony effect, and \omega is the averaging effect.

Value

Returns an object of class 'comstab'.

An object of class 'comstab' is a list containing the following components:

• 'CVs' a named vector of calculated coefficient of variations. CVe is the CV of an average species, CVtilde is the mean of species CVs weighted by their relative abundances, CVa is the expected community CV if the community was stabilized by species asynchrony only, and CVc is the observed community CV.

• 'Stabilization' a named vector of the stabilizing effects. tau is the total stabilization, Delta is the dominance effect, Psi is the asynchrony effect, and omega is the averaging effect.

• 'Relative' a named vector of the relative contributions of each stabilizing effect to the total stabilization. Delta_cont, Psi_cont, and omega_cont are the relative contribution of respectively, the dominance, asynchrony, and averaging effects to the total stabilization. Returns a vector of NAs if any Stabilizing effect is higher than 1.

Author(s)

Jules Segrestin, [e-mail]

References

Segrestin et al. (2024) A unified framework for partitioning the drivers of stability of ecological communities. Global Ecology and Biogeography, 33(5), e13828. https://doi.org/10.1111/geb.13828

Examples

require(stats)

# Simulates a custom community time series using 'comTS()':
z <- comTS(nsp = 10, ny = 30, even = 0.6, mvs = 1.5, sync = "0")

# Runs the partitioning of the community coefficient of variation:
partitionR(z)