calc_dissim

internal

Standardises and facilitates the use of eleven established stability properties that have been used to assess systems’ responses to press or pulse disturbances at different ecological levels (e.g. population, community). There are two sets of functions. The first set corresponds to functions that measure stability at any level of organisation, from individual to community and can be applied to a time series of a system’s state variables (e.g., body mass, population abundance, or species diversity). The properties included in this set are: invariability, resistance, extent and rate of recovery, persistence, and overall ecological vulnerability. The second set of functions can be applied to Jacobian matrices. The functions in this set measure the stability of a community at short and long time scales. In the short term, the community’s response is measured by maximal amplification, reactivity and initial resilience (i.e. initial rate of return to equilibrium). In the long term, stability can be measured as asymptotic resilience and intrinsic stochastic invariability. Figueiredo et al. (2025) <doi:10.32942/X2M053>.

Ludmilla Figueiredo

estar

Ecological Stability Metrics

Viktoriia Radchuk

Cédric Scherer

calc_dissim function

<dl><dt>df</dt>
<dd>dataframe with "temporal community data": species abundances of the
baseline and disturbed communities over time.</dd>
<dt>comm_t</dt>
<dd>the name of the time variable in comm_b and comm_d.</dd>
<dt>method</dt>
<dd>a string identifying the dissimilarity index to be used to
calculate dissimilarity. For more options, see <code>?vegdist</code>.
Defaults to "bray".</dd>
<dt>binary</dt>
<dd>a boolean stating whether presence/absence standardization
should be performed before calculating the dissimilarity. For more options,
see <code>?vegdist</code>. Defaults to "bray".</dd></dl>

Arguments

Calculate dissimilarity — calc_dissim

<dl>

<dt>df</dt>
<dd>dataframe with "temporal community data": species abundances of the
baseline and disturbed communities over time.</dd>


<dt>comm_t</dt>
<dd>the name of the time variable in comm_b and comm_d.</dd>


<dt>method</dt>
<dd>a string identifying the dissimilarity index to be used to
calculate dissimilarity. For more options, see <code>?vegdist</code>.
Defaults to "bray".</dd>


<dt>binary</dt>
<dd>a boolean stating whether presence/absence standardization
should be performed before calculating the dissimilarity. For more options,
see <code>?vegdist</code>. Defaults to "bray".</dd>

</dl>

calc_dissim: Calculate dissimilarity

Description

Usage

Arguments