colfun0

Simulates colonization events - events occur as a binomial random process with probability ilogit(p), and populations are seeded with abundance exp(A).

colonization

Includes a collection of functions presented in "Measuring stability in ecological systems without static equilibria" by Clark et al. (2022) <doi:10.1002/ecs2.4328> in Ecosphere.
These can be used to estimate the parameters of a stochastic state space model (i.e. a model where
a time series is observed with error). The goal of this package is to estimate the variability
around a deterministic process, both in terms of observation error - i.e. variability due to
imperfect observations that does not influence system state - and in terms of process noise - i.e.
stochastic variation in the actual state of the process. Unlike classical methods for estimating
variability, this package does not necessarily assume that the deterministic state is fixed (i.e.
a fixed-point equilibrium), meaning that variability around a dynamic trajectory can be estimated
(e.g. stochastic fluctuations during predator-prey dynamics).

Adam Clark

pttstability

Particle-Takens Stability

colfun0 function

<dl><dt>co</dt>
<dd>a numeric vector of length two (p, A), specifying the logit-transformed colonization probability when abundance is zero, and the log-transformed abundance observed immediately after a colonization event</dd>
<dt>xt</dt>
<dd>a number or numeric vector of abundances at time t, before colonization has occurred</dd></dl>

Arguments

default colonization function — colfun0

<dl>

<dt>co</dt>
<dd>a numeric vector of length two (p, A), specifying the logit-transformed colonization probability when abundance is zero, and the log-transformed abundance observed immediately after a colonization event</dd>


<dt>xt</dt>
<dd>a number or numeric vector of abundances at time t, before colonization has occurred</dd>

</dl>

colfun0: default colonization function

Description

Usage

Value

Arguments