indexsort

Sorts outputs of particle filter based on index - returns a sorted list of particles, based on the
sampling trajectory through time. This is a somewhat more accurate estiamte of the true posterior than
are the stepwise samples provided by the filter.

filter

particle

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

indexsort function

<dl><dt>fulltracemat</dt>
<dd>full output of particles from the particleFilterLL function</dd>
<dt>fulltraceindex</dt>
<dd>full output of particle indices from the particleFilterLL function</dd>
<dt>nsmp</dt>
<dd>number of particle paths to sample - defaults to NULL, which samples all paths</dd></dl>

Arguments

Sort output of particle filter — indexsort

<dl>

<dt>fulltracemat</dt>
<dd>full output of particles from the particleFilterLL function</dd>


<dt>fulltraceindex</dt>
<dd>full output of particle indices from the particleFilterLL function</dd>


<dt>nsmp</dt>
<dd>number of particle paths to sample - defaults to NULL, which samples all paths</dd>

</dl>

indexsort: Sort output of particle filter

Description

Usage

Value

Arguments