replicates
Number of replicate simulation runs.
time_steps
Number of simulation time steps.
populations
Number of populations.
stages
Number of life cycle stages.
compartments
Number of disease compartments (e.g., 3 for a
SIR model).
abundance_threshold
A quasi-extinction threshold at
which a population becomes extinct.
mortality
A vector of mortality rates, one for each
combination of stages and compartments.
mortality_unit
A vector indicating whether mortality rates
are daily or seasonal. 1 indicates seasonal, 0 indicates daily.
fecundity
A vector of fecundity rates, one for each
combination of stages and compartments for which fecundity applies.
fecundity_unit
A vector indicating whether fecundity rates
are daily or seasonal. 1 indicates seasonal, 0 indicates daily.
fecundity_mask
A vector indicating which stages and
compartments reproduce.
transmission
A vector of transmission rates, one for each
combination of stages and compartment for which transmission applies (see
transmission_mask
below.
transmission_unit
A vector indicating whether mortality
rates are daily or seasonal. 1 indicates seasonal, 0 indicates daily.
transmission_mask
A vector indicating which stages and
compartments are subject to transmission (i.e., classes susceptible to
infection.)
recovery
A vector of recovery rates, one for each
combination of stages and compartment for which recovery applies (see
recovery_mask
below.)
recovery_unit
A vector indicating whether mortality rates
are daily or seasonal. 1 indicates seasonal, 0 indicates daily.
recovery_mask
A vector indicating which compartments are
subject to recovery (i.e., infected classes that can recover.)
r
Simulation replicate.
tm
Simulation time step.
carrying_capacity
Array of carrying capacity values for
each population at time step.
breeding_season_length
Array of breeding season lengths in
days for each population at time step.
segment_abundance
Matrix of (current) abundance for each
stage-compartment combo (rows) and population (columns) at time step.
occupied_indices
Array of indices for populations occupied
at (current) time step.
simulator
poems::SimulatorReference
object with
dynamically accessible attached and results lists.
additional attributes
Additional attributes when the
transformation is optionally nested in a list.