Package index

Defining population dynamics models

dynamics() update(<dynamics>) is.dynamics()

Create and update population dynamics objects

Simulating population dynamics

simulate(<dynamics>) is.simulation() is.simulation_list()

Simulate single or multispecies population dynamics in R

Summarising population dynamics

pr_extinct()

Calculate (quasi-)extinction risk for a simulate object

emps()

Calculate expected minimum population size (EMPS) for a simulate object

risk_curve()

Calculate (quasi-)extinction risk at multiple thresholds for a simulate object

exps()

Calculate expected population size for a simulate object based on generic functions (ExPS)

get_pdf()

Calculate the probability density of a summary statistic across all iterations of a simulate object

get_cdf()

Calculate the cumulative distribution function of a summary statistic across all iterations of a simulate object

Adding density dependence

density_dependence() density_dependence_n()

Specify density dependence in models of population dynamics

beverton_holt() ricker()

Common forms of density dependence

Altering the population vector

add_remove_pre() add_remove_post()

Specify additions or removals in models of population dynamics

Adding stochasticity

environmental_stochasticity() demographic_stochasticity()

Specify environmental and demographic stochasticity in models of population dynamics

Adding covariates

covariates() format_covariates()

Specify covariate dependence in models of population dynamics

replicated_covariates()

Specify replicate-specific covariate dependence in models of population dynamics

Subsetting population matrices

reproduction() survival() transition() all_cells() all_classes() combine()

Isolate elements of population dynamics models

Updating population abundances

update_crossprod() update_binomial_leslie() update_multinomial()

Functions for a single time-step update

Adding metapopulation structure

metapopulation() is.metapopulation()

Create a metapopulation dynamics object

dispersal()

Specify dispersal between populations in a metapopulation model

Modelling multiple species

multispecies() is.multispecies() is.interaction()

Create a population dynamics object with multiple species

pairwise_interaction()

Specify interactions between two species

Helpers

rmultiunit() rmultiunit_from_real() runit_from_real() runit() unit_to_real()

Random number generators not available in existing R packages