Package index • mpmsim

Simulation of Lefkovitch MPMs

Functions for simulating Lefkovitch matrix models.

generate_mpm_set(): Generate lists of Lefkovitch matrix population models (MPMs) based on life history archetypes

rand_lefko_mpm(): Generate random Lefkovitch matrix population models (MPMs) based on life history archetypes

rand_lefko_set(): Generate lists of Lefkovitch matrix population models (MPMs) based on life history archetypes

random_mpm(): Generate random Lefkovitch matrix population models (MPMs) based on life history archetypes

Simulation of Leslie MPMs

Functions for simulating Leslie matrix models.

make_leslie_mpm(): Create a Leslie matrix population model

rand_leslie_set(): Generate a set of random Leslie Matrix Population Models

reorganise_matrices(): Reorganise Matrix Population Models

Model demographic trajectories

Functions for modelling demographic trajectories.

model_fecundity() model_fertility() model_reproduction(): Model reproductive output with age using set functional forms

model_survival() model_mortality(): Model mortality hazard, survivorship and age-specific survival probability using a mortality model

Understanding error

Functions for calculating and propagating error.

add_mpm_error(): Add sampling error to matrix population models (MPMs) based on expected values of transition rates and sample sizes

calculate_errors(): Calculate error (standard error or 95%CI) in elements of a matrix population model.

compute_ci(): Compute 95% confidence intervals for derived estimates from a matrix population model

compute_ci_U(): Compute 95% confidence intervals for derived estimates from the U submatrix of a matrix population model

Drivers of dynamics

Functions for simulating drivers of dynamics.

driven_vital_rate(): Calculate driven vital rates

Utilities

Utility functions.

plot_matrix(): Plot a matrix as a heatmap

summarise_mpms(): Summarise Matrix Population Models

All functions

All functions listed alphabetically.

add_mpm_error(): Add sampling error to matrix population models (MPMs) based on expected values of transition rates and sample sizes

calculate_errors(): Calculate error (standard error or 95%CI) in elements of a matrix population model.

compute_ci(): Compute 95% confidence intervals for derived estimates from a matrix population model

compute_ci_U(): Compute 95% confidence intervals for derived estimates from the U submatrix of a matrix population model

driven_vital_rate(): Calculate driven vital rates

generate_mpm_set(): Generate lists of Lefkovitch matrix population models (MPMs) based on life history archetypes

make_leslie_mpm(): Create a Leslie matrix population model

model_fecundity() model_fertility() model_reproduction(): Model reproductive output with age using set functional forms

model_survival() model_mortality(): Model mortality hazard, survivorship and age-specific survival probability using a mortality model

plot_matrix(): Plot a matrix as a heatmap

rand_lefko_mpm(): Generate random Lefkovitch matrix population models (MPMs) based on life history archetypes

rand_lefko_set(): Generate lists of Lefkovitch matrix population models (MPMs) based on life history archetypes

rand_leslie_set(): Generate a set of random Leslie Matrix Population Models

random_mpm(): Generate random Lefkovitch matrix population models (MPMs) based on life history archetypes

reorganise_matrices(): Reorganise Matrix Population Models

summarise_mpms(): Summarise Matrix Population Models