Life history traits

Functions for calculating life history traits.

entropy_d()

Calculate Demetrius' entropy from trajectories of age-specific survivorship and fecundity

entropy_k()

Calculate Keyfitz's entropy from a trajectory of age-specific survivorship

gen_time()

Calculate generation time from a matrix population model

life_expect_mean() life_expect_var() life_expect()

Calculate mean and variance of life expectancy from a matrix population model

longevity()

Calculate longevity from a matrix population model

net_repro_rate()

Calculate net reproductive value (R0) from a matrix population model

mature_prob() mature_age() mature_distrib()

Age of reproductive maturity

shape_rep()

Calculate shape of reproduction over age

shape_surv()

Calculate shape of survival over age

Vital rates

Functions for calculating vital rates.

vital_rates()

Derive mean vital rates from a matrix population model

vr_survival() vr_growth() vr_shrinkage() vr_stasis() vr_dorm_enter() vr_dorm_exit() vr_fecundity()

Derive mean vital rates from a matrix population model

vr_mat_U() vr_mat_R()

Derive survival-independent vital rates for growth, stasis, shrinkage, and reproduction

vr_vec_survival() vr_vec_growth() vr_vec_shrinkage() vr_vec_stasis() vr_vec_dorm_enter() vr_vec_dorm_exit() vr_vec_reproduction()

Derive stage-specific vital rates from a matrix population model

Life tables

Functions for calculating life tables.

mpm_to_mx() mpm_to_lx() mpm_to_px() mpm_to_hx()

Calculate age-specific traits from a matrix population model

lx_to_px() lx_to_hx() px_to_lx() px_to_hx() hx_to_lx() hx_to_px()

Convert between age-specific survivorship, survival, or mortality hazard

mpm_to_table()

Generate a life table from a matrix population model

qsd_converge()

Calculate time to reach quasi-stationary stage distribution

Perturbation analysis

Functions for perturbation analysis.

perturb_matrix()

Perturbation analysis of a matrix population model

perturb_stochastic()

Calculate stochastic elasticities from a time-series of matrix population models and corresponding population vectors

perturb_trans()

Perturbation analysis of transition types within a matrix population model

perturb_vr()

Perturbation analysis of vital rates in a matrix population model

pop_vectors()

Derive a hypothetical set of population vectors corresponding to a time-series of matrix population models

MPM transformation

Functions for transforming matrices.

mpm_collapse()

Collapse a matrix population model to a smaller number of stages

mpm_rearrange()

Rearrange stages of a matrix population model to segregate reproductive and non-reproductive stages

mpm_split()

Convert matrix population model into U, F and C matrices

mpm_standardize() mpm_standardise()

Transform a matrix population model to a standardized form

name_stages()

Add stage names to matrices

repro_stages()

Identify which stages in a matrix population model are reproductive

standard_stages()

Identify stages corresponding to different parts of the reproductive life cycle

Visualisation

Functions for visualising matrices.

plot_life_cycle()

Plot a life cycle diagram from a matrix population model

All functions

All functions listed alphabetically.

mpm_to_mx() mpm_to_lx() mpm_to_px() mpm_to_hx()

Calculate age-specific traits from a matrix population model

entropy_d()

Calculate Demetrius' entropy from trajectories of age-specific survivorship and fecundity

entropy_k()

Calculate Keyfitz's entropy from a trajectory of age-specific survivorship

gen_time()

Calculate generation time from a matrix population model

life_expect_mean() life_expect_var() life_expect()

Calculate mean and variance of life expectancy from a matrix population model

lx_to_px() lx_to_hx() px_to_lx() px_to_hx() hx_to_lx() hx_to_px()

Convert between age-specific survivorship, survival, or mortality hazard

longevity()

Calculate longevity from a matrix population model

mpm1

Example matrix population model (MPM)

mpm_collapse()

Collapse a matrix population model to a smaller number of stages

mpm_rearrange()

Rearrange stages of a matrix population model to segregate reproductive and non-reproductive stages

mpm_split()

Convert matrix population model into U, F and C matrices

mpm_standardize() mpm_standardise()

Transform a matrix population model to a standardized form

mpm_to_table()

Generate a life table from a matrix population model

name_stages()

Add stage names to matrices

net_repro_rate()

Calculate net reproductive value (R0) from a matrix population model

perturb_matrix()

Perturbation analysis of a matrix population model

perturb_stochastic()

Calculate stochastic elasticities from a time-series of matrix population models and corresponding population vectors

perturb_trans()

Perturbation analysis of transition types within a matrix population model

perturb_vr()

Perturbation analysis of vital rates in a matrix population model

plot_life_cycle()

Plot a life cycle diagram from a matrix population model

pop_vectors()

Derive a hypothetical set of population vectors corresponding to a time-series of matrix population models

qsd_converge()

Calculate time to reach quasi-stationary stage distribution

mature_prob() mature_age() mature_distrib()

Age of reproductive maturity

repro_stages()

Identify which stages in a matrix population model are reproductive

shape_rep()

Calculate shape of reproduction over age

shape_surv()

Calculate shape of survival over age

standard_stages()

Identify stages corresponding to different parts of the reproductive life cycle

vital_rates()

Derive mean vital rates from a matrix population model

vr_survival() vr_growth() vr_shrinkage() vr_stasis() vr_dorm_enter() vr_dorm_exit() vr_fecundity()

Derive mean vital rates from a matrix population model

vr_mat_U() vr_mat_R()

Derive survival-independent vital rates for growth, stasis, shrinkage, and reproduction

vr_vec_survival() vr_vec_growth() vr_vec_shrinkage() vr_vec_stasis() vr_vec_dorm_enter() vr_vec_dorm_exit() vr_vec_reproduction()

Derive stage-specific vital rates from a matrix population model