Function reference • Rage

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
`entropy_k_age()`	Calculate Keyfitz entropy for an age-based matrix population model
`entropy_k_stage()`	Calculate Keyfitz entropy for a stage-based matrix population model
`gen_time()`	Calculate generation time from a matrix population model
`life_elas()`	Calculate Keyfitz's entropy from a trajectory of age-specific survivorship
`life_expect_mean()` `life_expect_var()`	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 rate (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.
`is_leslie_matrix()`	Determine if a matrix is a Leslie matrix population model
`leslie_collapse()`	Aggregate a Leslie matrix
`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
`entropy_k_age()`	Calculate Keyfitz entropy for an age-based matrix population model
`entropy_k_stage()`	Calculate Keyfitz entropy for a stage-based matrix population model
`gen_time()`	Calculate generation time from a matrix population model
`is_leslie_matrix()`	Determine if a matrix is a Leslie matrix population model
`leslie_collapse()`	Aggregate a Leslie matrix
`leslie_mpm1`	Example Leslie matrix population model (MPM)
`life_elas()`	Calculate Keyfitz's entropy from a trajectory of age-specific survivorship
`life_expect_mean()` `life_expect_var()`	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 rate (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

Reference

Life history traits

Vital rates

Life tables

Perturbation analysis

MPM transformation

Visualisation

All functions