R: Life History Metrics from Matrix Population Models

# Life History Metrics from Matrix Population Models

## Documentation for package ‘Rage’ version 1.9.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

age_from_stage | 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
evenness_shannon | Shannon Evenness (Pielou's J)
gen_time | Calculate generation time from a matrix population model
hx_to_lx | Convert between age-specific survivorship, survival, or mortality hazard
hx_to_px | Convert between age-specific survivorship, survival, or mortality hazard
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)
lifetable_convert | Convert between age-specific survivorship, survival, or mortality hazard
life_elas | Calculate Keyfitz's entropy from a trajectory of age-specific survivorship
life_expect_mean | Calculate mean and variance of life expectancy from a matrix population model
life_expect_var | Calculate mean and variance of life expectancy from a matrix population model
longevity | Calculate longevity from a matrix population model
lx_to_hx | Convert between age-specific survivorship, survival, or mortality hazard
lx_to_px | Convert between age-specific survivorship, survival, or mortality hazard
mature_age | Age of reproductive maturity
mature_distrib | Age of reproductive maturity
mature_prob | Age of reproductive maturity
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_standardise | Transform a matrix population model to a standardized form
mpm_standardize | Transform a matrix population model to a standardized form
mpm_to_hx | Calculate age-specific traits from a matrix population model
mpm_to_lx | Calculate age-specific traits from a matrix population model
mpm_to_mx | Calculate age-specific traits from a matrix population model
mpm_to_px | Calculate age-specific traits from a matrix population model
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
px_to_hx | Convert between age-specific survivorship, survival, or mortality hazard
px_to_lx | Convert between age-specific survivorship, survival, or mortality hazard
qsd_converge | Calculate time to reach quasi-stationary stage distribution
repro_maturity | Age of reproductive maturity
repro_stages | Identify which stages in a matrix population model are reproductive
scale_mpm_to_lambda1 | Scale a matrix population model so that lambda equals 1
shape_rep | Calculate shape of reproduction over age
shape_surv | Calculate shape of survival over age
stage_at_death_dist | Compute distribution of stage at death from a stage-structured MPM
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 | Derive mean vital rates from a matrix population model
vr_dorm_enter | Derive mean vital rates from a matrix population model
vr_dorm_exit | Derive mean vital rates from a matrix population model
vr_fecundity | Derive mean vital rates from a matrix population model
vr_growth | Derive mean vital rates from a matrix population model
vr_mat | Derive survival-independent vital rates for growth, stasis, shrinkage, and reproduction
vr_mat_R | Derive survival-independent vital rates for growth, stasis, shrinkage, and reproduction
vr_mat_U | Derive survival-independent vital rates for growth, stasis, shrinkage, and reproduction
vr_shrinkage | Derive mean vital rates from a matrix population model
vr_stasis | Derive mean vital rates from a matrix population model
vr_survival | Derive mean vital rates from a matrix population model
vr_vec | Derive stage-specific vital rates from a matrix population model
vr_vec_dorm_enter | Derive stage-specific vital rates from a matrix population model
vr_vec_dorm_exit | Derive stage-specific vital rates from a matrix population model
vr_vec_growth | Derive stage-specific vital rates from a matrix population model
vr_vec_reproduction | Derive stage-specific vital rates from a matrix population model
vr_vec_shrinkage | Derive stage-specific vital rates from a matrix population model
vr_vec_stasis | Derive stage-specific vital rates from a matrix population model
vr_vec_survival | Derive stage-specific vital rates from a matrix population model