Life History Metrics from Matrix Population Models

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Documentation for package ‘Rage’ version 1.6.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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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
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_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
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	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