Package: Rage 1.9.0

Rage: Life History Metrics from Matrix Population Models

Functions for calculating life history metrics using matrix population models ('MPMs'). Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.

Authors:Patrick Barks [aut], Danny Buss [ctb], Pol Capdevila [aut], Hal Caswell [aut], Judy P. Che-Castaldo [aut], Richard A. Hinrichsen [aut], John Jackson [aut], Tamora James [aut], Owen Jones [aut, cre], Sam Levin [aut], William K. Petry [aut], Roberto Salguero-Gomez [aut], Caroline Schuette [ctb], Iain Stott [aut], Chelsea C. Thomas [aut], Christina M. Hernández [aut], Lotte de Vries [aut], Stefano Giaimo [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rage/json (API)

# Install 'Rage' in R:
install.packages('Rage', repos = c('https://jonesor.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jonesor/rage/issues

Pkgdown/docs site:https://jonesor.github.io

Datasets:
  • leslie_mpm1 - Example Leslie matrix population model
  • mpm1 - Example matrix population model

On CRAN:

Conda:

8.81 score 12 stars 1 packages 103 scripts 816 downloads 1 mentions 63 exports 73 dependencies

Last updated from:e4f1b981ec. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK186
source / vignettesOK201
linux-release-x86_64OK223
macos-release-arm64OK180
macos-oldrel-arm64OK165
windows-develOK104
windows-releaseOK107
windows-oldrelOK114
wasm-releaseOK168

Exports:entropy_dentropy_kentropy_k_ageentropy_k_stageevenness_shannongen_timehx_to_lxhx_to_pxis_leslie_matrixleslie_collapselife_elaslife_expect_meanlife_expect_varlongevitylx_to_hxlx_to_pxmature_agemature_distribmature_probmpm_collapsempm_rearrangempm_splitmpm_standardisempm_standardizempm_to_hxmpm_to_lxmpm_to_mxmpm_to_pxmpm_to_tablename_stagesnet_repro_rateperturb_matrixperturb_stochasticperturb_transperturb_vrplot_life_cyclepop_vectorspx_to_hxpx_to_lxqsd_convergerepro_stagesscale_mpm_to_lambda1shape_repshape_survstage_at_death_diststandard_stagesvital_ratesvr_dorm_entervr_dorm_exitvr_fecundityvr_growthvr_mat_Rvr_mat_Uvr_shrinkagevr_stasisvr_survivalvr_vec_dorm_entervr_vec_dorm_exitvr_vec_growthvr_vec_reproductionvr_vec_shrinkagevr_vec_stasisvr_vec_survival

Dependencies:base64encbitbit64bslibcachemclicliprcodacpp11crayonDiagrammeRdigestdplyrevaluateexpmfarverfastmapfontawesomefsgenericsgluehighrhmshtmltoolshtmlwidgetsigraphjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmemoisemimepillarpkgconfigpopdemoprettyunitsprogresspurrrquantregR6rappdirsRColorBrewerreadrrlangrmarkdownrstudioapisassscalesSparseMstringistringrsurvivaltibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevisNetworkvroomwithrxfunyaml

Getting started with Rage
Overview | Recap: Assumed knowledge | R.1. Basic anatomy of life cycles and MPMs | R.2. Projecting population change | R.3. Analysis of population equilibrium (eigenanalysis) | Representing and loading MPMs in Rage | Families of Rage functions for life history analysis | 1. Standardized vital rates | 2. Deriving life tables from MPMs for age-from-stage analyses | 3. Perturbation analyses | 4. Deriving life history traits | 5. Transforming MPMs | References
Rendered froma01_GettingStarted.Rmdusingknitr::rmarkdown

Last update: 2024-12-21
Started: 2021-02-21

Deriving life history traits from an MPM
Introduction | Loading MPMs and basic anatomy | Survival and lifespan traits | Reproduction and maturation traits | Life table component traits | Shape of mortality and fecundity | References
Rendered froma03_LifeHistoryTraits.Rmdusingknitr::rmarkdown

Last update: 2024-03-30
Started: 2021-03-13

Age-from-stage analyses
Introduction | Preliminaries | Age-from-stage methods with a single matrix population model | Extending to many matrix population models | References
Rendered froma04_AgeFromStage.Rmdusingknitr::rmarkdown

Last update: 2023-05-23
Started: 2021-03-13

Deriving vital rates from an MPM
Introduction | Preliminaries: Constructing an MPM from lower-level vital rates | Deriving vital rates of survival | Deriving vital rates conditional on survival | Summarizing vital rates within stages | Growth, shrinkage, stasis, and dormancy | Fecundity | Summarizing vital rates across stages | Simple average across stage classes | Weighted average across stage classes | Distinguishing between possible and impossible transitions | References
Rendered froma02_VitalRates.Rmdusingknitr::rmarkdown

Last update: 2023-04-09
Started: 2021-02-21

Suggested quality control
Introduction | Types of issue | Missing data | Excessive zeros | Excessive survival | Excessive mortality | Irreducibility and ergodicity | Singularity of the U matrix | Matrix split errors | Function requirement summaries | Other issues | Finally... | References
Rendered froma05_SuggestedQualityControl.Rmdusingknitr::rmarkdown

Last update: 2023-01-17
Started: 2021-10-14

Readme and manuals

Help Manual

Help pageTopics
Calculate age-specific traits from a matrix population modelage_from_stage mpm_to_hx mpm_to_lx mpm_to_mx mpm_to_px
Calculate Demetrius' entropy from trajectories of age-specific survivorship and fecundityentropy_d
Calculate Keyfitz's entropy from a trajectory of age-specific survivorshipentropy_k
Calculate Keyfitz entropy for an age-based matrix population modelentropy_k_age
Calculate Keyfitz entropy for a stage-based matrix population modelentropy_k_stage
Shannon Evenness (Pielou's J)evenness_shannon
Calculate generation time from a matrix population modelgen_time
Determine if a matrix is a Leslie matrix population modelis_leslie_matrix
Aggregate a Leslie matrixleslie_collapse
Example Leslie matrix population model (MPM)leslie_mpm1
Calculate Keyfitz's entropy from a trajectory of age-specific survivorshiplife_elas
Calculate mean and variance of life expectancy from a matrix population modellife_expect_mean life_expect_var
Convert between age-specific survivorship, survival, or mortality hazardhx_to_lx hx_to_px lifetable_convert lx_to_hx lx_to_px px_to_hx px_to_lx
Calculate longevity from a matrix population modellongevity
Collapse a matrix population model to a smaller number of stagesmpm_collapse
Rearrange stages of a matrix population model to segregate reproductive and non-reproductive stagesmpm_rearrange
Convert matrix population model into U, F and C matricesmpm_split
Transform a matrix population model to a standardized formmpm_standardise mpm_standardize
Generate a life table from a matrix population modelmpm_to_table
Example matrix population model (MPM)mpm1
Add stage names to matricesname_stages
Calculate net reproductive rate (R0) from a matrix population modelnet_repro_rate
Perturbation analysis of a matrix population modelperturb_matrix
Calculate stochastic elasticities from a time-series of matrix population models and corresponding population vectorsperturb_stochastic
Perturbation analysis of transition types within a matrix population modelperturb_trans
Perturbation analysis of vital rates in a matrix population modelperturb_vr
Plot a life cycle diagram from a matrix population modelplot_life_cycle
Derive a hypothetical set of population vectors corresponding to a time-series of matrix population modelspop_vectors
Calculate time to reach quasi-stationary stage distributionqsd_converge
Age of reproductive maturitymature_age mature_distrib mature_prob repro_maturity
Identify which stages in a matrix population model are reproductiverepro_stages
Scale a matrix population model so that lambda equals 1scale_mpm_to_lambda1
Calculate shape of reproduction over ageshape_rep
Calculate shape of survival over ageshape_surv
Compute distribution of stage at death from a stage-structured MPMstage_at_death_dist
Identify stages corresponding to different parts of the reproductive life cyclestandard_stages
Derive mean vital rates from a matrix population modelvital_rates
Derive mean vital rates from a matrix population modelvr vr_dorm_enter vr_dorm_exit vr_fecundity vr_growth vr_shrinkage vr_stasis vr_survival
Derive survival-independent vital rates for growth, stasis, shrinkage, and reproductionvr_mat vr_mat_R vr_mat_U
Derive stage-specific vital rates from a matrix population modelvr_vec vr_vec_dorm_enter vr_vec_dorm_exit vr_vec_growth vr_vec_reproduction vr_vec_shrinkage vr_vec_stasis vr_vec_survival