Package: aae.pop 0.2.0.9000

Jian Yen

aae.pop: Flexible Population Dynamics Simulations

Simulate population dynamics from realistically complex matrix population models in a plug-and-play fashion. Supports aspatial and spatially implicit models with one or more species and time-varying covariates, stochasticity, density dependence, additions or removals of individuals, interspecific interactions, and metapopulations.

Authors:Jian Yen [aut, cre, cph], Arthur Rylah Institute for Environmental Research [fnd]

aae.pop_0.2.0.9000.tar.gz
aae.pop_0.2.0.9000.zip(r-4.7)aae.pop_0.2.0.9000.zip(r-4.6)aae.pop_0.2.0.9000.zip(r-4.5)
aae.pop_0.2.0.9000.tgz(r-4.6-any)aae.pop_0.2.0.9000.tgz(r-4.5-any)
aae.pop_0.2.0.9000.tar.gz(r-4.7-any)aae.pop_0.2.0.9000.tar.gz(r-4.6-any)
aae.pop_0.2.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
aae.pop/json (API)
NEWS

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

Bug tracker:https://github.com/aae-stats/aae.pop/issues

Pkgdown/docs site:https://aae-stats.github.io

On CRAN:

Conda:

5.44 score 1 stars 8 scripts 222 downloads 42 exports 88 dependencies

Last updated from:0a4c975df5. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK177
source / vignettesOK237
linux-release-x86_64OK187
macos-release-arm64OK185
macos-oldrel-arm64OK191
windows-develOK147
windows-releaseOK126
windows-oldrelOK140
wasm-releaseOK137

Exports:add_remove_postadd_remove_preall_cellsall_classesbeverton_holtcombinecovariatesdemographic_stochasticitydensity_dependencedensity_dependence_ndispersaldynamicsempsenvironmental_stochasticityexpsformat_covariatesget_cdfget_pdfis.dynamicsis.interactionis.metapopulationis.multispeciesis.simulationis.simulation_listmetapopulationmultispeciespairwise_interactionpr_extinctreplicated_covariatesreproductionrickerrisk_curvermultiunitrmultiunit_from_realrunitrunit_from_realsurvivaltransitionunit_to_realupdate_binomial_leslieupdate_crossprodupdate_multinomial

Dependencies:abindbackportsbootbroomcarcarDataclicodetoolscolorspacecorrplotcowplotcpp11cubatureDerivdigestdoBydplyrfarverforecastFormulafracdifffuturefuture.applygenericsggplot2ggpubrggrepelggsciggsignifglobalsgluegridExtragtableisobandlabelinglatticelifecyclelistenvlme4lmtestmagrittrMASSMatrixMatrixModelsmc2dmgcvmicrobenchmarkminqamodelrmvtnormnleqslvnlmenloptrnnetnumDerivparallellypbkrtestpillarpkgconfigpolynompurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrstatixS7scalesSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrzoo

Get started with aae.pop

Jian Yen

Rendered fromget_started.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-02-03
Started: 2020-11-02

Including demographic processes in a population model

Jian Yen

Rendered fromincluding_processes.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-01-27
Started: 2020-11-02

Modelling metapopulations

Jian Yen

Rendered frommetapopulations.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-01-27
Started: 2020-11-02

Models of interacting species

Jian Yen

Rendered frommultiple_species.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-01-27
Started: 2020-11-02

Moving beyond default settings in aae.pop

Jian Yen

Rendered frombeyond_defaults.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-01-27
Started: 2020-11-02

Readme and manuals

Help Manual

Help pageTopics
Specify additions or removals in models of population dynamicsadd_remove add_remove_post add_remove_pre
Specify covariate dependence in models of population dynamicscovariates format_covariates
Specify density dependence in models of population dynamicsdensity_dependence density_dependence_n
Common forms of density dependencebeverton_holt density_functions ricker
Specify dispersal between populations in a metapopulation modeldispersal
Create and update population dynamics objectsdynamics is.dynamics update.dynamics
Calculate expected minimum population size (EMPS) for a 'simulate' objectemps
Calculate expected population size for a 'simulate' object based on generic functions (ExPS)exps
Calculate the cumulative distribution function of a summary statistic across all iterations of a 'simulate' objectget_cdf
Calculate the probability density of a summary statistic across all iterations of a 'simulate' objectget_pdf
Isolate elements of population dynamics modelsall_cells all_classes combine masks reproduction survival transition
Create a metapopulation dynamics objectis.metapopulation metapopulation
Create a population dynamics object with multiple speciesis.interaction is.multispecies multispecies
Specify interactions between two speciespairwise_interaction
Calculate (quasi-)extinction risk for a 'simulate' objectpr_extinct
Specify replicate-specific covariate dependence in models of population dynamicsreplicated_covariates
Calculate (quasi-)extinction risk at multiple thresholds for a 'simulate' objectrisk_curve
Random number generators not available in existing R packagesrmultiunit rmultiunit_from_real rng runit runit_from_real unit_to_real
Simulate single or multispecies population dynamics in Ris.simulation is.simulation_list simulate simulate.dynamics
Specify environmental and demographic stochasticity in models of population dynamicsdemographic_stochasticity environmental_stochasticity stochasticity
Functions for a single time-step updateupdaters update_binomial_leslie update_crossprod update_multinomial