Package: adapt3 2.0.9

adapt3: Adaptive Dynamics and Community Matrix Model Projections

Runs projections of groups of matrix projection models (MPMs), allowing density dependence mechanisms to work across MPMs. This package was developed to run both adaptive dynamics simulations such as pairwise and multiple invasibility analyses, and community projections in which species are represented by MPMs. All forms of MPMs are allowed, including integral projection models (IPMs).

Authors:Richard P. Shefferson [aut, cre]

adapt3_2.0.9.tar.gz
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adapt3_2.0.9.tgz(r-4.6-x86_64)adapt3_2.0.9.tgz(r-4.6-arm64)adapt3_2.0.9.tgz(r-4.5-x86_64)adapt3_2.0.9.tgz(r-4.5-arm64)
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adapt3_2.0.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
adapt3/json (API)

# Install 'adapt3' in R:

install.packages('adapt3', repos = c('https://dormancy1.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dormancy1/adapt3/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

cypa_data - Demographic Dataset of _Cypripedium parviflorum_ Population, in Horizontal Format

On CRAN:

openblas cpp

5.34 score 7 scripts 214 downloads 6 exports 70 dependencies

Last updated from:52a613ea1d. Checks:11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	406
linux-devel-x86_64	NOTE	355
source / vignettes	OK	528
linux-release-arm64	NOTE	398
linux-release-x86_64	NOTE	366
macos-release-arm64	NOTE	485
macos-release-x86_64	NOTE	578
macos-oldrel-arm64	NOTE	514
macos-oldrel-x86_64	NOTE	525
windows-devel	NOTE	431
windows-release	NOTE	431
windows-oldrel	NOTE	355
wasm-release	OK	197

Exports:batch_project3 equiv_input invade3 project3 ta_skeleton trait_axis

Dependencies:backports BH boot broom cli colorspace cowplot cpp11 Deriv doBy dplyr farver forecast fracdiff generics ggplot2 glmmTMB glue gtable insight isoband labeling lattice lefko3 lifecycle lme4 lmtest magrittr MASS Matrix mgcv microbenchmark minqa modelr MuMIn nlme nloptr nnet numDeriv pbkrtest pillar pkgconfig pscl purrr R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang S7 sandwich scales stringi stringr tibble tidyr tidyselect timeDate TMB urca utf8 vctrs VGAM viridisLite withr zoo

Pairwise invasibility analysis

Rendered frominvasion.Rmdusingknitr::rmarkdown

Last update: 2026-02-12
Started: 2026-02-11

Community matrix projection

Organisms and populations | Dataset preparation | Community projection with pre-existing MPMs | Acknowledgements | Literature cited

Rendered fromcomproj.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adaptive Dynamics and Community Matrix Model Projections	adapt3-package adapt3
Project Multiple MPMs In Batches With Varying Starting Conditions	batch_project3
Demographic Dataset of _Cypripedium parviflorum_ Population, in Horizontal Format	cypa_data
Create an Equivalence Vector for Each Population	equiv_input
Run Pairwise and Multiple Invasibility Analysis	invade3
Create Contour Plot of Pairwise Invasibility Analysis Results	plot.adaptInv
Create Plot of Community Projection	plot.adaptProj
Project Multiple MPMs With or Without Density Dependence	project3
Summarize adaptInv Objects	summary.adaptInv
Summarize adaptProj Objects	summary.adaptProj
Summarize adaptProjBatch Objects	summary.adaptProjBatch
Create Skeleton Data Frame for Trait Variation for Invasion Analysis	ta_skeleton
Create a Data Frame of Trait Data for Invasion Analysis	trait_axis