Organism and population | Dataset preparation | Pairwise invasibility analysis focused on matrix element manipulation | Pairwise invasibility analysis focused on vital rate model manipulation | Acknowledgements | Literature cited
This package is considered a duplicate. The official version of this package is found at:https://dormancy1.r-universe.dev/adapt3
Package: adapt3 2.0.9
Richard P. Shefferson
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:
adapt3_2.0.9.tar.gz
adapt3_2.0.9.zip(r-4.7-x86_64)adapt3_2.0.9.zip(r-4.7-arm64)adapt3_2.0.9.zip(r-4.6-x86_64)adapt3_2.0.9.zip(r-4.6-arm64)
adapt3_2.0.9.tar.gz(r-4.7-arm64)adapt3_2.0.9.tar.gz(r-4.7-x86_64)adapt3_2.0.9.tar.gz(r-4.6-arm64)adapt3_2.0.9.tar.gz(r-4.6-x86_64)
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://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dormancy1/adapt3/issues
Datasets:
- cypa_data - Demographic Dataset of _Cypripedium parviflorum_ Population, in Horizontal Format
Last updated from:8435b23e46. Checks:8 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | NOTE | 315 | ||
| linux-devel-x86_64 | NOTE | 316 | ||
| source / vignettes | OK | 512 | ||
| linux-release-arm64 | NOTE | 338 | ||
| linux-release-x86_64 | NOTE | 334 | ||
| windows-devel-arm64 | NOTE | 408 | ||
| windows-devel-x86_64 | NOTE | 515 | ||
| windows-release-arm64 | NOTE | 471 | ||
| windows-release-x86_64 | NOTE | 361 | ||
| wasm-release | OK | 173 |
Exports:batch_project3equiv_inputinvade3project3ta_skeletontrait_axis
Dependencies:backportsBHbootbroomclicolorspacecowplotcpp11DerivdoBydplyrfarverforecastfracdiffgenericsggplot2glmmTMBgluegtableinsightisobandlabelinglatticelefko3lifecyclelme4lmtestmagrittrMASSMatrixmgcvminqamodelrMuMInnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpsclpurrrR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangRTMBS7sandwichscalesstringistringrtibbletidyrtidyselecttimeDateTMBurcautf8vctrsVGAMviridisLitewithrzoo
Pairwise invasibility analysis
Last update: 2026-02-13
Started: 2025-07-16
Community matrix projection
Organisms and populations | Dataset preparation | Community projection with pre-existing MPMs | Acknowledgements | Literature cited
Last update: 2026-02-09
Started: 2025-07-16
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 |