Package: ppgm 1.0.3
Alexandra Howard
ppgm: PaleoPhyloGeographic Modeling of Climate Niches and Species Distributions
Reconstruction of paleoclimate niches using phylogenetic comparative methods and projection reconstructed niches onto paleoclimate maps. The user can specify various models of trait evolution or estimate the best fit model, include fossils, use one or multiple phylogenies for inference, and make animations of shifting suitable habitat through time. This model was first used in Lawing and Polly (2011), and further implemented in Lawing et al (2016) and Rivera et al (2020). Lawing and Polly (2011) <doi:10.1371/journal.pone.0028554> "Pleistocene climate, phylogeny and climate envelope models: An integrative approach to better understand species' response to climate change" Lawing et al (2016) <doi:10.1086/687202> "Including fossils in phylogenetic climate reconstructions: A deep time perspective on the climatic niche evolution and diversification of spiny lizards (Sceloporus)" Rivera et al (2020) <doi:10.1111/jbi.13915> "Reconstructing historical shifts in suitable habitat of Sceloporus lineages using phylogenetic niche modelling.".
Authors:
ppgm_1.0.3.tar.gz
ppgm_1.0.3.tar.gz(r-4.5-noble)ppgm_1.0.3.tar.gz(r-4.4-noble)
ppgm_1.0.3.tgz(r-4.4-emscripten)ppgm_1.0.3.tgz(r-4.3-emscripten)
ppgm.pdf |ppgm.html✨
ppgm/json (API)
NEWS
| # Install 'ppgm' in R: |
| install.packages('ppgm', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- occurrences - Sceloporus occurrence data
- paleoclimate - Paleoclimate Data for ppgm examples
- sampletrees - Sample of Sceloporus phylogenies
- scel_fossils - Sceloporus fossil data
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 months agofrom:af3640e9be. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 10 2024 |
| R-4.5-linux | OK | Sep 10 2024 |
Exports:addFossilgetBioclimVarsgetEnvelopesgetGeoRategetLineageClimategetTimeSlicenodeEstimatenodeEstimateEnvelopesplotAnimatedPPGMplotAnimatedPPGMMultiPhyloplotGeoRatesplotGeoRatesConplotTraitGramplotTraitGramMultiPhyloppgmppgmConsensusppgmMESS
Dependencies:animationapeclassclassIntcliclusterGenerationcodacodetoolscolorspacecombinatcpp11curlDBIDEoptimdeSolvedigestdoParalleldotCall64e1071expmfastmatchfieldsforeachgeigergenericsglueigraphiteratorsKernSmoothlatticelifecyclemagickmagrittrmapsMASSMatrixmnormtmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspkgconfigproxyquadprogRcpprlangs2scatterplot3dsfspspamstringisubplexunitsvctrsviridisLitewk
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| addFossil | addFossil |
| getBioclimVars | getBioclimVars |
| getEnvelopes | getEnvelopes |
| getGeoRate | getGeoRate |
| getLineageClimate | getLineageClimate |
| getTimeSlice | getTimeSlice |
| nodeEstimate | nodeEstimate |
| nodeEstimateEnvelopes | nodeEstimateEnvelopes |
| Sceloporus occurrence data | occurrences |
| Paleoclimate Data for ppgm examples | paleoclimate |
| plotAnimatedPPGM | plotAnimatedPPGM |
| plotAnimatedPPGMMultiPhylo | plotAnimatedPPGMMultiPhylo |
| plotGeoRates | plotGeoRates |
| plotGeoRatesCon | plotGeoRatesCon |
| plotTraitGram | plotTraitGram |
| plotTraitGramMultiPhylo | plotTraitGramMultiPhylo |
| ppgm | ppgm |
| ppgmConsensus | ppgmConsensus |
| ppgmMESS | ppgmMESS |
| Sample of Sceloporus phylogenies | sampletrees |
| Sceloporus fossil data | scel_fossils |