Package: treats 1.1
treats: Trees and Traits Simulations
A modular package for simulating phylogenetic trees and species traits jointly. Trees can be simulated using modular birth-death parameters (e.g. changing starting parameters or algorithm rules). Traits can be simulated in any way designed by the user. The growth of the tree and the traits can influence each other through modifiers objects providing rules for affecting each other. Finally, events can be created to modify both the tree and the traits under specific conditions ( Guillerme, 2024 <doi:10.1111/2041-210X.14306>).
Authors:
treats_1.1.tar.gz
treats_1.1.zip(r-4.5)treats_1.1.zip(r-4.4)treats_1.1.zip(r-4.3)
treats_1.1.tgz(r-4.4-any)treats_1.1.tgz(r-4.3-any)
treats_1.1.tar.gz(r-4.5-noble)treats_1.1.tar.gz(r-4.4-noble)
treats_1.1.tgz(r-4.4-emscripten)treats_1.1.tgz(r-4.3-emscripten)
treats.pdf |treats.html✨
treats/json (API)
NEWS
| # Install 'treats' in R: |
| install.packages('treats', repos = c('https://tguillerme.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tguillerme/treats/issues
Last updated 9 days agofrom:af6cf46375. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 11 2024 |
| R-4.5-win | OK | Nov 11 2024 |
| R-4.5-linux | OK | Nov 11 2024 |
| R-4.4-win | OK | Nov 11 2024 |
| R-4.4-mac | OK | Nov 11 2024 |
| R-4.3-win | OK | Nov 11 2024 |
| R-4.3-mac | OK | Nov 11 2024 |
Exports:age.conditionbd.params.updateBM.processbranch.lengthbranch.length.traitcrude.bd.estdiscrete.processdispRitreatsdrop.fossilsdrop.livingsdrop.singlesdrop.thingsdrop.tip.treatsevents.conditionevents.modificationfounding.eventkeep.tip.treatslink.traitsmake.bd.paramsmake.eventsmake.modifiersmake.traitsmake.treatsmap.traitsmodifiersmodifiers.updatemulti.peak.processno.processOU.processparent.traitsplot.treatsprint.treatsrandom.extinctionrepulsion.processselectionspeciationspeciation.traittaxa.conditiontrait.conditiontrait.extinctiontrait.processtraits.updatetransition.matrixtreats
Dependencies:abindade4apebase64encbslibcachemcastorCladdisclicliprclusterclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdispRitydoParallelellipseevaluateexpmfansifarverfastmapfastmatchfontawesomeforeachfsfuturefuture.applygeigergenericsgeometrygeoscaleGETggplot2globalsgluegmpgridExtragtablehighrhtmltoolshtmlwidgetsigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclelinproglistenvlpSolvemagicmagrittrmapsMASSmathjaxrMatrixmemoisemgcvmimemnormtmulticoolmunsellmvtnormnaturalsortncbitnlmenumDerivoptimParallelparallellypartitionspbapplypermutephangornphyclustphylolmphytoolspillarpixmappkgconfigpolynomquadprogR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressRdpackrglrlangrmarkdownRSpectrasassscalesscatterplot3dsetsspstrapsubplextibbletinytexutf8vctrsveganviridisLitewithrxfunyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Crudely estimates extinction and speciation | crude.bd.est |
| dispRity interface for treats objects | dispRitreats |
| Drop things from a treats object | drop.fossils drop.livings drop.singles drop.things |
| drop.tip.treats | drop.tip.treats keep.tip.treats |
| events.conditions | age.condition events.condition events.conditions taxa.condition trait.condition |
| Events modifications | bd.params.update events.modification events.modifications founding.event modifiers.update random.extinction trait.extinction traits.update |
| link.traits | link.traits |
| Make birth death parameters | make.bd.params |
| make.events | make.events |
| make.modifiers | make.modifiers |
| make.traits | make.traits |
| Make a treats object | make.treats |
| Maps a trait on a tree | map.traits |
| Modifiers | branch.length branch.length.trait modifiers selection speciation speciation.trait |
| Get parent traits | parent.traits |
| Plot treats objects | plot.treats |
| Prints a 'treats' object. | print.treats |
| Trait processes | BM.process discrete.process multi.peak.process no.process OU.process repulsion.process trait.process |
| Makes a transition matrix | transition.matrix |
| Diversity and disparity simulator | treats |
