Package: DAMOCLES 3.1
Rampal S. Etienne
DAMOCLES: Dynamic Assembly Model of Colonization, Local Extinction and Speciation
Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account phylogenetic history.
Authors:
DAMOCLES_3.1.tar.gz
DAMOCLES_3.1.zip(r-4.5)DAMOCLES_3.1.zip(r-4.4)DAMOCLES_3.1.zip(r-4.3)
DAMOCLES_3.1.tgz(r-4.4-x86_64)DAMOCLES_3.1.tgz(r-4.4-arm64)DAMOCLES_3.1.tgz(r-4.3-x86_64)DAMOCLES_3.1.tgz(r-4.3-arm64)
DAMOCLES_3.1.tar.gz(r-4.5-noble)DAMOCLES_3.1.tar.gz(r-4.4-noble)
DAMOCLES_3.1.tgz(r-4.4-emscripten)DAMOCLES_3.1.tgz(r-4.3-emscripten)
DAMOCLES.pdf |DAMOCLES.html✨
DAMOCLES/json (API)
| # Install 'DAMOCLES' in R: |
| install.packages('DAMOCLES', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rsetienne/damocles/issues
Pkgdown:https://rsetienne.github.io
- NWPrimates_data - Dated phylogenetic tree of the New World Primates in nexus format and presence-absence matrix for species in Manu
Last updated 7 days agofrom:cef97a6533. Checks:OK: 9. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 26 2024 |
| R-4.5-win-x86_64 | OK | Nov 26 2024 |
| R-4.5-linux-x86_64 | OK | Nov 26 2024 |
| R-4.4-win-x86_64 | OK | Nov 26 2024 |
| R-4.4-mac-x86_64 | OK | Nov 26 2024 |
| R-4.4-mac-aarch64 | OK | Nov 26 2024 |
| R-4.3-win-x86_64 | OK | Nov 26 2024 |
| R-4.3-mac-x86_64 | OK | Nov 26 2024 |
| R-4.3-mac-aarch64 | OK | Nov 26 2024 |
Exports:DAMOCLES_bootstrapDAMOCLES_loglikDAMOCLES_MLDAMOCLES_simHERACLES_ImportanceSampling
Dependencies:apebackportsbase64encBHbslibcachemcapercheckmatecliclusterclusterGenerationcodacodetoolscolorspacecombinatcpp11data.tableDDDDEoptimdeSolvedigestdoParallelevaluateexpmfansifarverfastmapfontawesomeforeachforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrmapsMASSMatrixmatrixStatsmemoisemgcvmimemnormtmunsellmvtnormnlmennetnumDerivoptimParallelpermutephangornphytoolspicantepillarpkgconfigquadprogR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrlangrmarkdownrpartrstudioapisassscalesscatterplot3dSparseMstringistringrsubplextibbletinytexutf8vctrsveganviridisviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Phylogenetic community structure hypothesis test | DAMOCLES_bootstrap |
| Likelihood for DAMOCLES model | DAMOCLES_loglik |
| Maximization of the loglikelihood under the DAMOCLES model | DAMOCLES_ML |
| Simulating DAMOCLES | DAMOCLES_sim |
| Importance Sampling from the HERACLES model | HERACLES_ImportanceSampling |
| Dated phylogenetic tree of the New World Primates in nexus format and presence-absence matrix for species in Manu | NWPrimates_data |
