Package: DAMOCLES 2.3
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_2.3.tar.gz
DAMOCLES_2.3.zip(r-4.5)DAMOCLES_2.3.zip(r-4.4)DAMOCLES_2.3.zip(r-4.3)
DAMOCLES_2.3.tgz(r-4.4-any)DAMOCLES_2.3.tgz(r-4.3-any)
DAMOCLES_2.3.tar.gz(r-4.5-noble)DAMOCLES_2.3.tar.gz(r-4.4-noble)
DAMOCLES_2.3.tgz(r-4.4-emscripten)DAMOCLES_2.3.tgz(r-4.3-emscripten)
DAMOCLES.pdf |DAMOCLES.html✨
DAMOCLES/json (API)
| # Install 'DAMOCLES' in R: |
| install.packages('DAMOCLES', repos = c('https://rsetienne.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rsetienne/damocles/issues
- NWPrimates_data - Dated phylogenetic tree of the New World Primates in nexus format and presence-absence matrix for species in Manu
Last updated 4 years agofrom:05fbf008d9. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 04 2024 |
| R-4.5-win | WARNING | Nov 04 2024 |
| R-4.5-linux | WARNING | Nov 04 2024 |
| R-4.4-win | WARNING | Nov 04 2024 |
| R-4.4-mac | WARNING | Nov 04 2024 |
| R-4.3-win | WARNING | Nov 04 2024 |
| R-4.3-mac | WARNING | Nov 04 2024 |
Exports:DAMOCLES_bootstrapDAMOCLES_loglikDAMOCLES_MLDAMOCLES_sim
Dependencies:apebackportsbase64encBHbslibcachemcapercheckmatecliclusterclusterGenerationcodacodetoolscolorspacecombinatcpp11data.tableDDDDEoptimdeSolvedigestdoParallelevaluateexpmfansifarverfastmapfastmatchfontawesomeforeachforeignFormulafsgenericsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsigraphisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrmapsMASSMatrixmatrixStatsmemoisemgcvmimemnormtmunsellmvtnormnlmennetnumDerivoptimParallelpermutephangornphytoolspicantepillarpkgconfigquadprogR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownrpartrstudioapisassscalesscatterplot3dSparseMstringistringrsubplextibbletinytexutf8vctrsveganviridisviridisLitewithrxfunyaml
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 |
| Dated phylogenetic tree of the New World Primates in nexus format and presence-absence matrix for species in Manu | NWPrimates_data |
