Package: DAMOCLES 2.3

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:Rampal S. Etienne & Alex L. Pigot

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://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rsetienne/damocles/issues

Datasets:

NWPrimates_data - Dated phylogenetic tree of the New World Primates in nexus format and presence-absence matrix for species in Manu

On CRAN:

4 exports 1 stars 4.39 score 101 dependencies 39 mentions 10 scripts 266 downloads

Last updated 4 years agofrom:05fbf008d9. Checks:OK: 1 WARNING: 6. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Aug 24 2024
R-4.5-win	WARNING	Aug 24 2024
R-4.5-linux	WARNING	Aug 24 2024
R-4.4-win	WARNING	Aug 24 2024
R-4.4-mac	WARNING	Aug 24 2024
R-4.3-win	WARNING	Aug 24 2024
R-4.3-mac	WARNING	Aug 24 2024

Exports:DAMOCLES_bootstrap DAMOCLES_loglik DAMOCLES_ML DAMOCLES_sim

Dependencies:ape backports base64enc BH bslib cachem caper checkmate cli cluster clusterGeneration coda codetools colorspace combinat cpp11 data.table DDD DEoptim deSolve digest doParallel evaluate expm fansi farver fastmap fastmatch fontawesome foreach foreign Formula fs generics ggplot2 ggseqlogo glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets igraph isoband iterators jquerylib jsonlite knitr labeling lattice lifecycle magrittr maps MASS Matrix matrixStats memoise mgcv mime mnormt munsell mvtnorm nlme nnet numDeriv optimParallel permute phangorn phytools picante pillar pkgconfig quadprog R6 rappdirs RColorBrewer Rcpp RcppEigen rlang rmarkdown rpart rstudioapi sass scales scatterplot3d SparseM stringi stringr subplex tibble tinytex utf8 vctrs vegan viridis viridisLite withr xfun yaml

Citation

Development and contributors

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

Usage by other packages (reverse dependencies)