Two shape statistics, two processes | Reaching target values | A grid of tree shapes | Placing an empirical tree on the same scale | References
Package: treeshapesim 0.2.1
treeshapesim: Simulate Trees with Separately Controlled Imbalance and Branching Times
Simulates rooted, binary, ultrametric trees in which topological imbalance and the distribution of branching times are set by separate parameters. The topology is drawn from Aldous' beta-splitting model and the internode intervals from a pure-birth process in which each of k lineages splits at rate k^c. Because the gamma statistic depends only on the internode intervals and the Colless index only on the topology, beta mainly controls imbalance and c mainly controls gamma.
Authors:
treeshapesim_0.2.1.tar.gz
treeshapesim_0.2.1.zip(r-4.7-any)treeshapesim_0.2.1.zip(r-4.6-any)treeshapesim_0.2.1.zip(r-4.5-any)
treeshapesim_0.2.1.tgz(r-4.6-any)treeshapesim_0.2.1.tgz(r-4.5-any)
treeshapesim_0.2.1.tar.gz(r-4.7-any)treeshapesim_0.2.1.tar.gz(r-4.6-any)
treeshapesim_0.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
treeshapesim/json (API)
| # Install 'treeshapesim' in R: |
| install.packages('treeshapesim', repos = c('https://diogoprov.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/diogoprov/treeshapesim/issues
Pkgdown/docs site:https://diogoprov.github.io
phylogeneticsphylogenetic-treestree-shapetree-balancetree-imbalancegamma-statisticcolless-indexbeta-splittingdiversificationsimulationmacroevolutioncommunity-phylogeneticsr-universe
Last updated from:ac28f2c041 (on main). Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 141 | ||
| source / vignettes | OK | 436 | ||
| linux-release | OK | 127 | ||
| macos-release | OK | 108 | ||
| macos-oldrel | OK | 134 | ||
| windows-devel | OK | 110 | ||
| windows-release | OK | 108 | ||
| windows-oldrel | OK | 86 | ||
| wasm-release | OK | 111 |
Exports:assign_agescalibrate_shapefit_shapeintervals_lineage_ratertopology_betashape_gridshape_paramssim_tree_shapesim_tree_targettree_shape
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Assign node ages to a topology from internode intervals | assign_ages |
| Calibrate the shape parameters for a number of tips | calibrate_shape |
| Estimate the shape parameters of a tree | fit_shape |
| Internode intervals of a pure-birth process with lineage-dependent rates | intervals_lineage_rate |
| Random topology under Aldous' beta-splitting model | rtopology_beta |
| Grid of tree shapes | shape_grid |
| Shape parameters that give target mean values of gamma and Colless | shape_params |
| Ultrametric trees with given imbalance and branching-time parameters | sim_tree_shape |
| Simulate trees near target values of gamma and Colless | sim_tree_target |
| Gamma statistic and Colless index of a tree | tree_shape |