Package: diverge 2.0.6
Sean A. S. Anderson
diverge: Evolutionary Trait Divergence Between Sister Species and Other Paired Lineages
Compares the fit of alternative models of continuous trait differentiation between sister species and other paired lineages. Differences in trait means between two lineages arise as they diverge from a common ancestor, and alternative processes of evolutionary divergence are expected to leave unique signatures in the distribution of trait differentiation in datasets comprised of many lineage pairs. Models include approximations of divergent selection, drift, and stabilizing selection. A variety of model extensions facilitate the testing of process-to-pattern hypotheses. Users supply trait data and divergence times for each lineage pair. The fit of alternative models is compared in a likelihood framework.
Authors:
diverge_2.0.6.tar.gz
diverge_2.0.6.tar.gz(r-4.5-noble)diverge_2.0.6.tar.gz(r-4.4-noble)
diverge_2.0.6.tgz(r-4.4-emscripten)diverge_2.0.6.tgz(r-4.3-emscripten)
diverge.pdf |diverge.html✨
diverge/json (API)
| # Install 'diverge' in R: |
| install.packages('diverge', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
- all_birds - Example Tree
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:399a318a7a. Checks:OK: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 16 2024 |
| R-4.5-linux | NOTE | Dec 16 2024 |
Exports:bootstrap_ciexpected_valextract_sistersfind_mlelikelihood_funcmodel_error_ratemodel_generatormodel_selectparam_gridrandom_walksre_estimatorsimulate_div
Dependencies:truncnorm
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Evolutionary Trait Divergence Between Sister Species and Other Paired Lineages | diverge-package diverge |
| Estimate confidence intervals using bootstrap | bootstrap_ci |
| Example Tree | all_birds |
| Expected value through time | expected_val |
| Extract sister pairs | extract_sisters |
| Find Maximum Likelihood Estimates | find_mle |
| Functions for negative log likelihood | likelihood_func |
| Calculate error rate in model selection | model_error_rate |
| Generate parameter~gradient linear models | model_generator |
| Select the best fit model of trait divergence | model_select |
| Generate parameter grid | param_grid |
| Simulate and plot trait evolution through time | random_walks |
| Estimate model parameters | re_estimator |
| Simulate trait divergence | simulate_div |