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diverge (version 2.0.4)

Evolutionary Trait Divergence Between Sister Species and Other Paired Lineages

Description

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.

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Version

Install

install.packages('diverge')

Monthly Downloads

240

Version

2.0.4

License

GPL (>= 2)

Maintainer

Sean S. Anderson

Last Published

January 19th, 2022

Functions in diverge (2.0.4)

model_generator

Generate parameter~gradient linear models
find_mle

Find Maximum Likelihood Estimates
likelihood_func

Functions for negative log likelihood
diverge-package

Evolutionary Trait Divergence Between Sister Species and Other Paired Lineages
bootstrap_ci

Estimate confidence intervals using bootstrap
extract_sisters

Extract sister pairs
model_error_rate

Calculate error rate in model selection
model_select

Select the best fit model of trait divergence
expected_val

Expected value through time
diverge-data

Example Tree
param_grid

Generate parameter grid
random_walks

Simulate and plot trait evolution through time
simulate_div

Simulate trait divergence
re_estimator

Estimate model parameters