Analysis of Convergent Evolution
Converts taxon names to tip/edge numbers
Calculates maxdist for all pairs of taxa in a phylogeny.
Extracts lineages leading to two tips, t1 and t2, from their most rece...
Calculates all phenotypic changes that occur on all branches of a phyl...
Quantifies convergent evolution by the ratio of the current to maximum...
Computes Ct-metric scores for putatively convergent tips (or groups of...
Calculates the C1-C4 measures of convergent evolution between two line...
Computes Ct values for a pair of tips. Internal, called in calcConv.
Quantify convergence by the number of convergent events
Assess the significance of convergent evolution using simulations and ...
Quantifies convergent evolution using the C1, C2, C3, and C4 measures ...
Tests the signifiance of convergent evolution by the ratio of the curr...
Uses simulations to assess the significance of C1-C4 measures of conve...
Computes and conducts significance tests on Ct-metric scores for putat...
Find the ancestor of a given node in a phylogeny
Calculates the maximum phenotypic distance between the lineages leadin...
Reconstructs ancestral states for multiple characters
Plots calcConv or convSig output as a two-dimensional time series.
Plots calcConv or convSig output.
Plots an ellipse
Extracts a vector of ancestors for a given taxon. Code written by Jona...
Calculates the number of measurements that can be made between two lin...
Quantifies and assesses the significance of convergent evolution using multiple methods and measures as described in Stayton (2015) <DOI: 10.1111/evo.12729> and Grossnickle et al. 2023. Also displays results in various ways.