Parsimony lengths of trees in posterior distribution

Source: R/Parsimony.R

For each project and model combination, computes the parsimony step count of each posterior tree (under equal weights and implied-weights concavities of k = 10 and k = 1) relative to the most-parsimonious tree, then caches the result to ParsimonyFile().

PosteriorTreeSteps(projects, models)

Arguments

projects

Character vector of project IDs to process.

models

Character vector of script/model IDs to process.

Value

A data frame with columns ew, k10, k1 (step-length ratios relative to the MPT), pID, and scriptID, with one row per posterior tree.

Details

The following must have been run before calling this function:

  • MCMC sampling and tree-sample assembly: trees must be present at TreeSampleFile() (created via UpdateRecords()).

  • Parsimony search: .trees files for k = 1, k = 10, and k = Inf must be present in AnalysisDir(pID, "by_ki") (fetched with FetchResults() or submitted via TreeSearch()).

  • Nexus character matrices (.neo.nex / .trans.nex) must be present in the same analysis directory.