timePlotter: Rboretum Time-Dependent Signal Plotter

In BobLiterman/Rboretum: Compare Phylogenetic Trees and Alignment Support Values

Rboretum Time-Dependent Signal Plotter

Description

This function takes information about node ages and node support, and plots relative changes in node support over time among datasets.

Usage

timePlotter(
  node_age_df,
  tree_support,
  plot_datasets,
  all_sites_col,
  lm_alpha,
  wrap,
  wrap_scales,
  return_stats
)

Arguments

node_age_df	Output from extractNodeAges(phylo) or extractNodeAges(multiPhylo,return_summary = 'mean' or 'median') [Or a two-column dataframe containing (1) semicolon separated clades and (2) estimated node ages]
tree_support	Output from getAlignmentSupport with information about all clades in node_age_df and 2+ alignment support columns
plot_datasets	OPTIONAL: Character vector specifying the datasets desired for the plot (Must be 2+ and present in 'tree_support')
all_sites_col	OPTIONAL (Very special case): If the alignments from tree_support contain overlapping sites AND there is is a column in the data corresponding to all non-overlapping sites, specify the column name for all nonoverlapping sites to be used when calculating proportions
lm_alpha	OPTIONAL: Run linear models at this alpha level (must be > 0 and < 1; Alpha will be automatically Bonferroni corrected based on dataset count) [Default: Do not run linear models]
wrap	OPTIONAL (TRUE/FALSE); Plot datasets in separate facets [Default: FALSE; do not wrap and produce 1 plot]
wrap_scales	OPTIONAL ('free'/'fixed'): If wrapping, allow free or fixed scales on each facet [Default: 'fixed']
return_stats	OPTIONAL (TRUE/FALSE): In addition to returning the plot, also return the statistical output from linear models in a list

Value

Plot or list (depending on return_stats)

BobLiterman/Rboretum documentation built on July 6, 2023, 7:46 p.m.