plot_ltt_summary: Lineage through time plots of all chronograms in multiphylo...

In phylotastic/datelifeplot: Methods to plot chronograms

Lineage through time plots of all chronograms in multiphylo object and its summaries.

Description

Lineage through time plots of all chronograms in multiphylo object and its summaries.

Usage

plot_ltt_summary(
  taxon,
  phy,
  phy_sdm,
  phy_median,
  file_name = NULL,
  file_dir = NULL,
  height = 3.5,
  width = 7,
  add_legend = TRUE,
  add_title = FALSE,
  col_sdm = "#00AFBB",
  col_median = "#CC79A7",
  tax_datedotol = NULL,
  ...
)

Arguments

taxon	Character vector indicating the name of the taxon or lineage that the chronograms in phy belong to.
phy	A phylo or multiphylo object with chronograms (trees with branch lengths proportional to geologic time), ideally.
phy_sdm	A multiphylo object with chronograms from a SDM summary.
phy_median	A multiphylo object with chronograms from a median summary.
file_name	A character string giving the name of the pdf file.
file_dir	A character string giving the path to write the file to.
height	Height of the plot
width	Width of the plot
add_legend	Boolean
add_title	Boolean
col_sdm	Color of the SDM tree
col_median	Color of the median tree
tax_datedotol	A chronogram to compare other chronograms to.
...	Arguments passed on to ape::ltt.plot xlab a character string (or a variable of mode character) giving the label for the x-axis (default is "Time"). ylab idem for the y-axis (default is "N"). backward a logical value: should the time axis be traced from the present (the default), or from the root of the tree? tol a numeric value (see details).

phylotastic/datelifeplot documentation built on July 14, 2022, 12:35 p.m.