phylo.spindles {paleoDiv}

Plots a phylogenetic tree with spindle-diagrams, optimized for showing taxonomic diversity.

Description

Plots a phylogenetic tree with spindle-diagrams, optimized for showing taxonomic diversity.

Usage

phylo.spindles(
  phylo0,
  occ,
  stat = divdistr_,
  prefix = "sptab_",
  pos = NULL,
  ages = NULL,
  xlimits = NULL,
  res = 1,
  weights = 1,
  dscale = 0.002,
  col = add.alpha("black"),
  fill = col,
  lwd = 1,
  lty = 1,
  cex.txt = 1,
  col.txt = add.alpha(col, 1),
  axis = TRUE,
  labels = TRUE,
  txt.y = 0.5,
  txt.x = NULL,
  adj.x = 0,
  add = FALSE,
  tbmar = 0.2,
  smooth = 0,
  italicize = character()
)

Arguments

phylo0

A time-calibrated phylogenetic tree to plot with spindle diagrams, or a character vector of taxonomic names for which to plot spindle diagrams.

occ

Either a list()-object containing taxon-range tables for plotting diversity, or a matrix() or data.frame()-object that contains numerical plotting statistics. If the latter is provided, the default use of divdistr_() is overridden and the function will look for a column named "x" and columns matching the phylogeny tip.labels to plot the spindles.

stat

Plotting statistic to be passed on to viol(). Defaults to use divdistr_().

prefix

Prefix for taxon-range tables in occ. Defaults to "sptab_"

pos

Position at which to draw spindles. If NULL (default), then spindles are drawn at c(1:n) where n is the number of taxa in phylo0.

ages

Optional matrix with lower and upper age limits for each spindle, formatted like the output of tree.ages() (most commonly the same calibration matrix used to time-calibrate the tree)

xlimits

Limits for plotting the on the x axis.

res

Temporal resolution of diversity estimation (if occ is a matrix or data.frame containing plotting statistics, this is ignored)

weights

Weights for diversity estimation. Must have the same length as the range of xlimits divided by res. For details, see divdistr_()

dscale

Scale value of the spindles on the y axis. Should be adjusted manually to optimize visibility of results.

col

Color to use for the border of the plotted spindles

fill

Color to use for the fill of the plotted spindles. Defaults to col.

lwd

Line width for the plotted spindles.

lty

Line type for the plotted spindles.

cex.txt

Adjustment for tip label text size

col.txt

tip label text color, defaults to be same as col, but with no transparency

axis

Logical indicating whether to plot (temporal) x axis (defaults to TRUE)

labels

Logical indicating whether to plot tip labels of phylogeny (defaults to TRUE)

txt.y

y axis alignment of tip labels

txt.x

x coordinates for plotting tip labels. Can be a single value applicable to all labels, or a vector of the same length as phylo0$tip.label

adj.x

Numeric value giving alignment on x axis, defaults to 0 (left-aligned) but can also be 0.5 (centered) or 1 (right-aligned).

add

Logical indicating whether to add to an existing plot, in which case only the spindles are plotted on top of an existing phylogeny, or not, in which case the phylogeny is plotted along with the spindles.

tbmar

Top and bottom margin around the plot. Numeric of either length 1 or 2

smooth

Smoothing parameter to be passed on to divdistr_()

italicize

Character or numeric vector specifying which labels to italicize, if any.

Details

The phylo.spindles() function allows the plotting of a phylogeny with spindle diagrams at each of its terminal branches. Various data can be represented (e.g. disparity, abundance, various diversity measures, such as those output by the divDyn package, etc.) depending on the settings for occ and stat, but the function is optimized to plot the results of divdistr_() and does so by default. If another function is used as an argument to stat, it has to be able to take the sequence resulting from xlimits and res as its first, and occ as its 'table' argument and return a vector of the same length as range(xlimits)/res to be plotted. If occ is a list() object containing multiple dataframes, occurrence datasets or taxon range tables are automatically converted to work with abdistr_() or divdistr_() respectively (if the plot contains a phylogeny). If occ is a matrix or data.frame, the x values must already be converted (e.g. using tsconv()) to match the phylogeny.

Value

A plotted phylogeny with spindle diagrams plotted at each of its terminal branches.

Examples

data(archosauria)
data(tree_archosauria)
data(ages_archosauria)
data(diversity_table)
phylo.spindles(tree_archosauria,occ=archosauria,dscale=0.005,ages=ages_archosauria,txt.x=66)
phylo.spindles(tree_archosauria,occ=diversity_table,dscale=0.005,ages=ages_archosauria,txt.x=66)