plotShifts: plotShifts

Description Usage Arguments

View source: R/plotShifts.R

Description

Plots the locations of the origins of scalars from the postprocessor output of bayestraits. CURRENTLY WORKS ONLY FOR DELTAS.

Usage

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plotShifts(PP, scalar, threshold = 0, threshold2 = 0, nodecex = 2,
  scaled = "time", scalebar = TRUE, measure = "median",
  excludeones = FALSE, relativetrans = FALSE, nodescaling = TRUE,
  transparency = FALSE, gradientcols = c("dodgerblue", "firebrick1"),
  rate.edges = NULL, colour = "red", colour2 = "green", shp = 21,
  tips = FALSE, ...)

Arguments

PP

The psotprocessor (localscalrPP) output.

scalar

The scalar to find and plot from the post processor - delta/lambda/kappa/node/branch

threshold

Threshold of probability in posterior to display deltas for, defaults to zero (i.e. shows all deltas shaded proportionally to the posterior probability)

nodecex

The scaling factor for the size of the node circles

scaled

Plot the original tree (scaled = "time", the default), or the mean/sclaed tree (scaled = "mean") or plot the tree scaled only by scalars present above the threshold (scaled = "threshold")?

scalebar

Include scale bar?

measure

When plotting "siginficant" tree, what measure of the parameter? Median (default), mode or mean.

relativetrans

If TRUE (defaults to FALSE) the scale of transparency will go from the threshold (totally transparent) to the maximum presence (full opacity).

nodescaling

Scale node symbols according to posterior probability of shift (default).

transparency

Adjust node symbol transparency according to posterior probability? Defaults to FALSE.

gradientcols

A vector of two colours - the min and max colours used when colouring the tree according to percentage time rate scaled (when threshold = 0) or using rate.edges.

rate.edges

Takes a numeric value between 0 and 1. If NULL (default) then node shapes are plotted for a transformation. If equal to zero then node shapes are plotted along with a colour gradient on the branches for rates (if in the posterior), and if set to a threshold then the branches are coloured black/red for whether there is a scalar over the threshold (red) along with node scalars.

colour

The colour to use for the node circles

shp

The shape of the node markers (uses the usual pch index).

tips

Show tip labels?

exludeones

If plotting according to a threshold of significance, should 1s (i.e. no scalar) be excluded from the posterior when calculating average scalar?


hferg/bayestraitr documentation built on May 28, 2019, 8:55 p.m.