Plots the locations of the origins of scalars from the postprocessor output of bayestraits. CURRENTLY WORKS ONLY FOR DELTAS.
1 2 3 4 5 6 | 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, ...)
|
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? |
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