plot_distribution_tree | R Documentation |
This functions plots the posterior distribution of a state in the tree used as base_tree on map_posterior_distribution.
The legend shows the colors representing the incidence of state
given as parameter in the trees analysize in map
. The NA values means that there are no sufficient data to compute the values for the branch given the confidence interval (conf_level
parameter). In other words, the branch is not present in a sufficient number of the analysed trees.
plot_distribution_tree(map, state='all', type='emr', conf_level=95, number_of_ticks=20
, tip_states=NULL, fsize=0.7, ftype="i", lwd=3, tip.label=NULL)
map |
A result of a map_posterior_distribution execution; |
state |
The state to be plotted. NULL means that the program should consider all states. This makes more sense for "muration rate" then other types of plot. |
type |
|
conf_level |
An integer representing the confidence level desired, ranging from 0 to 100. Defaults to 95 percent; |
number_of_ticks |
The number of intervals in which the data will be divided. Defaults to 20; |
tip_states |
tip states as provided to |
fsize |
relative font size for tip labels; |
ftype |
font type - options are "reg", "i" (italics), "b" (bold), or "bi" (bold-italics); |
lwd |
line width for three branches. |
tip.label |
A vector containing the tip names. Defaults to NULL, meaning tip names will be get from the |
Returns the tree plotted, with the data used in the plot stored in tree\$maps
.
Diego Pasqualin dpasqualin@inf.ufpr.br
map_posterior_distribution
sm <- sfreemap(sfreemap.corals.trees, sfreemap.corals.tips, parallel=FALSE)
map <- map_posterior_distribution(sm[[1]], sm, parallel=FALSE)
tree <- plot_distribution_tree(map, state='colonial', tip_states=sfreemap.corals.tips)
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