phytools (version 2.1-1)

edge.widthMap: Map continuous trait evolution on the tree

Description

Maps a discrete character onto the edges of the tree using variable edge widths.

Usage

edge.widthMap(tree, x, ...)
# S3 method for edge.widthMap
plot(x, max.width=0.9, legend="trait value", ...)

Value

edge.widthMap returns an object of class "edge.widthMap".

plot.edge.widthMap can be used to plot this object.

Arguments

tree

object of class "phylo".

x

a numerical vector of phenotypic trait values for species. names(x) should contain the species names and match tree$tip.label. Or, for plot.edge.widthMap, an object of class "edge.widthMap".

max.width

maximum edge width in plot units.

legend

label for the plot legend.

...

optional arguments - especially for the plot method. Perhaps the most important of these is min.width, which defaults to 0 but could probably be increased for many datasets and graphical devices. Other arguments are passed internally to plotTree.

Author

Liam Revell

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

contMap, fastAnc

Examples

## load data from Garland et al. (1992)
data(mammal.tree)
data(mammal.data)
## extract character of interest
ln.bodyMass<-log(setNames(mammal.data$bodyMass,
    rownames(mammal.data)))
## create "edge.widthMap" object
mammal.ewMap<-edge.widthMap(mammal.tree,ln.bodyMass,
    min.width=0.05)
## plot it
plot(mammal.ewMap,legend="log(body mass)")
par(mar=c(5.1,4.1,4.1,2.1)) ## reset margins to default