MultiScale.simmap {ontophylo}

Multidimensional scaling of character states from one stochastic character map

Description

Performs multidimensional scaling (MDS) based on hamming distances among character state vectors from one stochastic character map.

Usage

MultiScale.simmap(tree.merge, add.noise = NULL)

Arguments

tree.merge

simmap object. A stochastic character map after being processed by the discr_Simmap and merge_tree_cat functions.

add.noise

numeric. A vector of length 2 or NULL. Indicates if noise should be added or not. Useful if there are many identical states occupying the same points in the 2D coordinates of the morphospace plot. The noise is calculated as var(V)*add.noise.

Value

A list of tibbles – Points, Lines, and Edge.map – correponding to tree branch information to plot.

Author(s)

Sergei Tarasov

Examples

data("hym_stm_mds")
# Select a few taxa from main lineages of Hymenoptera.
tax <- c("Xyela", "Tenthredo", "Orussus", "Pimpla",
         "Ceraphron", "Evania", "Pison",
         "Ibalia", "Proctotrupes", "Chiloe") 
drop_tax <- hym_stm_mds$tip.label[!hym_stm_mds$tip.label %in% tax]
hym_stm_mds <- phytools::drop.tip.simmap(hym_stm_mds, drop_tax)
# Get a sample of amalgamated stochastic map (phenome).
tree <- merge_tree_cat(hym_stm_mds)


  # Multidimensional scaling for an arbitrary tree.
  MD <- suppressWarnings(MultiScale.simmap(tree))