comparetree {networktree}

comparetree

Description

Quickly compares two partitions of a networktree object

Usage

comparetree(
  tree,
  id1 = 2L,
  id2 = 3L,
  transform = "detect",
  highlights = 5,
  plot = FALSE,
  plot.type = c("compare", "subtract"),
  layout = "constrained",
  ...
)

Arguments

tree

a networktree object

id1

the first partition

id2

the second partition

transform

should stored correlation matrices be transformed to partial correlations or graphical lasso? Can be set to "cor", "pcor", or "glasso". Defaults to automatic detection

highlights

the number of comparisons to highlight

plot

plot a comparison of the two partitions?

plot.type

"compare" or "subtract". "compare" plots the two networks side by side. "subtract" subtracts network 2 from network 1, and plots a network where edge weights indicate the difference

layout

layout for the plots. The default "constrained" uses a FR layout from the full dataset

...

additional arguments passed to qgraph

Examples

set.seed(1)
d <- data.frame(trend = 1:200, foo = runif(200, -1, 1))
d <- cbind(d, rbind(
  mvtnorm::rmvnorm(100, mean = c(0, 0, 0),
          sigma = matrix(c(1, 0.5, 0.5, 0.5, 1, 0.5, 0.5, 0.5, 1), ncol = 3)),
  mvtnorm::rmvnorm(100, mean = c(0, 0, 0),
          sigma = matrix(c(1, 0, 0.5, 0, 1, 0.5, 0.5, 0.5, 1), ncol = 3))
))
colnames(d)[3:5] <- paste0("y", 1:3)

## Generate a networktree
tree1 <- networktree(nodevars=d[,3:5], splitvars=d[,1:2])

## Print out the structure
tree1

## Compare any two partitions
comparetree(tree1, id1=2, id2=3, highlights=3)

## Add a comparison plot
comparetree(tree1, id1=2, id2=3, plot=TRUE)