comparetree — comparetree • networktree

Quickly compares two partitions of a networktree object

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
#> Network tree object
#> 
#> Model formula:
#> y1 + y2 + y3 ~ trend + foo
#> 
#> Fitted party:
#> [1] root
#> |   [2] trend <= 104
#> |   [3] trend > 104
#> 
#> Number of inner nodes:    1
#> Number of terminal nodes: 2
#> Number of parameters per node: 3
#> Objective function: 791.619

## Compare any two partitions
comparetree(tree1, id1=2, id2=3, highlights=3)
#> $highlights
#>   node1 node2       id1        id2  (id1 - id2)
#> 1    y1    y2 0.5192754 -0.1396285  0.658903871
#> 2    y1    y3 0.5060213  0.4191285  0.086892783
#> 3    y2    y3 0.4634213  0.4709230 -0.007501688
#> 
#> $matrix
#>            y1           y2           y3
#> y1 0.00000000  0.658903871  0.086892783
#> y2 0.65890387  0.000000000 -0.007501688
#> y3 0.08689278 -0.007501688  0.000000000
#> 
#> attr(,"class")
#> [1] "comparetree"

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

#> $highlights
#>   node1 node2       id1        id2  (id1 - id2)
#> 1    y1    y2 0.5192754 -0.1396285  0.658903871
#> 2    y1    y3 0.5060213  0.4191285  0.086892783
#> 3    y2    y3 0.4634213  0.4709230 -0.007501688
#> 4    y1    y1 0.0000000  0.0000000  0.000000000
#> 5    y2    y2 0.0000000  0.0000000  0.000000000
#> 
#> $matrix
#>            y1           y2           y3
#> y1 0.00000000  0.658903871  0.086892783
#> y2 0.65890387  0.000000000 -0.007501688
#> y3 0.08689278 -0.007501688  0.000000000
#> 
#> attr(,"class")
#> [1] "comparetree"