networktree {networktree}

networktree: Partitioning of network models

Description

Computes a tree model with networks at the end of branches. Can use model-based recursive partitioning or conditional inference.

Wraps the mob() and ctree() functions from the partykit package.

Usage

networktree(...)

## Default S3 method:
networktree(
  nodevars,
  splitvars,
  method = c("mob", "ctree"),
  model = "correlation",
  transform = c("cor", "pcor", "glasso"),
  na.action = na.omit,
  weights = NULL,
  ...
)

## S3 method for class 'formula'
networktree(
  formula,
  data,
  transform = c("cor", "pcor", "glasso"),
  method = c("mob", "ctree"),
  na.action = na.omit,
  model = "correlation",
  ...
)

Arguments

...

additional arguments passed to mob_control (mob) or ctree_control (ctree)

nodevars

the variables with which to compute the network. Can be vector, matrix, or dataframe

splitvars

the variables with which to test split the network. Can be vector, matrix, or dataframe

method

"mob" or "ctree"

model

can be any combination of c("correlation", "mean", "variance") splits are determined based on the specified characteristics

transform

should stored correlation matrices be transformed to partial correlations or a graphical lasso for plotting? Can be set to "cor" (default), "pcor", or "glasso"

na.action

a function which indicates what should happen when the data contain missing values (NAs).

weights

weights

formula

A symbolic description of the model to be fit. This should either be of type y1 + y2 + y3 ~ x1 + x2 with node vectors y1, y2, and y3 or y ~ x1 + x2 with a matrix response y. x1 and x2 are used as partitioning variables.

data

a data frame containing the variables in the model

References

Jones, P.J., Mair, P., Simon, T., Zeileis, A. (2020). Network trees: A method for recursively partitioning covariance structures. Psychometrika, 85(4), 926-945. https://doi.org/10.1007/s11336-020-09731-4

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)

## Now use the function
tree1 <- networktree(nodevars=d[,3:5], splitvars=d[,1:2])

## Formula interface
tree2 <- networktree(y1 + y2 + y3 ~ trend + foo, data=d)

## plot 
plot(tree2)
plot(tree2, terminal_panel = "box")
plot(tree2, terminal_panel = "matrix")


## Conditional version
tree3 <- networktree(nodevars=d[,3:5], splitvars=d[,1:2], 
                     method="ctree")

## Change control arguments
tree4 <- networktree(nodevars=d[,3:5], splitvars=d[,1:2],
                     alpha=0.01)