Plot a post-hoc tree of all tests or all significant tests on 2x2 discretized contingency tables. See vignettes for examples.
MultiTree(xy, x = NULL, y = NULL, fit, show.all = FALSE,
max.node.size = 5, min.node.size = 2.5, use.pval = NULL,
images.path = NULL, node.name = "node", filename = NULL,
filetype = "pdf")A list (optional), whose first element corresponds to the matrix x as below, and
its second element corresponds to the matrix y as below.
if xy is not specified, x and y need to be assigned. If xy,
x and y are missing or NULL, the tree nodes are blank. If
xy or x and y are provided, nodes are png images of the marginal
scatter plots that are associated with each test.
A matrix (optional), number of columns = dimension of random vector,
number of rows = number of observations. If xy,
x and y are missing or NULL, the tree nodes are blank. If
xy or x and y are provided, nodes are png images of the marginal
scatter plots that are associated with each test.
A matrix (optional), number of columns = dimension of random vector,
number of rows = number of observations. If xy,
x and y are missing or NULL, the tree nodes are blank. If
xy or x and y are provided, nodes are png images of the marginal
scatter plots that are associated with each test.
An object generated by multiFit.
Logical. If TRUE, all tests are shown. If FALSE
only tests who were ranked in each resolution amongst the top M ranking tests
are shown. See ?multiFit for an explanation about the parameter M and see
documentation for further information.
Numeric. Maximal node size. All nodes are scaled between min.node.size and
max.node.size, where larger nodes are associated smaller p-values of the corresponding tests
on 2x2 contingency tables.
Numeric. Minimal node size. All nodes are scaled between min.node.size and
max.node.size, where larger nodes are associated smaller p-values of the corresponding tests
on 2x2 contingency tables.
String, choose between "H" (for Holm), "Hcorrected"
(for Holm on corrected p-values) or "MH" for modified Holm.
If left NULL, the order of preference is "MH", "Hcorrected" and
then "H", according to which is present in the object fit.
String, path to save png images of nodes to. If not
specified, images are saved to tempdir().
String, prefix for file names for nodes pngs.
String, file name for tree output. If left NULL, file name
is prefixed by multiTree and ends with system time. See documentation of
qgraph::qgraph for further information.
String, default is pdf, See documentation of
qgraph::qgraph for further information.
The main output of multiTree is a pdf file with the directed acyclic graph
showing tests as nodes.
In addition, the function returns a list. Its elements are:
qgraph.object, the graphical object generated by the qgraph function. See
the qgraph package documentation for further details.
qgraph.call, the call for the tree generating function. Arguments for
the call: adj, the adjacency matrix, nodes.size, a numeric vector with the
scaled sizes of the nodes, images, the file names of the nodes images (may be
NULL), filename as passed to multiTree and passed over to qgraph,
and filetype as passed to multiTree and passed over to qgraph.
Other elements of the returned list are pvs.attributes, the attributes summarizing the
data and the tests performed as stored in fit, and n.nodes, the number of nodes.