summary.rgcca {RGCCA}

Summary of a fitted object from the RGCCA package

Description

'summary.rgcca()' summarizes a fitted RGCCA object. Some information about the model are displayed like model parameters or criterion.

'summary.rgcca_cv()' summarizes a fitted rgcca_cv object. Parameters of the analysis, tuning parameters and statistics for each set of parameters are displayed.

'summary.rgcca_permutation()' summarizes a fitted rgcca_permutation object. Parameters of the analysis, tuning parameters and statistics for each set of parameters are displayed.

'summary.rgcca_bootstrap()' summarizes a fitted rgcca_bootstrap object. Parameters of the analysis and bootstrap statistics are displayed.

'summary.rgcca_stability()' calls 'summary.rgcca()' on the fitted RGCCA model returned by 'rgcca_stability()'.

Usage

## S3 method for class 'rgcca'
summary(object, ...)

## S3 method for class 'rgcca_cv'
summary(object, type = c("sd", "quantile"), ...)

## S3 method for class 'rgcca_permutation'
summary(object, ...)

## S3 method for class 'rgcca_bootstrap'
summary(
  object,
  block = seq_along(object$rgcca$call$blocks),
  comp = 1,
  type = c("weights", "loadings"),
  empirical = TRUE,
  display_order = FALSE,
  adj.method = "fdr",
  ...
)

## S3 method for class 'rgcca_stability'
summary(object, ...)

Arguments

object

An object to be summarized (output of functions rgcca, rgcca_cv, rgcca_permutation, rgcca_bootstrap, or rgcca_stability).

...

Further arguments passed to other methods (for the displaying of matrices).

type

A character string indicating the type of the summarized object (see details).

block

A numeric corresponding to the block(s) to summarize.

comp

A numeric vector indicating the component(s) to consider.

empirical

A logical value indicating if the bootstrap confidence intervals and p-values are derived from the empirical distribution. (default: TRUE)

display_order

A logical value for ordering the variables. If TRUE, variables are ordered from highest to lowest absolute value. If FALSE, the block order is used. Default is TRUE.

adj.method

A string indicating the method used to adjust the p-values. It must be a method handled by the p.adjust function. Default is "fdr".

Details

Argument type can take two values in 'summary.cval':

• "sd" (default): mean values of the cross-validated scores are reported, as well as means plus or minus standard deviations.

• "quantiles": median values, 25% and 75% quantiles of the cross-validated scores are reported.

Argument type can take two values in 'summary.bootstrap':

• "weights" (default): statistics about the block-weight vectors are reported.

• "loadings": statistics about the block-loading vectors are reported.

Value

none

Examples

## Summary of an rgcca object
data(Russett)
blocks <- list(
  agriculture = Russett[, seq(3)],
  industry = Russett[, 4:5],
  politic = Russett[, 6:8]
)
C <- matrix(c(0, 0, 1, 0, 0, 1, 1, 1, 0), 3, 3)
res <- rgcca(blocks,
  connection = C, ncomp = rep(2, 3), tau = c(1, 1, 1),
  scheme = "factorial", scale = TRUE, verbose = FALSE
)
summary(res)

## Summary of an rgcca_cv object
res <- rgcca_cv(blocks,
  response = 3, method = "rgcca", par_type = "tau",
  par_value = c(0, 0.2, 0.3), n_run = 1, n_cores = 1,
  verbose = TRUE
)
summary(res)

## Summary of an rgcca_permutation object
perm.out <- rgcca_permutation(blocks,
  par_type = "tau",
  n_perms = 5, n_cores = 1,
  verbose = TRUE
)
summary(perm.out)

## Summary of an rgcca_bootstrap object
fit.rgcca <- rgcca(blocks, ncomp = c(2, 1, 2))
boot.out <- rgcca_bootstrap(fit.rgcca, n_boot = 20, n_cores = 2,
                            verbose = TRUE)
summary(boot.out)

## Summary of an rgcca_stability object
fit.sgcca <- rgcca(blocks, sparsity = c(.8, .9, .6))
res <- rgcca_stability(fit.sgcca, n_boot = 10, verbose = TRUE)
summary(res)