Parameter correlation/covariance matrix heatmap

Visualizes the parameter correlation (or covariance) matrix as a heatmap, filling a gap left behind in translation from xpose4. Values come from get_cov_matrix(), which has built-in support for nonmem and nlmixr2 models; rendering is done with the generic xplot_heatmap() template.

Usage

cormat(
  xpdb,
  type = c("correlation", "covariance"),
  .problem = NULL,
  .subprob = NULL,
  .method = NULL,
  drop_fixed = TRUE,
  digits,
  title,
  subtitle = "Ofv: @ofv, Condition number: @condn",
  caption = "@dir",
  tag = NULL,
  quiet,
  ...
)

Arguments

xpdb: <xp_xtras> or <xpose_data> object
type: <character> Either "correlation" (default) or "covariance"
.problem: <numeric> Problem number to use. Uses the xpose default if not provided.
.subprob: <numeric> Subproblem number to use. Uses the xpose default if not provided.
.method: <character> Method to use. Uses the xpose default if not provided.
drop_fixed: <logical> Passed to get_cov_matrix()
digits: Number of significant digits to display in cell labels. Defaults to reportable_digits()
title: Plot title
subtitle: Plot subtitle
caption: Plot caption
tag: Plot tag
quiet: Silence extra debugging output
...: Additional aesthetics, passed to xplot_heatmap()

Value

The desired plot

Details

Only the upper triangle of the matrix is drawn, as it is symmetric. Fixed-effect (theta) and random-effect (omega/sigma) parameters are both included for nonmem models, when available and not fixed. For nlmixr2 models, only fixed effects are included, as nlmixr2 does not report uncertainty for random effects. See get_cov_matrix() for further details on availability; if the covariance step was not run, or did not complete successfully, an informative error is raised.

Examples

cormat(xpdb_x)
#> Returning data from run001.cor, $prob no.1, subprob no.1, method foce

cormat(xpdb_x, type = "covariance")
#> Returning data from run001.cov, $prob no.1, subprob no.1, method foce