nmxml: Import model estimates from a NONMEM xml file

In mrgsolve: Simulate from ODE-Based Models

Import model estimates from a NONMEM xml file

Description

Import model estimates from a NONMEM xml file

Usage

nmxml(
  run = numeric(0),
  project = character(0),
  file = character(0),
  path = character(0),
  root = c("working", "cppfile"),
  theta = TRUE,
  omega = TRUE,
  sigma = TRUE,
  olabels = NULL,
  slabels = NULL,
  oprefix = "",
  sprefix = "",
  tname = "THETA",
  oname = "...",
  sname = "...",
  index = "last",
  xpath = ".//nm:estimation",
  env = NULL
)

Arguments

run	run number.
project	project directory.
file	deprecated; use path instead.
path	the complete path to the run.xml file.
root	the directory that path and project are relative to; this is currently limited to the working directory or cppdir, the directory where the model file is located.
theta	logical; if TRUE, the ⁠$THETA⁠ vector is returned.
omega	logical; if TRUE, the ⁠$OMEGA⁠ matrix is returned.
sigma	logical; if TRUE, the ⁠$SIGMA⁠ matrix is returned.
olabels	labels for ⁠$OMEGA⁠.
slabels	labels for ⁠$SIGMA⁠.
oprefix	prefix for ⁠$OMEGA⁠ labels.
sprefix	prefix for ⁠$SIGMA⁠ labels.
tname	name for ⁠$THETA⁠.
oname	name for ⁠$OMEGA⁠.
sname	name for ⁠$SIGMA⁠.
index	the estimation number to return; "last" will return the last estimation results; otherwise, pass an integer indicating which estimation results to return.
xpath	xml path containing run results; if the default doesn't work, consider using ⁠.//estimation⁠ as an alternative; see details.
env	internal use only.

Details

If run and project are supplied, the .xml file is assumed to be located in run.xml, in directory run off the project directory. If file is supplied, run and project arguments are ignored.

This function requires that the xml2 package be installed and loadable. If requireNamespace("xml2") fails, an error will be generated.

nmxml usually expects to find run results in the xpath called ⁠.//nm:estimation⁠. Occasionally, the run results are not stored in this namespace but no namespaces are found in the xml file. In this case, the user can specify the xpath containing run results. Consider trying ⁠.//estimation⁠ as an alternative if the default fails.

Value

A list with theta, omega and sigma elements, depending on what was requested.

See Also

nmext

Examples

if(requireNamespace("xml2")) {
  proj <- system.file("nonmem", package = "mrgsolve")
  mrgsolve:::nmxml(run = 1005, project = proj)
}

mrgsolve documentation built on Oct. 18, 2024, 5:12 p.m.