nmxml: 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
)

Value

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

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.

Examples

Run this code


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