Import model estimates from a NONMEM xml file

Source: R/nmxml.R

Import model estimates from a NONMEM xml file

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.

Value

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

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.

See also

nmext

Examples


if(requireNamespace("xml2")) {
  proj <- system.file("nonmem", package = "mrgsolve")
  mrgsolve:::nmxml(run = 1005, project = proj)
}
#> $theta
#> $theta$THETA1
#> [1] 9.507886
#> 
#> $theta$THETA2
#> [1] 22.79099
#> 
#> $theta$THETA3
#> [1] 0.07143366
#> 
#> $theta$THETA4
#> [1] 3.474506
#> 
#> $theta$THETA5
#> [1] 113.2767
#> 
#> $theta$THETA6
#> [1] 1.024354
#> 
#> $theta$THETA7
#> [1] 1.192118
#> 
#> 
#> $omega
#> $...
#>            [,1]        [,2]        [,3]
#> 1:   0.21387884  0.12077020 -0.01162777
#> 2:   0.12077020  0.09451047 -0.03720637
#> 3:  -0.01162777 -0.03720637  0.04656315
#> 
#> 
#> $sigma
#> $...
#>           [,1]      [,2]
#> 1:  0.04917071 0.0000000
#> 2:  0.00000000 0.2017688
#> 
#> 
#> $file
#> [1] "/tmp/Rtmp5Jqf1L/temp_libpath1efe701eb88814/mrgsolve/nonmem/1005/1005.xml"
#> 
#> attr(,"class")
#> [1] "NMXMLDATA"