Get THETA, OMEGA and SIGMA from a completed NONMEM run

Get THETA, OMEGA and SIGMA from a completed NONMEM run

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

Arguments

run	run number
project	project directory
file	the complete path to the run.xml file
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
...	not used

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.

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
#> 
#> 
#> attr(,"class")
#> [1] "NMXMLDATA"