xyplot.ext: Plot the Parameter Search History for a NONMEM 7 Run

In metrumrg: Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting

Description

NONMEM7 produces, for run n, the file n.ext, containing the values of parameter estimates at specified iterations. Terminal estimates are included, and possibly standard errrors. This function plots the parameter estimates vs. iteration. 95 percent CI is plotted if standard errors are available. Terminal estimate is indicated.

Usage

xyplotExt(
	x, 
	data = read.table(file, skip = 1, header = TRUE, check.names = FALSE), 
	project = getwd(), 
	rundir = filename(project, x), 
	file = filename(rundir, x, '.ext'), 
	as.table = TRUE, 
	auto.key = TRUE, 
	layout = c(1, 4), 
	scales = list(relation = 'free'), 
	type = 'l', 
	panel = panel.superpose, 
	panel.groups = function(
		x, 
		y, 
		group.number, 
		type,
		...
	){
		if (group.number == 3) type <- 'p'
		panel.xyplot(x = x, y = y, type = type, ...)
	}, 
	...
)

Arguments

x	run name (number)
data	a data.frame representing an *.ext file
project	parent of run directory
rundir	run directory
file	path to .ext file
as.table	passed to xyplot
auto.key	passed to xyplot
layout	passed to xyplot
scales	passed to xyplot
type	passed to xyplot
panel	passed to xyplot
panel.groups	passed to xyplot
...	passed to xyplot

Details

If data is supplied, x,project,rundir,file are irrelevant. data is reshaped, and passed to xyplot with remaining arguments, all of which may be overridden.

Value

a trellis object

Author(s)

Tim Bergsma

References

http://metrumrg.googlecode.com

See Also

• as.pxml.ext

Examples

ext <- c(
'TABLE NO.  1: First Order: Goal Function=MINIMUM VALUE OF OBJECTIVE FUNCTION',
' ITERATION    THETA1       THETA2       THETA3       SIGMA(1,1)   OMEGA(1,1)   OBJ',
'            0  1.70E+0  1.02E-1  2.90E+1  0.00E+0  1.17E+0  11.570086639848398',
'            2  1.78E+0  1.06E-1  3.05E+1  0.00E+0  1.08E+0  9.377909428896904',
'            4  1.91E+0  1.05E-1  3.14E+1  0.00E+0  8.96E-1  8.983605357031118',
'            6  1.94E+0  1.01E-1  3.20E+1  0.00E+0  9.06E-1  8.940731060922468',
'            8  1.93E+0  1.01E-1  3.20E+1  0.00E+0  8.99E-1  8.940110966224346',
'           10  1.94E+0  1.01E-1  3.20E+1  0.00E+0  8.99E-1  8.940101673144566',
'           11  1.94E+0  1.01E-1  3.20E+1  0.00E+0  8.99E-1  8.940101673144566',
'  -1000000000  1.94E+0  1.01E-1  3.20E+1  0.00E+0  8.99E-1  8.940101673144566',
'  -1000000001  6.28E-1  7.36E-3  1.25E+0  0.00E+0  5.44E-1  0.'
)
file <- textConnection(ext)
data <- read.table(file, skip = 1, header = TRUE, check.names = FALSE)
close(file)
xyplotExt(data=data)

metrumrg documentation built on May 2, 2019, 5:55 p.m.