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

Description Usage Arguments Details Value Author(s) References See Also Examples

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
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.