dataSynthesis: Build a Standard Plotting Data Set for a Given NONR Run

In anniejw6/metrumrg: Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting

Description

dataSynthesis scavenges columns from the ‘TAB’ file, the ‘par.TAB’ file, and the underlying dataset (all required), returning just observation records (EVID==0) that are not commented. The second two files are limited to the first record per ID. Columns to scavenge are supplied by grp, cont.cov, cat.cov, par.list, and eta.list. All ‘TAB’ file columns are returned, plus first instance of ‘scavenge’ columns from either the ‘par’ file or the parent data set (in that order) unless already present. Exception: par.list and eta.list items are not sought in the underlying dataset.

Usage

  dataSynthesis(
	run, 
	project=getwd(), 
	logtrans = FALSE,
	grp = NULL, 
	grpnames = NULL,
	cont.cov = NULL,
	cat.cov = NULL,
	par.list = NULL,
	eta.list = NULL,
	missing = -99,
	rundir  = filename(project, run),
	ctlfile = filename(rundir,run,'.ctl'),
	outfile = filename(rundir,run,'.lst'),
	datfile = getdname(ctlfile),
	...
)

Arguments

run	a control stream name, typically integer
project	the directory containing the NONMEM run directories
logtrans	whether to transform the NONMEM output variables DV, PRED, NPRED, CPRED, CPREDI, EPRED, IPRE, IPRED, PREDI, CIPRED, IPREDI, IPRD, and EIPRED. Default: FALSE.
grp	item in NONMEM datafile or output table file that can be used to condition plots generated by PLOTR. Default value is NULL. Example: grp=c('SEX'). Can be more than one, e.g,. grp=c('SEX','TRT').
grpnames	optional vector of names for grp item. Vector length must equal number of conditions in grp and must have an order corresponding to an increasing sort of grp. Default value is NULL. Example: grpnames=c('Male','Female')
cont.cov	vector of continuous covariate names. Names must match those used as column headers in datfile. Values are retrieved from datfile so they do not need to be part of the NONMEM $TABLE step. Default value is NULL. Example: cont.cov=c('AGE','WT','CLCR')
cat.cov	vector of categorical covariate names. Names must match those used as column headers in datfile. Values are retrieved from datfile so they do not need to be part of the NONMEM $TABLE step. Default value is NULL. Example: cat.cov=c('SEX','FOOD')
par.list	vector of NONMEM model parameter names. Values are retrieved from ‘*par.TAB’ created in NONMEM. Default value is NULL. This can be a superset of parameters but only those present in NONMEM output table will be used. Example: par.list=c('CL','V','V2','Q')
eta.list	vector of NONMEM model random effect names. Values are retrieved from ‘*par.TAB’ created in NONMEM. Default value is NULL. This can be a superset of random parameters but only those present in NONMEM output table will be used. Example: eta.list=c('ETA1','ETA2','ETA3','ETA4')
missing	numeric item that defines value used to represent missing items in the NONMEM data file. Default value is '-99'.
ctlfile	Path and filename for the NONMEM control stream (‘*.ctl’).
outfile	Path and filename for the NONMEM output file (‘*.lst’).
datfile	Path and filename for the source dataset, as in DATA record in ‘*.ctl’.
rundir	Path for the NONMEM run directory (‘project/*’).
...	extra arguments

Value

data.frame

Author(s)

Tim Bergsma

References

http://metrumrg.googlecode.com

See Also

• diagnosticPlots

• dataFormat

anniejw6/metrumrg documentation built on May 10, 2019, 11:50 a.m.