dataSynthesis: Build a Standard Plotting Data Set for a Given NONR Run
In metrumresearchgroup/metrumrg: Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting

Description Usage Arguments Value Author(s) References See Also

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.

  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),
	...
)

`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