as.partab.modelname: Create a Parameter Table from Model Name

In bergsmat/partab: Make a Parameter Table from NONMEM Output

Description

Creates a parameter table from a model name. Pass the project argument or set the project option.

Usage

## S3 method for class 'modelname'
as.partab(x, verbose = FALSE, lo = "5", hi = "95",
  project = if (is.null(opt)) getwd() else opt, opt = getOption("project"),
  rundir = file.path(project, x), metafile = file.path(rundir, paste0(x,
  ".def")), xmlfile = file.path(rundir, paste0(x, ".xml")),
  ctlfile = file.path(rundir, paste0(x, ".ctl")), bootcsv,
  strip.namespace = TRUE, skip = 28, check.names = FALSE, digits = 3,
  ci = TRUE, open = "(", close = ")", sep = ", ", format = TRUE,
  fields = c("symbol", "label", "unit"), relative = TRUE,
  percent = relative, nonzero = TRUE, ...)

Arguments

x	a model name (numeric or character)
verbose	set FALSE to suppress messages
lo	the PsN bootstrap lower confidence limit (%)
hi	the PsN bootstrap upper confidence limit (%)
project	parent directory of model directories
opt	alternative argument for setting project
rundir	specific model directory
metafile	optional metadata for parameter table (see also: fields)
xmlfile	path to xml file
ctlfile	path to control stream
bootcsv	path to PsN bootstrap_results.csv
strip.namespace	whether to strip e.g. nm: from xml elements for easier xpath syntax
skip	number of lines to skip in bootstrap_results.csv
check.names	passed to bootstrap reader
digits	limits numerics to significant digits (use NULL to suppress)
ci	combine bootstrap lo and hi into an enclosed interval
open	first character for bootstrap interval
close	last character for bootstrap interval
sep	separator for bootstrap interval
format	format numerics as character
fields	metadata fields to read from control stream. See details.
relative	transform standard errors to relative standard errors: rse replaces se
percent	if relative is true, express as percent (else ignore): prse replaces se
nonzero	limit random effects to those with nonzero estimates
...	passed to other functions

Details

Normally you can just call the generic. Suitable defaults are supplied, but much customization is supported by means of arguments documented here and in called functions.

Metadata can be added to the parameter table two ways: as markup in the control stream, and as a *.def file in the model directory. See vignette('parameter-table') for details.

Value

object of class partab, data.frame

See Also

as.docx.partab

as.flextable.partab

as.xml_document.modelname

as.bootstrap.modelname

as.nmctl.modelname

write.csv

read.csv

as.csv

Examples

library(magrittr)
options(project = system.file('project/model',package='partab'))
1001 %>% as.partab

bergsmat/partab documentation built on May 12, 2019, 3:09 p.m.