partab.character: Create a Parameter Table from Model Name
In nonmemica: Create and Evaluate NONMEM Models in a Project Context

partab.character

R Documentation

Create a Parameter Table from Model Name

Description

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

Usage

## S3 method for class 'character'
partab(
  x,
  verbose = FALSE,
  lo = "5",
  hi = "95",
  metafile = modelpath(x, "def", ...),
  xmlfile = modelpath(x, "xml", ...),
  ctlfile = modelfile(x, ...),
  bootcsv,
  strip.namespace = TRUE,
  skip = 28,
  check.names = FALSE,
  digits = 3,
  ci = TRUE,
  open = "(",
  close = ")",
  sep = ", ",
  format = TRUE,
  fields = getOption("fields", default = c("symbol", "label", "unit")),
  relative = TRUE,
  percent = relative,
  nonzero = TRUE,
  shrinkage = FALSE,
  correlation = FALSE,
  ...
)

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 (%)
`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
`shrinkage`	whether to include percent shrinkage on random effects
`correlation`	whether to include correlation of random effects (as percent if `percent` is true)
`...`	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

Examples

library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% partab
1001 %>% partab(shrinkage = TRUE, correlation = TRUE)

nonmemica documentation built on Oct. 26, 2024, 1:06 a.m.