eta.cov.GOF: Covariate and pairs ETA GOFs

In nonmem2R: Loading NONMEM Output Files with Functions for Visual Predictive Checks (VPC) and Goodness of Fit (GOF) Plots

Covariate and pairs ETA GOFs

Description

ETA's vs numerical covariates (eta.cov.GOF) and ETA's vs categorical covariates GOF plots on multiple or single pages with reflines, data smoother, and caption added as reurned by get.caption.

eta.pairs.GOF provides a pairs plot of all ETA's.

Usage

eta.cov.GOF(
  data,
  covariates = c("AGE", "BWT"),
  ETA.subset = NULL,
  exclude.zero.ETA = FALSE,
  title = "",
  drop.fixed = TRUE,
  id.column = "ID",
  standardize = TRUE,
  refline = TRUE,
  type = c("all-in-one", "covariate-by-page", "eta-by-page"),
  layout = c("ETAbyROW", "ETAbyCOL"),
  add.loess = TRUE,
  control = GOF.control()
)

eta.cat.GOF(
  data,
  covariates = c("SEXM"),
  ETA.subset = NULL,
  exclude.zero.ETA = FALSE,
  title = "",
  drop.fixed = TRUE,
  id.column = "ID",
  standardize = TRUE,
  refline = TRUE,
  type = c("all-in-one", "covariate-by-page", "eta-by-page"),
  layout = c("ETAbyROW", "ETAbyCOL"),
  add.points = TRUE,
  control = GOF.control()
)

eta.pairs.GOF(
  data,
  ETA.subset = NULL,
  title = "",
  drop.fixed = TRUE,
  id.column = "ID",
  density2D = c("none", "upper", "lower"),
  standardize = TRUE,
  control = GOF.control()
)

Arguments

data	data.frame to plot
covariates	covariates, list of character strings
ETA.subset	index for subset of ETA's to plot. If NULL (default) all ETA's are plotted.
exclude.zero.ETA	If set to TRUE any ETA==0 is excluded before plotting. This option is useful if the model have full shrinkage for subset of individuals e.g. for ETA on ED50 in patents on placebo or on dose==0.
title	title
drop.fixed	drop ETA's that are fixed, i.e. any ETA with the same value in all subjects
id.column	column name that indicate subject identifier
standardize	Standardize all ETA's (e.g. scale to unit variance)
refline	add reference line (default =TRUE) or not (FALSE)
type	do all ETA's and covariates on one page (all-in-one), one page for each covariate (covariate-by-page), or one page for each ETA (eta-by-page)
layout	Layout for ETA's and covariates
add.loess	add loess smoother to plot (TRUE), or not (FALSE)
control	an optional list of control settings. See GOF.control for the names of the settable control values and their effect.
add.points	add jittered points of data (TRUE), or not (FALSE)
density2D	add 2D-density above (upper) or below (lower), or don't add (none)

Examples

# Get path to the example files included in nonmem2R package
file1 <- system.file("extdata", "sdtab999", package = "nonmem2R")
sdtab<-read.table(file=file1,skip=1,header=TRUE)
set.script.name("MyScript.R")
eta.cov.GOF(sdtab,covariates=c("AGE","BWT"))
# Get path to the example files included in nonmem2R package
file1 <- system.file("extdata", "sdtab999", package = "nonmem2R")
sdtab<-read.table(file=file1,skip=1,header=TRUE)
set.script.name("MyScript.R")
eta.cat.GOF(sdtab,covariates=c("SEXM"))
# Get path to the example files included in nonmem2R package
file1 <- system.file("extdata", "sdtab999", package = "nonmem2R")
sdtab<-read.table(file=file1,skip=1,header=TRUE)
set.script.name("MyScript.R")
eta.pairs.GOF(sdtab)

nonmem2R documentation built on May 29, 2024, 8:58 a.m.