eta.cov.GOF {nonmem2R}

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)