Basic 4- and 6-panel GOF

basic.GOF4 provides a 4-panel GOF plot showing
i) Observations (DV) vs population predictions (PRED)
ii) Observations (DV) vs individual predictions (IPRED)
iii) sqrt(abs(CWRES)) vs individual predictions (IPRED), and
iV) CWRES vs TIME or other columns as set by idv

basic.GOF6 provides 2 additional GOF's showing histogram and qqnorm GOF's for CWRES.

Caption is added as reurned by get.caption

basic.GOF4(
  data,
  residual = "CWRES",
  idv1 = "IPRED",
  idv2 = "TIME",
  title = "",
  color = "",
  log.scale = FALSE,
  global.ggplot.options = NULL,
  refline = TRUE,
  add.loess = TRUE,
  control = GOF.control()
)

basic.GOF6(
  data,
  residual = "CWRES",
  idv1 = "IPRED",
  idv2 = "TIME",
  title = "",
  color = "",
  log.scale = FALSE,
  global.ggplot.options = NULL,
  refline = TRUE,
  add.loess = TRUE,
  bins = NA,
  control = GOF.control()
)

Arguments

data

data.frame to plot

residual

column name for residuals, default="CWRES"

idv1

independent variable for plot of sqrt of absolute CWRES

idv2

independent variable for plot of CWRES

title

title

color

data columns to set different colors in plot, interpreted as factor

log.scale

use log scale for DV, IPRED and PRED (TRUE) or normal scale (FALSE)

global.ggplot.options

ggplot option added to each ggplot before plotting/returning object

refline

add reference line (default =TRUE) or not (FALSE)

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.

bins

number of histogram bins, if NA, bins are set using Sturges' formula

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")
## Example 4 panel basic GOF
basic.GOF4(subset(sdtab,DV>0),idv2="TAPD")
#> `geom_smooth()` using formula = 'y ~ x'
#> `geom_smooth()` using formula = 'y ~ x'
#> `geom_smooth()` using formula = 'y ~ x'
#> Warning: The following aesthetics were dropped during statistical transformation: x and
#> y.
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?
#> `geom_smooth()` using formula = 'y ~ x'
#> `geom_smooth()` using formula = 'y ~ x'

## Example 6 panel basic GOF
basic.GOF6(subset(sdtab,DV>0),idv1="TAPD",idv2="PRED")
#> `geom_smooth()` using formula = 'y ~ x'
#> `geom_smooth()` using formula = 'y ~ x'
#> `geom_smooth()` using formula = 'y ~ x'
#> Warning: `stat(density)` was deprecated in ggplot2 3.4.0.
#> ℹ Please use `after_stat(density)` instead.
#> ℹ The deprecated feature was likely used in the nonmem2R package.
#>   Please report the issue to the authors.
#> Warning: The following aesthetics were dropped during statistical transformation: x and
#> y.
#> ℹ This can happen when ggplot fails to infer the correct grouping structure in
#>   the data.
#> ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
#>   variable into a factor?
#> `geom_smooth()` using formula = 'y ~ x'
#> `geom_smooth()` using formula = 'y ~ x'