Introduction
Herein is a demo of functions for GOF plots in the nonmem2R R-package. The functions provide building blocks for doing GOF plots with flexibility for user specific formatting and or layout. There are also functions for combining single GOF’s into one and there are basic GOF’s combining a specific type of GOF’s into one single plot, e.g. the function basic.GOF4 which generated the example below.
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
## `geom_smooth()` using formula 'y ~ x'
The GOF functions build on ggplot2 and as far as possible return an ggplot-object that can be further modified by adding ggplot formatting. However, some functions use grid.arrange from the R-package gridExtra to combine different type of GOF’s. These functions plot the combined set of GOF’s but does not return an ggplot object, and hence the plots can therefore not be easily further modified/formatted. To still provide options to add ggplot formatting these functions have an argument global.ggplot.options which can be used to add extra ggplot functions on each individual GOF before the GOF’s are combined into one graph by grid.arrange.
Formatting of e.g. lines and plot symbols can also be controlled by the argument control and the function GOF.control or using set.GOF.params to affect all GOF’s.
Axis labels are set for most common NONMEM variables, e.g. CWRES is by default labelled “Cond. weighted res” and TIME is by default labelled “Time after first dose(h)”. See examples in section Labels and formatting options with further details on controling axis labels, changing the caption text and other formatting of the GOF plots.
All GOF functions will by default add a caption in the bottom of the graph to indicate date when figure was generated together with the full path to the script. However, this require that the script name has been set using set.script.name, and then the script name will be pasted together with the date and path as derived from getwd. If script name has not been set no caption will be added. Each GOF plot will have a red dashed reference line and blue solid lines are smoother’s representing the actual data.
All functions require a data.frame as input and thus NONMEM output tables, e.g, sdtab, cotab,.., should be loaded prior using the functions, and if using multiple output tables it’s recommenced to just cbind all of them to a single sdtab data.frame.
