residual_scatter: Scatter residual plots

In ggPMX: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models

Scatter residual plots

Description

Scatter residual plots

DV vs PRED plot

DV vs IPRED plot

IWRES vs IPRED plot

|IWRES| vs IPRED plot

|IWRES| vs TIME plot

IWRES vs TIME plot

NPDE vs TIME plot

NPDE vs PRED plot

NPD vs TIME plot

NPD vs EPRED plot

NPD vs PRED plot

CWRES vs TIME plot

CWRES vs CPRED plot

CWRES vs PRED plot

Usage

residual_scatter(
  sim_blq,
  point,
  is.hline,
  hline,
  dname,
  bloq,
  filter,
  strat.facet,
  facets,
  strat.color,
  trans,
  pmxgpar,
  labels,
  axis.title,
  axis.text,
  ranges,
  is.smooth,
  smooth,
  is.band,
  band,
  is.draft,
  draft,
  is.identity_line,
  identity_line,
  scale_x_log10,
  scale_y_log10,
  color.scales,
  ...
)

pmx_plot_dv_pred(ctr, ...)

pmx_plot_dv_ipred(ctr, ...)

pmx_plot_iwres_ipred(ctr, ...)

pmx_plot_abs_iwres_ipred(ctr, ...)

pmx_plot_abs_iwres_time(ctr, ...)

pmx_plot_iwres_time(ctr, ...)

pmx_plot_npde_time(ctr, ...)

pmx_plot_npde_pred(ctr, ...)

pmx_plot_npd_time(ctr, ...)

pmx_plot_npd_epred(ctr, ...)

pmx_plot_npd_pred(ctr, ...)

pmx_plot_cwres_time(ctr, ...)

pmx_plot_cwres_cpred(ctr, ...)

pmx_plot_cwres_pred(ctr, ...)

Arguments

sim_blq	logical if TRUE uses sim_blq values for plotting. Only for Monolix 2018 and later.
point	list geom_point graphical parameters.
is.hline	logical if TRUE add horizontal line y=0 ( TRUE by default).
hline	list geom_hline graphical parameters.
dname	character name of dataset to be used. User can create his own dataset using set_data and pass it as dname to be plotted.
bloq	pmxBLOQ object created by pmx_bloq. pmx_update parameters
filter	expression filter which will be applied to plotting data.
strat.facet	formula optional stratification parameter by facetting. This split plot by strats(each strat in a facet)
facets	list facet_wrap parameters.
strat.color	character optional stratification parameter by grouping. This will split the plot by group (color) of strat.
trans	character define the transformation to apply on x or y or both variables
pmxgpar	a object of class pmx_gpar possibly the output of the pmx_gpar: Shared basic graphics parameters
labels	list list containing plot and/or axis labels: title, subtitle, x , y
axis.title	list containing element_text attributes to customize the axis title. (similar to ggplot2 axis.title theme)
axis.text	list containing element_text attributes to customize the axis text (similar to ggplot2 axis.text theme)
ranges	list limits of x/y ranges
is.smooth	logical if set to TRUE add smooth layer
smooth	list geom_smooth graphical/smoothing fun parameters
is.band	logical if TRUE add horizontal band
band	list horizontal band parameters. geom_hline graphical parameters.
is.draft	logical if TRUE add draft layer
draft	list draft layer parameters. geom_text graphical parameters.
is.identity_line	logical if TRUE add an identity line
identity_line	listgeom_abline graphical parameters.
scale_x_log10	logical if TRUE use log10 scale for x axis.
scale_y_log10	logical if TRUE use log10 scale for y axis.
color.scales	list define scales parameter in case of strat.color pmx_settings
...	others graphics parameters passed : pmx_gpar internal function to customize shared graphical parameters residual generic object for all residual (scatter) plots . pmx_update function. aess can be used to change time variable within the plot (e.g. aess = list(x="TADQBW")) residual parameters
ctr	pmx controller

Value

ggplot2 object

Examples

# NOTES ######################
# examples are availables for all residual plots:
# - pmx_plot_abs_iwres_ipred
# - pmx_plot_dv_ipred
# - pmx_plot_dv_pred
# - pmx_plot_iwres_ipred
# - pmx_plot_iwres_time
# - pmx_plot_npde_time


# basic use  ---------------------------------------

ctr <- theophylline()
p <- ctr %>% pmx_plot_dv_pred()
## p is a ggplot2 object you can add any layer here
p + ggplot2::theme_minimal()

# update graphical parameter  ----------------------

## update labels
ctr %>% pmx_plot_dv_pred(
  labels = list(title = "DV versus PRED new title")
)

## remove draft
ctr %>% pmx_plot_dv_pred(is.draft = FALSE)

## remove horizontal line
ctr %>% pmx_plot_dv_pred(is.hline = FALSE)

## custom point aes and static parameters
## we can customize any geom_point parameter
ctr %>% pmx_plot_dv_pred(
  point = list(aes(alpha = DV), color = "green", shape = 4)
)



# stratification  ----------------------------------

## continuous stratification
ctr %>% pmx_plot_dv_pred(strat.color = ~WT0)
## categorical stratification
ctr %>% pmx_plot_dv_pred(strat.facet = ~SEX)
## using formula notation
ctr %>% pmx_plot_dv_pred(strat.facet = STUD~SEX)

# subsetting  --------------------------------------

## we can use any expression involving the data
ctr %>% pmx_plot_dv_pred(filter = DV > mean(DV) & PRED < median(PRED))
## filter and stratify
ctr %>% pmx_plot_dv_pred(filter = SEX == 1, strat.facet = ~SEX)


# transformation  --------------------------------------

## apply a log transformation in y
ctr %>% pmx_plot_dv_pred(trans = "log10_y")

ggPMX documentation built on July 9, 2023, 7:45 p.m.