residual_scatter: Scatter residual plots

View source: R/pmx-plots-scatter.R

residual_scatterR Documentation

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 June 18, 2022, 1:05 a.m.