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Plot population overlay goodness-of-fit (GOF) plots

Source: R/plot_popgof.R
plot_popgof.Rd

Plot population overlay goodness-of-fit (GOF) plots

Usage

plot_popgof(
  data,
  time_vars = c(TIME = "TIME", NTIME = "NTIME"),
  output_vars = c(PRED = "PRED", IPRED = "IPRED", DV = "DV"),
  output_colors = c(PRED = "red", IPRED = "green", DV = "blue", OBS = "darkgrey"),
  timeu = "hours",
  grp_var = "ID",
  dose_var = "DOSE",
  loq = NULL,
  loq_method = 0,
  cent = "mean",
  obs_dv = TRUE,
  grp_dv = FALSE,
  dosenorm = FALSE,
  cfb = FALSE,
  ylab = "Concentration",
  log_y = FALSE,
  show_caption = TRUE,
  n_breaks = 8,
  theme = NULL
)

Arguments

data

Input dataset. Must contain required variables for mrgsim_df() other than those handled by other arguments.

time_vars

Names of actual and nominal time variables. Must be named character vector. Defaults is: c(TIME="TIME", NTIME="NTIME").

output_vars

Names of model outputs from model. Must be named character vector. Defaults is: c(PRED= "PRED", IPRED = "IPRED", DV= "DV").

output_colors

Colors for model outputs. Must be named character vector.

Defaults are:

  • PRED= "red"

  • IPRED="green",

  • DV="blue".

  • OBS="darkgrey"

timeu

Character string specifying units for the time variable. Passed to breaks_time and assigned to default x-axis label. Options include:

  • "hours" (default)

  • "days"

  • "weeks"

  • "months"

grp_var

Character string of the variable to map to the group aesthetic. Default is "ID"

dose_var

Character string of the variable to use in dosenormalization when dosenorm = TRUE. Default is "DOSE".

loq

Numeric value of the lower limit of quantification (LLOQ) for the assay. Must be coercible to a numeric if specified. Can be NULL if variable LLOQ is present in data Specifying this argument implies that DV is missing in data where < LLOQ.

loq_method

Method for handling data below the lower limit of quantification (BLQ) in the plot.

Options are:

+ `0` : No handling. Plot input dataset `DV` vs `TIME` as is. (default)
+ `1` : Impute all BLQ data at `TIME` <= 0 to 0 and all BLQ data at `TIME` > 0 to 1/2 x `loq`.
   Useful for plotting concentration-time data with some data BLQ on the linear scale
+ `2` : Impute all BLQ data at `TIME` <= 0 to 1/2 x `loq` and all BLQ data at `TIME` > 0 to 1/2 x `loq`.
   Useful for plotting concentration-time data with some data BLQ on the log scale where 0 cannot be displayed

cent

Character string specifying the central tendency measure to plot.

Options are:

  • Mean only: "mean" (default)

  • Mean +/- Standard Deviation (upper and lower error bar): "mean_sdl"

  • Mean + Standard Deviation (upper error bar only): "mean_sdl_upper"

  • Median only: "median"

  • Median +/- Interquartile Range: median_iqr

  • None: "none"

obs_dv

Logical indicating if observed data points should be shown. Default is TRUE.

grp_dv

Logical indicating if observed data points should be connected within a group (i.e., spaghetti plot). Default is FALSE.

dosenorm

logical indicating if observed data points should be dose normalized. Default is FALSE, Requires variable specified in dose_var to be present in data

cfb

Logical indicating if dependent variable is a change from baseline. Plots a reference line at y = 0. Default is FALSE.

ylab

Character string specifing the y-axis label: Default is "Concentration".

log_y

Logical indicator for log10 transformation of the y-axis.

show_caption

Logical indicating if a caption should be show describing the data plotted

n_breaks

Number of breaks requested for x-axis. Default is 5.

theme

Named list of aesthetic parameters to be supplied to the plot. Defaults can be viewed by running plot_dvtime_theme() with no arguments. Default width_errorbar is 2.5% of maximum NTIME. Defaults for observations updated in plot_popgof as follows:

 +`size_point_obs` = 1.25
 +`linewidth_obs` = 1
 + `alpha_line_obs` = 1

Value

A ggplot2 plot object

Examples

plot_popgof(data_sad_pkfit, output_vars = c(DV = "ODV"), dosenorm = TRUE, ylab = "Dose-norm Conc.")
#> Warning: Removed 205 rows containing non-finite outside the scale range
#> (`stat_summary()`).
#> Warning: Removed 205 rows containing non-finite outside the scale range
#> (`stat_summary()`).
#> Warning: Removed 205 rows containing missing values or values outside the scale range
#> (`geom_point()`).