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Plot a visual predictive check (VPC) with exact time bins

Source: R/plot_vpc_exactbins.R
plot_vpc_exactbins.Rd

plot_vpc_exactbins() is a wrapper function for vpc::vpc() that returns a ggplot2 object.

Usage

plot_vpc_exactbins(
  sim,
  pcvpc = FALSE,
  time_vars = c(TIME = "TIME", NTIME = "NTIME"),
  output_vars = c(PRED = "PRED", IPRED = "IPRED", SIMDV = "SIMDV", OBSDV = "OBSDV"),
  loq = NULL,
  strat_var = NULL,
  irep_name = "SIM",
  min_bin_count = 1,
  show_rep = TRUE,
  lower_bound = 0,
  shown = NULL,
  theme = NULL,
  timeu = "hours",
  n_breaks = 8,
  ...
)

Arguments

sim

Input dataset. Must contain the following variables: "ID", "TIME"

pcvpc

logical for prediction correction. Default is FALSE.

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").

loq

Numeric value of the lower limit of quantification (LLOQ) for the assay. Passed to lloq argument of vpc::vpc(). Specifying this argument implies that OBSDV is missing in sim where < LLOQ.

strat_var

Character string of stratification variable passed to stratify argument of vpc::vpc(). Currently, only a single stratifying variable is supported.

irep_name

Name of replicate variable in data. Must be a string. Default is "SIM".

min_bin_count

Minimum number of quantifiable observations in exact bin for inclusion in binned plot layers. This argument drops small bins from summary statistic calculation but retains these observations in the observed data points.

show_rep

Display number of replicates as a plot caption. Default is TRUE.

lower_bound

Lower bound of the dependent variable for prediction correction. Default is 0.

shown

Named list of logicals specifying which layers to include on the plot. Passed to show argument of vpc::vpc().

Defaults are:

  • Observed points: obs_dv = TRUE.

  • Observed quantiles: obs_ci = TRUE

  • Simulated inter-quantile range:pi = FALSE

  • Simulated inter-quantile area: pi_as_area = FALSE

  • Simulated Quantile CI: pi_ci = TRUE

  • Observed Median: obs_median = TRUE

  • Simulated Median: sim_median = FALSE

  • Simulated Median CI: sim_median_ci = TRUE

theme

Named list of aesthetic parameters for the plot.Passed to vpc_theme arumgent of vpc::vpc(). Defaults can be obtained by running vpc::new_vpc_theme() with no arguments.

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"

n_breaks

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

...

Other arguments passed to vpc::vpc().

Value

A list containing calculated VPC information (when vpcdb=TRUE), or a ggplot2 object (default)

Examples

model <- model_mread_load(model = "model")
#> Loading model from cache.
simout <- df_mrgsim_replicate(data = data_sad, model = model, replicates = 100,
dv_var = "ODV",
num_vars = c("CMT", "EVID", "MDV", "NTIME", "LLOQ", "WTBL", "FOOD"),
char_vars = c("USUBJID", "PART"),
irep_name = "SIM")

vpc_plot <- plot_vpc_exactbins(
sim = simout,
pcvpc = TRUE,
pi = c(0.05, 0.95),
ci = c(0.05, 0.95),
loq = 1)
#> Joining with `by = join_by(NTIME, CMT)`
#> Joining with `by = join_by(NTIME, CMT)`
#> Prediction-correction cannot be used together with censored data (<LLOQ or >ULOQ). VPC plot will be shown for non-censored data only!
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the vpc package.
#>   Please report the issue to the authors.