VPC based on ui model

vpc_ui(
  fit,
  data = NULL,
  n = 100,
  bins = "jenks",
  n_bins = "auto",
  bin_mid = "mean",
  show = NULL,
  stratify = NULL,
  pred_corr = FALSE,
  pred_corr_lower_bnd = 0,
  pi = c(0.05, 0.95),
  ci = c(0.05, 0.95),
  uloq = NULL,
  lloq = NULL,
  log_y = FALSE,
  log_y_min = 0.001,
  xlab = NULL,
  ylab = NULL,
  title = NULL,
  smooth = TRUE,
  vpc_theme = NULL,
  facet = "wrap",
  labeller = NULL,
  vpcdb = FALSE,
  verbose = FALSE,
  ...
)

# S3 method for nlmixrFitData
vpc(sim, ...)

# S3 method for nlmixrVpc
vpc(sim, ...)

# S3 method for ui
vpc(sim, ...)

Arguments

fit

nlmixr fit object

data

this is the data to use to augment the VPC fit. By default is the fitted data, (can be retrieved by getData), but it can be changed by specifying this argument.

n

Number of VPC simulations. By default 100

bins

either "density", "time", or "data", "none", or one of the approaches available in classInterval() such as "jenks" (default) or "pretty", or a numeric vector specifying the bin separators.

n_bins

when using the "auto" binning method, what number of bins to aim for

bin_mid

either "mean" for the mean of all timepoints (default) or "middle" to use the average of the bin boundaries.

show

what to show in VPC (obs_dv, obs_ci, pi, pi_as_area, pi_ci, obs_median, sim_median, sim_median_ci)

stratify

character vector of stratification variables. Only 1 or 2 stratification variables can be supplied.

pred_corr

perform prediction-correction?

pred_corr_lower_bnd

lower bound for the prediction-correction

pi

simulated prediction interval to plot. Default is c(0.05, 0.95),

ci

confidence interval to plot. Default is (0.05, 0.95)

uloq

Number or NULL indicating upper limit of quantification. Default is NULL.

lloq

Number or NULL indicating lower limit of quantification. Default is NULL.

log_y

Boolean indicting whether y-axis should be shown as logarithmic. Default is FALSE.

log_y_min

minimal value when using log_y argument. Default is 1e-3.

xlab

label for x axis

ylab

label for y axis

title

title

smooth

"smooth" the VPC (connect bin midpoints) or show bins as rectangular boxes. Default is TRUE.

vpc_theme

theme to be used in VPC. Expects list of class vpc_theme created with function vpc_theme()

facet

either "wrap", "columns", or "rows"

labeller

ggplot2 labeller function to be passed to underlying ggplot object

vpcdb

Boolean whether to return the underlying vpcdb rather than the plot

verbose

show debugging information (TRUE or FALSE)

...

Args sent to rxSolve

sim

this is usually a data.frame with observed data, containing the independent and dependent variable, a column indicating the individual, and possibly covariates. E.g. load in from NONMEM using read_table_nm. However it can also be an object like a nlmixr or xpose object

Value

Simulated dataset (invisibly)

Author

Matthew L. Fidler