vpc_cens: VPC function for left- or right-censored data (e.g. BLOQ...

Description Usage Arguments Value See Also Examples

View source: R/vpc_cens.R

Description

Creates a VPC plot from observed and simulation data for censored data. Function can handle both left- (below lower limit of quantification) and right-censored (above upper limit of quantification) data.

Usage

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vpc_cens(
  sim = NULL,
  obs = NULL,
  psn_folder = NULL,
  bins = "jenks",
  n_bins = 8,
  bin_mid = "mean",
  obs_cols = NULL,
  sim_cols = NULL,
  software = "auto",
  show = NULL,
  stratify = NULL,
  stratify_color = NULL,
  ci = c(0.05, 0.95),
  uloq = NULL,
  lloq = NULL,
  plot = FALSE,
  xlab = "Time",
  ylab = "Probability of <LOQ",
  title = NULL,
  smooth = TRUE,
  vpc_theme = NULL,
  facet = "wrap",
  labeller = NULL,
  vpcdb = FALSE,
  verbose = FALSE
)

Arguments

sim

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

obs

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

psn_folder

instead of specifying "sim" and "obs", specify a PsN-generated VPC-folder

bins

either "density", "time", or "data", or a numeric vector specifying the bin separators.

n_bins

number of bins

bin_mid

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

obs_cols

observation dataset column names (list elements: "dv", "idv", "id", "pred")

sim_cols

simulation dataset column names (list elements: "dv", "idv", "id", "pred")

software

name of software platform using (e.g. nonmem, phoenix)

show

what to show in VPC (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.

stratify_color

variable to stratify and color lines for observed data. Only 1 stratification variables can be supplied.

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.

plot

Boolean indicating whether to plot the ggplot2 object after creation. Default is FALSE.

xlab

ylab as numeric vector of size 2

ylab

ylab as numeric vector of size 2

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)

Value

a list containing calculated VPC information, and a ggplot2 object

See Also

sim_data, vpc, vpc_tte, vpc_cat

Examples

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## See vpc.ronkeizer.com for more documentation and examples
library(vpc)

vpc_cens(sim = simple_data$sim, obs = simple_data$obs, lloq = 30)
vpc_cens(sim = simple_data$sim, obs = simple_data$obs, uloq = 120)

vpc documentation built on Jan. 16, 2021, 5:44 p.m.