Plot a dependent variable versus time

Source: R/plot_dvtime.R

Plot a dependent variable versus time

plot_dvtime(
  data,
  dv_var = c(DV = "DV"),
  time_vars = c(TIME = "TIME", NTIME = "NTIME"),
  timeu = "hours",
  col_var = NULL,
  grp_var = "ID",
  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
)

Arguments

data

Input dataset. Must contain the variables: "ID", "DV" "MDV".

dv_var

Character string of the dependent variable. Default is "DV".

time_vars

Names of actual and nominal time variables. Must be named character vector. Defaults are "TIME" and "NTIME".

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"

col_var

Character string of the name of the variable to map to the color aesthetic.

grp_var

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

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 DVis 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: "mean_sdl"

  • 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 DOSE 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.

Value

A ggplot2 plot object

Examples

data <- dplyr::mutate(data_sad, Dose = factor(DOSE))
plot <- plot_dvtime(data, dv_var = c(DV = "ODV"), cent = "median", col_var = "Dose")
#> Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
#> ℹ Please use the `fun` argument instead.
#> ℹ The deprecated feature was likely used in the pmxhelpr package.
#>   Please report the issue at <https://github.com/ryancrass/pmxhelpr/issues>.
plot
#> 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()`).