Skip to contents

Plot a dependent variable versus time

Source: R/plot_dvtime.R
plot_dvtime.Rd

Plot a dependent variable versus time

Usage

plot_dvtime(
  data,
  dv_var = "DV",
  time_var = "TIME",
  ntime_var = "NTIME",
  col_var = NULL,
  id_var = NULL,
  dose_var = "DOSE",
  loq = NULL,
  loq_method = 0,
  cent = c("mean", "mean_sdl", "mean_sdl_upper", "median", "median_iqr", "none"),
  dosenorm = FALSE,
  ref = NULL,
  log_y = FALSE,
  show_caption = TRUE,
  theme = NULL
)

Arguments

data

Input dataset.

dv_var

Column containing the dependent variable. Accepts bare names or strings. Default is DV.

time_var

Column containing the actual time variable. Accepts bare names or strings. Default is TIME.

ntime_var

Column containing the nominal time variable. Accepts bare names or strings. Default is NTIME.

col_var

Column to map to the color aesthetic. Accepts bare names or strings. Default is NULL.

id_var

Column to group observations for spaghetti lines. Accepts bare names or strings. Default is NULL (no spaghetti lines). Specifying a column (e.g., id_var = ID) enables spaghetti lines connecting observations within each level of the variable.

dose_var

Column to use in dosenormalization when dosenorm = TRUE. Accepts bare names or strings. 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:

+ No handling: `0` or `"none"`, Plot input dataset `DV` vs `TIME` as is. (default)
+ Impute Post-dose: `1` or `"postdose"`, 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
+ Impute All: `2` or `"all"`,Impute all BLQ data 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"

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

ref

Numeric y-intercept for a horizontal reference line, or NULL for no reference line. For example, ref = 0 draws a baseline reference for change-from-baseline data.

log_y

Logical indicator for log10 transformation of the y-axis. Also controls whether the caption reports arithmetic or geometric mean when show_caption = TRUE.

show_caption

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

theme

Theme object created by plot_dvtime_theme(). Defaults can be viewed by running plot_dvtime_theme() with no arguments. Default error bar width is 2.5% of maximum NTIME.

Value

A ggplot2 plot object

See also

Other exploratory analysis: plot_dvconc(), plot_dvconc_theme(), plot_dvtime_theme()

Examples

data_sad_pk <- dplyr::filter(data_sad, CMT %in% c(1,2))
data <- dplyr::mutate(data_sad_pk, Dose = var_addn(DOSE, ID, sep = "mg"))
plot_dvtime(data, dv_var = ODV, cent = "median", col_var = Dose)
#> Warning: Removed 169 rows containing non-finite outside the scale range
#> (`stat_summary()`).
#> Warning: Removed 169 rows containing non-finite outside the scale range
#> (`stat_summary()`).
#> Warning: Removed 169 rows containing missing values or values outside the scale range
#> (`geom_point()`).