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#' [Stable]

Plot PM_valid objects.

Usage

# S3 method for PM_valid
plot(
  x,
  type = "vpc",
  tad = FALSE,
  outeq = 1,
  line = TRUE,
  marker = TRUE,
  legend = FALSE,
  log = FALSE,
  grid = TRUE,
  xlab,
  ylab,
  title,
  xlim,
  ylim,
  ...
)

Arguments

x

The name of an PM_valid data object generated by the make_valid fundtion, which is usually called by the $validate method for PM_result objects.

type

Default is "vpc" for a visual predictive check, but could be "pcvpc" for a prediction-corrected visual predictive check, or "npde" for a normalized prediction distribution error analysis/plot. Choosing npde will call npde::plot.NpdeObject. To modify this plot, supply argmuents as a named list: npde = (...). Available arguments are in the user manual for the npde package.

tad

Boolean operator to use time after dose rather than time after start. Default is FALSE.

outeq

Which output equation to plot. Default is 1.

line

A list of three elements $upper, $mid, and $lower, each of which controls characteristics of corresponding quantiles. The arguments to each of these list elements map to several plotly attributes. Each can be a boolean value or a list. TRUE will plot default characteristics. FALSE will suppress quantile plots. The elements of the list for each argument are as follows:

  • value The quantile value. Default for lower is 0.025, mid is 0.5, and upper is 0.975.

  • color The color for both the 95%CI region around simulated quantile vs. time, and the color of the line for the observation quantile vs. time. Default for lower and upper is "dodgerblue" and for mid it is "red".

  • dash The style of the obervation quantile line. See plotly::schema(), traces > scatter > attributes > line > dash > values. Default for lower and upper is "dash" and for mid it is "solid".

  • width Default is 1 for lower, mid, and upper.

  • opacity The opacity of the 95%CI region around simulated quantile vs. time. Default is 0.4 for lower, mid and upper, but can range between 0 (fully transparent) to 1 (fully opaque). Example: line = list(upper = list(value = 0.9, color = "red", dash = "longdash", opacity = 0.5, width = 2))

marker

Controls the plotting symbol for observations. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the marker with default characteristics. FALSE will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:

  • color Marker color.

  • symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values.

  • size Character size in points.

  • opacity Ranging between 0 (fully transparent) to 1 (fully opaque).

  • line A list of additional attributes governing the outline for filled shapes, most commonly color and width.

Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2))

legend

Controls display of legend. This argument maps to the plotly layout showlegend and legend arguments. It is either a boolean operator (most common) or a list of parameters to be supplied to plotly. See plotly::schema() > layout > layoutAttributes > legend and showlegend for more details on the available options for formatting. If legend is supplied as a list, the plotly layout > layoutAttributes > showlegend value will be set to TRUE automatically.

Examples:

  • legend = T

  • legend = list(orientation = "h", font = list(color = "blue"))

Default is FALSE

log

Boolean operator to plot the y axis in log base 10. This argument maps to the the yaxis type value in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > type.

Example: log = T

grid

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

  • grid = F

  • grid = list(gridcolor = "black", gridwidth = 2)

xlab

Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

  • xlab = "Time (h)"

  • xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))

  • xlab = list(text = "Time", font = list(bold = T))

Default is "Time" or "Time after dose" if tad = TRUE.

ylab

Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, and ylab is simply a character label, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

Default is "Output".

title

Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element. The default for bold is TRUE.

Examples:

  • title = "Observed vs. Predicted"

  • title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))

Default is to have no title.

xlim

Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > range.

Example: xlim = c(0,1)

ylim

Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > range.

Example: ylim = c(0,100)

...

If type is not "npde", the following apply. Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note that log, xlab, ylab, xlim, and ylim are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. See plotly::schema() layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.

Examples:

  • NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only

  • NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes

. . However, if type is "npde", to modify the appearance of the plot, supply a list of options, npde = list(...). See the documentation for the type argument above.

Value

Plots and returns the plotly object

Details

Generates a plot of outputs (typically concentrations) on the y axis and time on the x axis. If tad was set to TRUE when make_valid was called, then time may be either absolute (default) or time after dose, controlled by the tad argument to this plot function. The following items are included in the plot:

  • Observed outputs. These may be either as measured for type = "vpc" or prediction corrected for type = "pcvpc". Format of the observations is controlled by the marker argument. The default is list(color = "black", symbol = "circle-open", size = 8).

  • Quantiles vs. time for observations. These are plotted by default as dashed blue lines for the 2.5th and 97.5th percentiles and a solid red line for the median. Formatting and the value for each quantile can be controlled with the upper, mid, and lower arguments.

  • 95% CI around the same quantiles of combined simulations from each subject. The values and formatting for these quantile CIs are the same as for the observations, and also controlled with the upper, mid, and lower arguments.

Good vpc/pcvpc plots are considered to be those where the quantile lines for the oberservations lie within the 95%CI quantile regions for simulations, indicated that the model is "centered" on the data and faithfully captures the variability in the data. For an npde plot, one expects to see approximately normally distributed normalized prediction errors.

Author

Michael Neely

Examples

library(PmetricsData)
# VPC
NPex_val$valid$plot()

# pcVPC
NPex_val$valid$plot(type = "pcvpc")

# modify median line and marker
NPex_val$valid$plot(
  line = list(mid = list(color = "orange", dash = "dashdot")),
  marker = list(
    color = "blue", size = 12, symbol = "diamond",
    line = list(color = "navy")
  )
)