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Plot Pmetrics Final Cycle Parameter Value Distributions

Source: R/plotPMfinal.R
plot.PM_final.Rd

[Stable]

Plot R6 PM_final objects made by makeFinal and loaded as a field in the PM_result object, e.g. PM_result$final.

Usage

# S3 method for PM_final
plot(
  x,
  formula = NULL,
  line,
  marker = TRUE,
  standardize,
  legend,
  log,
  grid = TRUE,
  xlab,
  ylab,
  zlab,
  title,
  xlim,
  ylim,
  ...
)

Arguments

x

The name of an PM_final data object as a field in a PM_result R6 object, e.g PM_result$final.

formula

An optional formula of the form y ~ x, where y and x are two model parameters to plot in a 3-dimensional bivariate plot. See details.

line

Controls characteristics of lines. This argument maps to plotly line attributes. TRUE will plot default lines. FALSE will suppress lines. If a list, can control many line characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > line to see all the ways the line can be formatted. Most common will be:

  • color Line color.

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

  • width Thickness in points.

Example: line = list(color = "red", dash = "longdash", width = 2) The line argument is used to format:

  • the density line drawn over an NPAG PM_final object. Default is FALSE, which means no density line will be drawn. Use TRUE to draw the default line, which is black, solid, and of width 1, or specify as a list to control these elements, e.g. line = list(color = "red", width = 2, dash = "dash")

  • the drop lines from point to lower surface when a formula is specified to generate a bivariate plot from an NPAG PM_final object. In this case, default is line = TRUE. The default format is black, dashed, and of width 1.

  • the lines drawing the normal distribution of parameter values from an IT2B PM_Final object. Again, here the default is line = TRUE, and the format is black, solid, of width 1. See density. Ignored for IT2B output.

marker

See details for which objects the marker argument controls. 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 Fill color for NPAG bars, marker color for bivariate NPAG plots. Ignored for IT2B plots.

  • symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values. Only relevant for bivariate NPAG plots.

  • size Character size in points. Only relevant for bivariate NPAG plots.

  • opacity Bar fill color for univariate NPAG plots or marker opacity for bivariate NPAG plots. Ignored for IT2B plots. Ranges between 0 (fully transparent) to 1 (fully opaque).

  • line A list of additional attributes governing the outline for bars in univariate NPAG plots or markers in bivariate NPAG plots. Ignored for IT2B plots.

    • color Outline color. Default is "black".

    • width Outline width. Default is 1. Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2))

standardize

Standardize the normal parameter distribution plots from IT2B to the same scale x-axis. Ignored for NPAG output.

legend

Ignored for this plot.

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 the name of the plotted x-variable. Formatting can be controlled, but the text is recommended to not be changed.

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 "Probability" for univariate plots, and the name of the plotted y-variable for bivariate plots. Formatting can be controlled, but the text is recommended to not be changed.

zlab

Only for bivariate plots. Default is "Probability". Can be a list to control formatting or default text, as for xlab and zlab.

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 on plots.

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)

...

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

.

Value

Plots the object.

Details

If formula is omitted, this will generate a marginal plot for each parameter. For NPAG data, this will be a histogram of marginal values for each parameter and the associated probability of that value. For IT2B, this will be a series of normal distributions with mean and standard deviation equal to the mean and standard deviation of each parameter marginal distribution. IF formula IS specified, this will generate one of two plots.

On the other hand, if formula is two parameters, e.g. CL~V, this will generate a bivariate plot. For NPAG data, it will be support point with size proportional to the probability of each point. For IT2B, it will be an elliptical distribution of a bivariate normal distribution centered at the mean of each plotted variable and surrounding quantiles of the bivariate distribution plotted in decreasing shades of grey. Mulitvariate normal density code is borrowed from the mvtnorm package.

See also

PM_final, schema

Other PMplots: plot.MMopt(), plot.PM_cov(), plot.PM_cycle(), plot.PM_data(), plot.PM_model(), plot.PM_op(), plot.PM_pta(), plot.PM_sim(), plot.PM_valid()

Author

Michael Neely

Examples

library(PmetricsData)
# NPAG
NPex$final$plot()


NPex$final$plot(line = TRUE)


NPex$final$plot(Ke ~ V)


# IT2B
ITex$final$plot()


ITex$final$plot(Ke ~ V)