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Plot Cycle Information

Source: R/plotPMcycle.R
plot.PM_cycle.Rd

[Stable]

Plot PM_cycle objects. These objects are created by makeCycle as part of a PM_result object when PM_load is run.

Usage

# S3 method for PM_cycle
plot(
  x,
  line = TRUE,
  marker = TRUE,
  colors,
  linetypes,
  omit,
  grid = TRUE,
  xlab,
  ylab,
  ...
)

Arguments

x

The name of a PM_cycle object, e.g. PmetricsData::NPex$cycle.

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) Default = list(color = "dodgerblue", width = 2, dash = "solid"). Note The width will apply to all plots, but color and dash will only apply to the first three plots (log-likelihood, AIC, gamma/lambda). Use colors and linetypes below to control the appearance of the line traces for the normalized plots, because each of those traces is mapped to a parameter.

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)) Here, the observation controlled is the value of a given trace at a specific cycle number. Default = list(symbol = "circle", color = "dodgerblue", size = 4). Note the marker color for the normalized parameter value plots will be controlled by the colors parameter below, but size and symbol will apply to all plots.

colors

to use for normalized parameter value line traces. This can be a palette or a vector of colors. For accepted palette names see RColorBrewer::brewer.pal.info. Examples include "BrBG", or "Set2". An example vector could be c("red", "green", "blue"). It is not necessary to specify the same number of colors parameters to be plotted, as colors will be interpolated to generate the correct number. The default when color is not specified is the "Set2" palette.

linetypes

to use for normalized parameter value line traces. See plotly::schema(), traces > scatter > attributes > line > dash > values. An example vector could be c("solid", "dash", "longdash"). It is not necessary to specify the same number of linetype parameters to be plotted, as they will be recycled to generate the correct number. The default when linetypes is not specified is "solid".

omit

Decimal between 0 and 1 specifying the proportion of "burn-in" cycles to omit from the plots. If missing, the first 20% will be omitted.

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

Controls the formatting of the x-axis label. The text is fixed by the function and cannot be altered. 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 = list(bold = F, font = list(color = "red", family = "Arial", size = 10))

  • xlab = list(font = list(bold = T))

ylab

Format 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, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

...

Additional R plotting parameters.

Value

Plots a panel with the following windows: -2 times the log-likelihood at each cycle, gamma/lambda at each cycle; Akaike Information Criterion at each cyle and Bayesian (Schwartz) Information Criterion at each cycle, the mean parameter values at each cycle (normalized to starting values); the normalized standard deviation of the population distribution for each parameter at each cycle; and the normalized median parameter values at each cycle.

See also

makeCycle, PM_result, schema

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

Author

Michael Neely

Examples

library(PmetricsData)
NPex$cycle$plot()


NPex$cycle$plot(omit = 0, marker = list(symbol = "cross"), line = list(width = 1))


NPex$cycle$plot(
  linetypes = "dash", colors = "Blues", marker = list(size = 1),
  line = list(width = 3)
)


NPex$cycle$plot(
  grid = FALSE,
  xlab = list(bold = FALSE, font = list(color = "red", family = "Arial", size = 10))
)