AdhereR: plot.CMA1 – R documentation

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AdhereR

plot.CMA1

Plot CMA0-derived objects.

Description

Plots the event data and estimated CMA encapsulated in objects derived from CMA0.

Usage

## S3 method for class 'CMA1'
plot(
  x,
  ...,
  patients.to.plot = NULL,
  duration = NA,
  align.all.patients = FALSE,
  align.first.event.at.zero = TRUE,
  show.period = c("dates", "days")[2],
  period.in.days = 90,
  show.legend = TRUE,
  legend.x = "right",
  legend.y = "bottom",
  legend.bkg.opacity = 0.5,
  legend.cex = 0.75,
  legend.cex.title = 1,
  legend.medication.truncate = 15,
  legend.medication.truncate.side = c("left", "center", "right")[2],
  cex = 1,
  cex.axis = 0.75,
  cex.lab = 1,
  show.cma = TRUE,
  col.cats = rainbow,
  unspecified.category.label = "drug",
  lty.event = "solid",
  lwd.event = 2,
  pch.start.event = 15,
  pch.end.event = 16,
  show.event.intervals = TRUE,
  col.na = "lightgray",
  print.CMA = TRUE,
  CMA.cex = 0.5,
  plot.CMA = TRUE,
  CMA.plot.ratio = 0.1,
  CMA.plot.col = "lightgreen",
  CMA.plot.border = "darkgreen",
  CMA.plot.bkg = "aquamarine",
  CMA.plot.text = CMA.plot.border,
  highlight.followup.window = TRUE,
  followup.window.col = "green",
  highlight.observation.window = TRUE,
  observation.window.col = "yellow",
  observation.window.density = 35,
  observation.window.angle = -30,
  observation.window.opacity = 0.3,
  show.real.obs.window.start = TRUE,
  real.obs.window.density = 35,
  real.obs.window.angle = 30,
  print.dose = FALSE,
  cex.dose = 0.75,
  print.dose.outline.col = "white",
  print.dose.centered = FALSE,
  plot.dose = FALSE,
  lwd.event.max.dose = 8,
  plot.dose.lwd.across.medication.classes = FALSE,
  bw.plot = FALSE,
  min.plot.size.in.characters.horiz = 10,
  min.plot.size.in.characters.vert = 0.5,
  max.patients.to.plot = 100,
  export.formats = NULL,
  export.formats.fileprefix = "AdhereR-plot",
  export.formats.height = NA,
  export.formats.width = NA,
  export.formats.save.svg.placeholder = TRUE,
  export.formats.directory = NA,
  generate.R.plot = TRUE
)

## S3 method for class 'CMA2'
plot(...)

## S3 method for class 'CMA3'
plot(...)

## S3 method for class 'CMA4'
plot(...)

## S3 method for class 'CMA5'
plot(...)

## S3 method for class 'CMA6'
plot(...)

## S3 method for class 'CMA7'
plot(...)

## S3 method for class 'CMA8'
plot(...)

## S3 method for class 'CMA9'
plot(...)

Arguments

`x`	A `CMA0` or derived object, representing the CMA to plot
`...`	other possible parameters
`patients.to.plot`	A vector of strings containing the list of patient IDs to plot (a subset of those in the `cma` object), or `NULL` for all
`duration`	A number, the total duration (in days) of the whole period to plot; in `NA` it is automatically determined from the event data such that the whole dataset fits.
`align.all.patients`	Logical, should all patients be aligned (i.e., the actual dates are discarded and all plots are relative to the earliest date)?
`align.first.event.at.zero`	Logical, should the first event be placed at the origin of the time axis (at 0)?
`show.period`	A string, if "dates" show the actual dates at the regular grid intervals, while for "days" (the default) shows the days since the beginning; if `align.all.patients == TRUE`, `show.period` is taken as "days".
`period.in.days`	The number of days at which the regular grid is drawn (or 0 for no grid).
`show.legend`	Logical, should the legend be drawn?
`legend.x`	The position of the legend on the x axis; can be "left", "right" (default), or a numeric value.
`legend.y`	The position of the legend on the y axis; can be "bottom" (default), "top", or a numeric value.
`legend.bkg.opacity`	A number between 0.0 and 1.0 specifying the opacity of the legend background.
`legend.medication.truncate`	A number specifying the maximum length (in character) of the medication class showin in the legend (or `NA` for no truncation).
`legend.medication.truncate.side`	A string specifying how the medication truncation is done (if `legend.medication.truncate` is not `NA`); can be "left", "right" or "center".
`cex, cex.axis, cex.lab, legend.cex, legend.cex.title, CMA.cex`	numeric values specifying the `cex` of the various types of text.
`show.cma`	Logical, should the CMA type be shown in the title?
`col.cats`	A color or a function that specifies the single colour or the colour palette used to plot the different medication; by default `rainbow`, but we recommend, whenever possible, a colorblind-friendly palette such as `viridis` or `colorblind_pal`.
`unspecified.category.label`	A string giving the name of the unspecified (generic) medication category.
`lty.event, lwd.event, pch.start.event, pch.end.event`	The style of the event (line style, width, and start and end symbols).
`show.event.intervals`	Logical, should the actual event intervals be shown?
`col.na`	The colour used for missing event data.
`print.CMA`	Logical, should the CMA values be printed?
`plot.CMA`	Logical, should the CMA values be represented graphically?
`CMA.plot.ratio`	A number, the proportion of the total horizontal plot space to be allocated to the CMA plot.
`CMA.plot.col, CMA.plot.border, CMA.plot.bkg, CMA.plot.text`	Strings giving the colours of the various components of the CMA plot.
`highlight.followup.window`	Logical, should the follow-up window be plotted?
`followup.window.col`	The follow-up window's colour.
`highlight.observation.window`	Logical, should the observation window be plotted?
`observation.window.col, observation.window.density, observation.window.angle, observation.window.opacity`	Attributes of the observation window (colour, shading density, angle and opacity).
`show.real.obs.window.start, real.obs.window.density, real.obs.window.angle`	For some CMAs, the observation window might be adjusted, in which case should it be plotted and with that attributes?
`print.dose`	Logical, should the daily dose be printed as text?
`cex.dose`	Numeric, if daily dose is printed, what text size to use?
`print.dose.outline.col`	If `NA`, don't print dose text with outline, otherwise a color name/code for the outline.
`print.dose.centered`	Logical, print the daily dose centered on the segment or slightly below it?
`plot.dose`	Logical, should the daily dose be indicated through segment width?
`lwd.event.max.dose`	Numeric, the segment width corresponding to the maximum daily dose (must be >= lwd.event but not too big either).
`plot.dose.lwd.across.medication.classes`	Logical, if `TRUE`, the line width of the even is scaled relative to all medication classes (i.e., relative to the global minimum and maximum doses), otherwise it is scale relative only to its medication class.
`bw.plot`	Logical, should the plot use grayscale only (i.e., the `gray.colors` function)?
`min.plot.size.in.characters.horiz, min.plot.size.in.characters.vert`	Numeric, the minimum size of the plotting surface in characters; horizontally (min.plot.size.in.characters.horiz) referes to the the whole duration of the events to plot; vertically (min.plot.size.in.characters.vert) referes to a single event.
`max.patients.to.plot`	Numeric, the maximum patients to attempt to plot.
`export.formats`	What formats should the plot be exported to? It can be any subset of "svg" (an SVG file), "html" (a self-contained HTML document including an embedded SVG image, CSS and the needed JavaScript for some limited user interactions, plus an external placeholder JPEG image for those browsers not supporting SVGs), "jpg", "png", "webp", "ps" and "pdf". Default to NULL (i.e., no plot is exported).
`export.formats.fileprefix`	The file name prefix for the exported formats (defaults to "AdhereR-plot").
`export.formats.height, export.formats.width`	The desired dimensions of the exported figure (defaults to sane values).
`export.formats.save.svg.placeholder`	Logical: if TRUE (the default), save a JPG placeholder for the SVG image.
`export.formats.directory`	If exporting the plot, which directory to export to (if not given, uses a temporary directory).
`generate.R.plot`	Logical: should it generate a standard (base R) plot for plotting within R?

Details

Please note that this function plots objects inheriting from CMA0 but not objects of type CMA0 itself (these are plotted by plot.CMA0).

The x-axis represents time (either in days since the earliest date or as actual dates), with consecutive events represented as ascending on the y-axis.

Each event is represented as a segment with style lty.event and line width lwd.event starting with a pch.start.event and ending with a pch.end.event character, coloured with a unique color as given by col.cats, extending from its start date until its end date. Superimposed on these are shown the event intervals and gap days as estimated by the particular CMA method, more precisely plotting the start and end of the available events as solid filled-in rectangles, and the event gaps as shaded rectangles.

The follow-up and the observation windows are plotted as an empty rectangle and as shaded rectangle, respectively (for some CMAs the observation window might be adjusted in which case the adjustment may also be plotted using a different shading).

The CMA estimates can be visually represented as well in the left side of the figure using bars (sometimes the estimates can go above 100%, in which case the maximum possible bar filling is adjusted to reflect this).

When several patients are displayed on the same plot, they are organized vertically, and alternating bands (white and gray) help distinguish consecutive patients. Implicitely, all patients contained in the cma object will be plotted, but the patients.to.plot parameter allows the selection of a subset of patients.

Finally, the y-axis shows the patient ID and possibly the CMA estimate as well.

Examples

cma1 <- CMA1(data=med.events,
             ID.colname="PATIENT_ID",
             event.date.colname="DATE",
             event.duration.colname="DURATION",
             followup.window.start=30,
             observation.window.start=30,
             observation.window.duration=365,
             date.format="%m/%d/%Y"
            );
plot(cma1, patients.to.plot=c("1","2"));

AdhereR

Adherence to Medications

v0.6.1

GPL (>= 2)

Authors

Dan Dediu [aut, cre], Alexandra Dima [aut], Samuel Allemann [aut]

Initial release

plot.CMA1

Description

Usage

Arguments

Details

Examples

AdhereR

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