plot.CMA1: Plot CMA0-derived objects.

Description Usage Arguments Details Examples

Description

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

Usage

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## 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,
  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)

## 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.

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.

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

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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 documentation built on May 2, 2019, 12:40 p.m.