AEdotplot

0th

Percentile

AE (Adverse Events) dotplot of incidence and relative risk

A three-panel display of the most frequently occurring AEs in the active arm of a clinical study. The first panel displays their incidence by treatment group, with different symbols for each group. The second panel displays the relative risk of an event on the active arm relative to the placebo arm, with 95% confidence intervals for a $2\times2$ table. By default, the AEs are ordered by relative risk so that events with the largest increases in risk for the active treatment are prominent at the top of the display. By setting the argument sortbyRelativeRisk=FALSE, the AEs retain the order specified by the levels of the factor. The third panel displays the numerical values of number of patients for each treatment, number of adverse events for each treatment, and relative risk. The third panel can be suppressed by the print method.

Keywords
hplot, htest
Usage
AEdotplot(xr, ...)

## S3 method for class 'formula': AEdotplot(xr, groups=NULL, data=NULL, sortbyRelativeRisk=TRUE, ..., sub=list(deparse(this.call[1:4], width.cutoff=500), cex=.7))

Arguments
xr
For the formula method, a formula of the form AE ~ nAE/nTRT | OrgSys, where the condition variable is optional. For the formula method only, the variable names are not restricted. See
groups
Variable containing the treatment levels.
data
data.frame containing at least four variables: containing the AE name, the treatment level, the number of observed AE in that treatment level, the number of patients in that treatment group. It may also contain a fifth variable
sortbyRelativeRisk
logical. If TRUE, then make the Adverse Events an ordered factor ordering by relative risk. If FALSE, then make the Adverse Events an ordered factor retaining the order of the input levels.
sub
Subtitle for the plot. The default value is the command that generates the plot.
...
Any of the arguments listed in the calling sequence for the methods documented in AEdotplot.data.frame.
Details

The first panel is an ordinary dotplot of the percent of AE observed for each treatment by AE.

The second panel shows relative risk of an event on the Treatment B arm (usually the active compound) relative to the Treatment A arm (usually the placebo), with 95% confidence intervals for a $2\times2$ table. Confidence intervals on the log relative risk are calculated using the asymptotic standard error formula given as Equation 3.18 in Agresti A., Categorical Data Analysis. Wiley: New York, 1990.

By default the AEdotplot function sorts the events by relative risk. To retain the sort order implied by the levels of the AE factor, specify the argument sortbyRelativeRisk=FALSE. To control the sort order, make the AE factor in the input dataset an ordered factor and specify the levels in the order you want.

The third panel shows the numerical values of the number and percent of observed events on each arm and the relative risk. The display of third panel can be suppressed by specifying the panel.widths argument. See the discussion of the panel.widths in AEdotplot.data.frame.

Value

  • The primary interest is in the display of the plot.

    The function returns an AEdotplot object which is a list of three trellis objects, one for the the Percent plot, one for the Relative Risk plot, and one for the Text plot containing the table of input values. The object has attributes

    1. mainandsubhold the main and subtitles. Each must be a list containing the text in the first component.
    2. ae.keyis a key as described inxyplot.
    3. n.eventsis a vector containing the number of events in each subpanel.
    4. panel.widthsis a vector of relative widths of the three components of the graph. The numbers must sum to one. Zero values are permitted. The first width includes the left axis and the Percent plot. The second is the Relative Risk plot, and the third is the plot of the table values.
    5. AEtableis a table containing the data plotted on its row.

References

Ohad Amit, Richard M. Heiberger, and Peter W. Lane. (2008) ``Graphical Approaches to the Analysis of Safety Data from Clinical Trials''. Pharmaceutical Statistics, 7, 1, 20--35.http://www3.interscience.wiley.com/journal/114129388/abstract

See Also

AEdotplot.data.frame

Aliases
  • AEdotplot
  • AEdotplot.formula
Examples
## formula method.  See ?AEdotplot.data.frame for other methods.
data(AEdata)
head(AEdata)

AEdotplot(AE ~ nAE/nTRT, groups = TRT, data = AEdata)
AEdotplot(AE ~ nAE/nTRT | OrgSys, groups = TRT, data = AEdata)

AEdotplot(AE ~ nAE/nTRT | OrgSys, groups = TRT,
          data = AEdata[c(AEdata$OrgSys %in% c("GI","Resp")),])

## test sortbyRelativeRisk=FALSE
ABCD.12345 <- AEdata[1:12,]
head(ABCD.12345)
AEdotplot(AE ~ nAE/nTRT | OrgSys, groups=TRT, data=ABCD.12345)
AEdotplot(AE ~ nAE/nTRT | OrgSys, groups=TRT, data=ABCD.12345, sort=FALSE)

## suppress third panel
tmp <- AEdotplot(AE ~ nAE/nTRT, groups = TRT, data = AEdata)
print(tmp, AEtable=FALSE)
Documentation reproduced from package HH, version 3.1-19, License: GPL (>= 2)

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