ae.dotplot

AE (Adverse Events) dotplot of incidence and relative risk

A two-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. See the Details section for information on changing the sort order.

Usage

ae.dotplot(ae, ...)
ae.dotplot.long(xr,
                A.name = levels(xr$RAND)[1], B.name = levels(xr$RAND)[2],
                col.AB = c("red","blue"), pch.AB = c(16, 17),
                main.title = paste("Most Frequent On-Therapy Adverse Events",
                                   "Sorted by Relative Risk"),
                main.cex = 1,
                cex.AB.points = NULL, cex.AB.y.scale = 0.6,
                position.left = c(0, 0, 0.7, 1), position.right = c(0.61, 0, 0.98, 1),
                key.y = -0.2, CI.percent=95)
logrelrisk(ae, A.name, B.name, crit.value=1.96)
panel.ae.leftplot(x, y, groups, col.AB, ...)
panel.ae.rightplot(x, y, ..., lwd=6, lower, upper, cex=.7)
panel.ae.dotplot(x, y, groups, ..., col.AB, pch.AB, lower, upper) ## R only
aeReshapeToLong(aewide)

Details

The second panel shows relative risk of an event on the active arm (treatment B) relative to the placebo arm (treatment A), 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 ae.dotplot function sorts the events by relative risk. To change the sort order, you must redefine the ordering of the ordered factor PREF. See the examples below.

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. https://onlinelibrary.wiley.com/doi/10.1002/pst.254

See Also

AEdotplot for a three-panel version that also has an associated shiny app.

Aliases

• ae.dotplot
• AE.dotplot
• ae.dotplot.long
• aeReshapeToLong
• panel.ae.leftplot
• panel.ae.rightplot
• panel.ae.dotplot
• logrelrisk

Examples

# NOT RUN {
## variable names in the input data.frame aeanonym
## RAND   treatment as randomized
## PREF   adverse event symptom name
## SN     number of patients in treatment group
## SAE    number of patients  in each group for whom the event PREF was observed
##
## Input sort order is PREF/RAND

data(aeanonym)
head(aeanonym)

## Calculate log relative risk and confidence intervals (95% by default).
## logrelrisk sets the sort order for PREF to match the relative risk.
aeanonymr <- logrelrisk(aeanonym) ## sorts by relative risk
head(aeanonymr)

## construct and print plot on current graphics device
ae.dotplot(aeanonymr,
           A.name="TREATMENT A (N=216)",
           B.name="TREATMENT B (N=431)")
## export.eps(h2("stdt/figure/aerelrisk.eps"))
## This looks great on screen and exports badly to eps.
## We recommend drawing this plot directly to the postscript device:
##
## trellis.device(postscript, color=TRUE, horizontal=TRUE,
##                colors=ps.colors.rgb[
##                  c("black", "blue", "red", "green",
##                    "yellow", "cyan","magenta","brown"),],
##                onefile=FALSE, print.it=FALSE,
##                file=h2("stdt/figure/aerelrisk.ps"))
## ae.dotplot(aeanonymr,
##            A.name="TREATMENT A (N=216)",
##            B.name="TREATMENT B (N=431)")
## dev.off()

## To change the sort order, redefine the PREF factor.
## For this example, to plot alphabetically, use the statement
aeanonymr$PREF <- ordered(aeanonymr$PREF, levels=sort(levels(aeanonymr$PREF)))
ae.dotplot(aeanonymr,
           A.name="TREATMENT A (N=216)",
           B.name="TREATMENT B (N=431)",
           main.title="change the main title to reflect the new sort order")

# }
# NOT RUN {
## to restore the order back to the default, use
relrisk <- aeanonymr[seq(1, nrow(aeanonymr), 2), "relrisk"]
PREF <- unique(aeanonymr$PREF)
aeanonymr$PREF <- ordered(aeanonymr$PREF, levels=PREF[order(relrisk)])
ae.dotplot(aeanonymr,
           A.name="TREATMENT A (N=216)",
           B.name="TREATMENT B (N=431)",
           main.title="back to the original sort order")

## smaller artifical example with the wide format
aewide <- data.frame(Event=letters[1:6],
                     N.A=c(50,50,50,50,50,50),
                     N.B=c(90,90,90,90,90,90),
                     AE.A=2*(1:6),
                     AE.B=1:6)
aewtol <- aeReshapeToLong(aewide)
xr <- logrelrisk(aewtol)
ae.dotplot(xr)
# }