funnel.meta {meta} | R Documentation |
Draw a funnel or radial plot to assess funnel plot asymmetry in the active graphics window.
A contour-enhanced funnel plot can be produced for assessing causes of funnel plot asymmetry.
## Default S3 method: funnel(x, y, xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL, comb.fixed=FALSE, comb.random=FALSE, axes=TRUE, pch=21, text=NULL, cex=1, lty.fixed=2, lty.random=9, lwd=1, lwd.fixed=lwd, lwd.random=lwd, col="black", bg="darkgray", col.fixed="black", col.random="black", log="", yaxis="se", sm=NULL, contour.levels=NULL, col.contour, ref=ifelse(sm %in% c("RR", "OR", "HR"), 1, 0), level=NULL, studlab=FALSE, cex.studlab=0.8, ...) ## S3 method for class 'meta': funnel(x, y, xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL, comb.fixed=x$comb.fixed, comb.random=x$comb.random, axes=TRUE, pch=21, text=NULL, cex=1, lty.fixed=2, lty.random=9, lwd=1, lwd.fixed=lwd, lwd.random=lwd, col="black", bg="darkgray", col.fixed="black", col.random="black", log="", yaxis="se", sm=NULL, contour.levels=NULL, col.contour, ref=ifelse(x$sm %in% c("RR", "OR", "HR"), 1, 0), level=x$level, studlab=FALSE, cex.studlab=0.8, ...) radial(x, y, xlim=NULL, ylim=NULL, xlab="Inverse of standard error", ylab="Standardised treatment effect (z-score)", comb.fixed=TRUE, axes=TRUE, pch=1, text=NULL, cex=1, col=NULL, level=NULL, ...)
x |
An object of class meta , or estimated treatment
effect in individual studies. |
y |
Standard error of estimated treatment effect (mandatory if
x not of class meta ). |
xlim |
The x limits (min,max) of the plot. |
ylim |
The y limits (min,max) of the plot. |
xlab |
A label for the x axis. |
ylab |
A label for the y axis. |
comb.fixed |
A logical indicating whether the pooled fixed effect estimate should be plotted. |
comb.random |
A logical indicating whether the pooled random effects estimate should be plotted. |
axes |
A logical indicating whether axes should be drawn on the plot. |
pch |
The plotting symbol used for individual studies. |
text |
A character vector specifying the text to be used instead of plotting symbol. |
cex |
The magnification to be used for plotting symbol. |
lty.fixed |
Line type (pooled fixed effect estimate). |
lty.random |
Line type (pooled random effects estimate). |
col |
A vector with colour of plotting symbols. |
bg |
A vector with background colour of plotting symbols (only
used if pch in 21:25 ). |
col.fixed |
Color of line representign fixed effect estimate. |
col.random |
Color of line representign random effects estimate. |
lwd |
The line width for confidence intervals (if level is
not NULL ). |
lwd.fixed |
The line width for fixed effect estimate (if
comb.fixed is not NULL ). |
lwd.random |
The line width for random effects estimate (if
comb.random is not NULL ). |
log |
A character string which contains "x" if the x axis
is to be logarithmic, "y" if the y axis is to be logarithmic
and "xy" or "yx" if both axes are to be logarithmic
(applies only to function funnel ). |
yaxis |
A character string indicating which type of weights are
to be used. Either "se" , "invvar" , "invse" , or "size"
(applies only to function funnel ). |
sm |
A character string indicating underlying summary measure,
e.g., "RD" , "RR" , "OR" , "AS" , "MD" ,
"SMD" (applies only to function funnel ). |
contour.levels |
A numeric vector specifying contour levels to produce contour-enhanced funnel plot. |
col.contour |
Colour of contours. |
ref |
Reference value (null effect) used to produce contour-enhanced funnel plot. |
level |
The confidence level utilised in the plot. For the funnel
plot, confidence limits are not drawn if yaxis="size" . |
studlab |
A logical indicating whether study labels should be
printed in the graph. A vector with study labels can also be
provided (must be of same length as x$TE then). |
cex.studlab |
Size of study labels. |
... |
Graphical parameters as in par may also be
passed as arguments. |
A funnel plot or radial plot, also called Galbraith plot, is drawn in
the active graphics window. If comb.fixed
is TRUE, the pooled
estimate of the fixed effect model is plotted. If level
is not
NULL, the corresponding confidence limits are drawn.
In the funnel plot, if yaxis
is "se"
, the standard error
of the treatment estimates is plotted on the y axis which is likely to
be the best choice (Sterne & Egger, 2001). Other possible choices for
yaxis
are "invvar"
(inverse of the variance),
"invse"
(inverse of the standard error), and "size"
(study size).
For yaxis!="size"
, contour-enhanced funnel plots can be
produced (Peters et al., 2008) by specifying the contour levels
(argument contour.levels
). By default (argument
col.contour
missing), suitable gray levels will be used to
distinguish the contours. Different colours can be chosen by argument
col.contour
.
Guido Schwarzer sc@imbi.uni-freiburg.de, Petra Graham pgraham@efs.mq.edu.au
Galbraith RF (1988a), Graphical display of estimates having differing standard errors. Technometrics, 30, 271–281.
Galbraith RF (1988b), A note on graphical presentation of estimated odds ratios from several clinical trials. Statistics in Medicine, 7, 889–894.
Light RJ & Pillemer DB (1984), Summing Up. The Science of Reviewing Research. Cambridge: Harvard University Press.
Peters JL, Sutton AJ, Jones DR, Abrams KR, Rushton L (2008), Contour-enhanced meta-analysis funnel plots help distinguish publication bias from other causes of asymmetry. Journal of Clinical Epidemiology, 61, 991–996.
Sterne JAC & Egger M (2001), Funnel plots for detecting bias in meta-analysis: Guidelines on choice of axis. Journal of Clinical Epidemiology, 54, 1046–1055.
data(Olkin95) meta1 <- metabin(event.e, n.e, event.c, n.c, data=Olkin95, subset=c(41,47,51,59), studlab=paste(author, year), sm="RR", meth="I") ## ## Radial plot ## radial(meta1, level=0.95) oldpar <- par(mfrow=c(2, 2)) ## ## Funnel plots ## funnel(meta1) ## ## Same result as code above: ## funnel(meta1$TE, meta1$seTE, sm="RR") ## ## Funnel plot with confidence intervals, ## fixed effect estimate and contours ## cc <- funnel(meta1, comb.fixed=TRUE, level=0.95, contour=c(0.9, 0.95, 0.99))$col.contour legend(0.05, 0.05, c("0.1 > p > 0.05", "0.05 > p > 0.01", "< 0.01"), fill=cc) ## ## Contour-enhanced funnel plot with user-chosen colours ## funnel(meta1, comb.fixed=TRUE, level=0.95, contour=c(0.9, 0.95, 0.99), col.contour=c("darkgreen", "green", "lightgreen"), lwd=2, cex=2, pch=16, studlab=TRUE, cex.studlab=1.25) legend(0.05, 0.05, c("0.1 > p > 0.05", "0.05 > p > 0.01", "< 0.01"), fill=c("darkgreen", "green", "lightgreen")) par(oldpar)