Hello,
I am performing a diagnostic accuracy meta-analysis. As a check for
publication bias/small study effects I want to use the Deeks' funnel
plot asymmetry test for publication bias. I could not find a
implementation in a software program. Does anybody know if there is a
package that contains this test?
Probably, a little bit late, however, for the record and future queries. ;-)
I implemented the Deeks' test in R package *meta*. In order to use it
one has to conduct a meta-analysis with /metabin()/ using the diagnostic
odds ratio as summary measure. Then, R function /metabias()/ conducts
the linear regression test using the inverse of the square root of the
effective study size.
Using Wolfgang's example dataset:
dat <- read.table(header = TRUE, text = "
tp np? tn? nn
10 25? 47? 53
15 24? 29? 32
10 14? 44? 47
13 23 123 123
10 32? 55? 56
16 61 184 186
12 49 137 138
13 26? 66? 74
16 80? NA? NA
24 42? 55? 57
17 27? 85? 91
?5 22? 45? 46
18 31 240 245
24 28 104 104
26 55? 81? 89")
library(meta)
settings.meta(digits = 2)
## Drop study with missing information and conduct meta-analysis
##
dat.nomiss <- subset(dat, !is.na(tn))
##
m <- metabin(tp, np, nn - tn, nn, data = dat.nomiss,
???????????? sm = "DOR", addincr = TRUE)
## Funnel plot with inverse of square root of effective study size on y-axis
##
funnel(m, yaxis = "ess", xlim = c(1, 1100), ylim = c(0.15, 0), studlab =
TRUE)
## same result with meta, > 4.15-1:
## funnel(m, xlim = c(1, 1100), studlab = TRUE)
## Deeks' test for funnel plot asymmetry
##
metabias(m)
Best wishes, Guido