II tried to do a Funnel plot of a dataset for a disease-prevention paper, view dataset here.
Got the plot, but am worried it is wrong.The dataset contains the Hazard ratio(HR)
, Lower control limit(LCL)
, Upper control limit(UCL)
and the Standard Errors(SE)[of Ln(HR)]
values, and I used the SE values to calculate Variances(var
in the dataset). Here is the code I used:
library(metafor)
age <- read.csv("age.csv", header=TRUE)
age
res <- rma(yi=lnhr, vi=var, data=age)
res
funnel(res,xlab = "ln(HR)",ylab = "SE.ln(HR)")
The question I had was this:
In most studies I have seen, the Ln(HR) values are negative, whereas in the dataset I was working on, almost all are positive. So for the correct funnel, should I take yi=-lnhr
, or is yi=lnhr
the correct method, in the res object?
P.S:(According to the Metafor
repository linked here, yi
is effect-size, and vi
is the variance)
Update:Here are the results using the above code and dataset, taking yi=-lnhr
Random-Effects Model (k = 11; tau^2 estimator: REML)
tau^2 (estimated amount of total heterogeneity): 0.0001 (SE = 0.0002)
tau (square root of estimated tau^2 value): 0.0122
I^2 (total heterogeneity / total variability): 35.20%
H^2 (total variability / sampling variability): 1.54
Test for Heterogeneity:
Q(df = 10) = 16.8884, p-val = 0.0769**
Model Results:
estimate= -0.0379
se =0.0067
zval=-5.6850
pval<.0001
ci.lb=-0.0509
ci.ub=-0.0248 ***
And here is the funnel plot generated.