My wish is to use the meta r package's forest fucntion for presenting the OR and 95% confidence intervals in a forest plot. It is a non-meta-analysis task. However, the supplied confidence intervals are changed when they are plotted in a forest plot. As an example, you can see the following
forest(metagen(
TE = c(0.58, 0.04,0.26, 0.92, 0.3),
lower = c(0.21,0.02,0.16, 0.64, 0.0),
upper = c(1.59,0.08,0.42, 1.32, 1.2),
overall = F, random = F,
fixed=F,
sm = "OR"))
I get the following plot after running the above code. As you can see the calculated seTE (Standard error) is different from the one you would get using the formula SE = (upper limit – lower limit) / 3.92 and the confidence intervals are different from the ones I supplied in the lower and upper limit of my code above. It looks like metagen function of the meta r package calculates SE using the following formula: SE = sqrt(Q / df). That seems I shouldn't use meta r package for vizualizing odds ratios and confidence intervals for non-meta-analysis taks. Is it possible to force it using the supplied confidence intervals or force it calculate using this: SE = (upper limit – lower limit) / 3.92
You need to pass the log-transformed odds ratios and CI bounds to the function:
forest(metagen(
TE = log(c(0.58, 0.04,0.26, 0.92, 0.3)),
lower = log(c(0.21,0.02,0.16, 0.64, 0.0)),
upper = log(c(1.59,0.08,0.42, 1.32, 1.2)),
overall = F, random = F,
fixed=F,
sm = "OR"))