Michael Schmitz - 1 year ago 108

R Question

In the documentation of the

`metafor`

`psize`

- How does the metafor library calculate the point size from the confidence interval?
- How can I enlarge only the point size? also affects the text size.
`cex`

example

`library(metafor)`

model_data <- read.table(dec = ",", text="

OR lower upper

age 0,9678479 0,9326182 1,002493

sex 1,0679667 0,4987457 2,280504

ApacheeII 0,9288701 0,8728417 0,984529",

header=T)

forest(x=model_data$OR,

ci.lb=model_data$lower,

ci.ub=model_data$upper,

annotate=TRUE,

cex=1.2,

at=seq(0,6,1),

refline=1,

digits=c(3,1),

xlim=c(-1,2),

xlab="OR",

slab=rownames(model_data))

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Answer Source

**As for 1:**

The relevant line of code in `forest.default()`

is:

```
vi <- ((ci.ub - ci.lb) / (2*qnorm(alpha/2, lower.tail=FALSE)))^2
```

So, the function assumes you are supplying the bounds of a symmetric Wald-tye confidence interval (CI) to the function and then back-calculates the variance based on that. This would be appropriate for log odds ratios and the corresponding CI bounds on the log scale, but you are apparently directly applying the ORs and CI bounds on the raw scale to the function. Then this makes less sense. Usually, CIs for odds ratios are actually first calculated on the log scale (and are then exponentiated). This also appears to the case for these data:

```
round(with(model_data, log(upper) - log(OR)), 2)
round(with(model_data, log(OR) - log(lower)), 2)
```

This shows that on the log scale, the CI bounds are symmetric (around log(OR)). So, these CI bounds are very likely Wald-type CIs on the log scale. So, it would make more sense to do this:

```
dat <- log(model_data)
forest(x=dat$OR, ci.lb=dat$lower, ci.ub=dat$upper,
annotate=TRUE, cex=1.2, at=seq(-2,2,1), digits=c(3,1),
xlim=c(-5,7), xlab="OR", slab=rownames(dat), atransf=exp)
```

So, supply log(OR) and the corresponding CI bounds to the function and then use the `atransf`

argument for the back-transformation. In essence, this puts the x-axis on the log-scale.

**As for 2:**

You will have to compute the point sizes yourself and then supply them to the function via the `psize`

argument.