Calculate 95 % CI from ICC

icc-95ci.r

# Code by Ashe: https://stats.stackexchange.com/questions/184767/how-do-i-calculate-the-confidence-interval-of-an-icc

#Make some mocked data
library(lme4)
library(reshape2)
set.seed(2024)  #For the Bell Riots
id <- factor(seq(1, 15))
id.mu <- rnorm(15, 10, 5)
mydat <- NULL
for (a in 1:length(id)){
  score <- rnorm(2, id.mu[a], 3)
  id.fr <- data.frame(id=id[a], score1=score[1], score2=score[2])
  mydat <- rbind(mydat, id.fr)
}
mydat <- melt(mydat, id.vars='id', value.name='score')

#Create function to calculate ICC from fitted model
calc.icc <- function(y) {
  sumy <- summary(y)
  (sumy$varcor$id[1]) / (sumy$varcor$id[1] + sumy$sigma^2)
}

#Fit the random effects model and calculate the ICC
mymod <- lmer(score ~ 1 + (1|id), data=mydat)
summary(mymod)
calc.icc(mymod)

#Calculate the bootstrap distribution
boot.icc <- bootMer(mymod, calc.icc, nsim=1000)

#Draw from the bootstrap distribution the usual 95% upper and lower confidence limits
quantile(boot.icc$t, c(0.025, 0.975))

Hi, I found your demo, but I'm having trouble getting it to work (the function, specifically) on my data. I need to calculate the 95%CI for ICC. This is how I'm calculating the ICC.

Empty model

library(lme4)
M0 <- glmer(outcome ~ ( 1 | pracid), data=master, family = "binomial")
summary(M0)

icc <- M0@theta[1]^2/ (M0@theta[1]^2 + (3.14159^2/3))
icc # Intraclass correlation coefficient.

Thanks a ton! It's been a challenge!
Liz

Hi Liz,

I realize I haven't calculated that thing in seven years and the code above doesn't work anymore. Check out the Stack Overflow link (https://stats.stackexchange.com/questions/184767/how-do-i-calculate-the-confidence-interval-of-an-icc) and try to post the issue there.

All the best,
Peter

No worries, thanks for the reply.

…

On Wed, Mar 27, 2024 at 5:58 PM Peter M. Dahlgren ***@***.***> wrote: ***@***.**** commented on this gist. ------------------------------ Hi Liz, I realize I haven't calculated that thing in seven years and the code above doesn't work anymore. Check out the Stack Overflow link ( https://stats.stackexchange.com/questions/184767/how-do-i-calculate-the-confidence-interval-of-an-icc) and try to post the issue there. All the best, Peter — Reply to this email directly, view it on GitHub <https://gist.github.com/peterdalle/7bce0bbebc13c36180fbbac1353a5353#gistcomment-5003254> or unsubscribe <https://github.com/notifications/unsubscribe-auth/AZ2Q2KULYM7FJDGJ4JGZYFDY2MCDVBFKMF2HI4TJMJ2XIZLTSKBKK5TBNR2WLJDUOJ2WLJDOMFWWLO3UNBZGKYLEL5YGC4TUNFRWS4DBNZ2F6YLDORUXM2LUPGBKK5TBNR2WLJDHNFZXJJDOMFWWLK3UNBZGKYLEL52HS4DFVRZXKYTKMVRXIX3UPFYGLK2HNFZXIQ3PNVWWK3TUUZ2G64DJMNZZDAVEOR4XAZNEM5UXG5FFOZQWY5LFVA3TMNRRG4ZDSM5HORZGSZ3HMVZKMY3SMVQXIZI> . You are receiving this email because you commented on the thread. Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub> .