ICC

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Basic

ICC: intra-class correlation

  • https://en.wikipedia.org/wiki/Intraclass_correlation (the random effect [math]\displaystyle{ \alpha_j }[/math] in the one-way random model should be subjects, not raters)
    • It describes how strongly units in the same group resemble each other. (Cf ICC(1,1) model, the group has the same concept of subject. That is, ICC is used to measure to what extent are the ratings within a subject homogeneous.) So the dot plots shown on the wikipedia should be rotated in order to match with the row/column meaning in the real data matrix.
    • (Early def of ICC) In the case of paired data (N groups, each group has 2 values), The key difference between this ICC and the interclass (Pearson) correlation is that the data are pooled to estimate the mean and variance. The reason for this is that in the setting where an intraclass correlation is desired, the pairs are considered to be unordered.
    • Intraclass Correlation from Statistics How To
    • Shrout, P.E., Fleiss, J.L. (1979), Intraclass correlation: uses in assessing rater reliability, Psychological Bulletin, 86, 420-428.
    • ICC(1,1): each subject is measured by a different set of k randomly selected raters?;
    • ICC(2,1): k raters are randomly selected, then, each subject is measured by the same set of k raters;
    • ICC(3,1): similar to ICC(2,1) but k raters are fixed.
  • (Modern ICC definitions) [math]\displaystyle{ Y_{ij} = \mu + \alpha_i + \varepsilon_{ij}, }[/math] where [math]\displaystyle{ \alpha_i }[/math] is the random effect from subject i (or group/target but not rater/judge),
[math]\displaystyle{ ICC(1,1) = \frac{\sigma_\alpha^2}{\sigma_\alpha^2+\sigma_\varepsilon^2}. }[/math]
The intraclass correlation is the ratio of the variance attributable to subjects divided by the total of subject and error variances. See also the formula and estimation here. The intuition can be found in examples where the 1st case has large [math]\displaystyle{ \sigma_\alpha^2 }[/math] and the other does not.

R packages

The main input is a matrix of n subjects x p raters. Each rater is a class/group.

  • psych: ICC()
  • irr: icc() for one-way or two-way model. This works on my data 30k by 58. The default option gives ICC(1). It can also compute ICC(A,1)/agreement and ICC(C,1)/consistency.
  • psy: icc(). No options are provided. I got an error: vector memory exhausted (limit reached?) when the data is 30k by 58.
  • rptR:

Negative ICC

Examples

psych package data

It shows ICC1 = ICC(1,1) 

R> library(psych)
R> (o <- ICC(anxiety, lmer=FALSE) )
Call: ICC(x = anxiety, lmer = FALSE)

Intraclass correlation coefficients 
                         type  ICC   F df1 df2     p lower bound upper bound
Single_raters_absolute   ICC1 0.18 1.6  19  40 0.094     -0.0405        0.44
Single_random_raters     ICC2 0.20 1.8  19  38 0.056     -0.0045        0.45
Single_fixed_raters      ICC3 0.22 1.8  19  38 0.056     -0.0073        0.48
Average_raters_absolute ICC1k 0.39 1.6  19  40 0.094     -0.1323        0.70
Average_random_raters   ICC2k 0.43 1.8  19  38 0.056     -0.0136        0.71
Average_fixed_raters    ICC3k 0.45 1.8  19  38 0.056     -0.0222        0.73

 Number of subjects = 20     Number of Judges =  3

R> library(irr)
R> (o2 <- icc(anxiety, model="oneway")) # subjects be considered as random effects
 Single Score Intraclass Correlation

   Model: oneway 
   Type : consistency 

   Subjects = 20 
     Raters = 3 
     ICC(1) = 0.175

 F-Test, H0: r0 = 0 ; H1: r0 > 0 
   F(19,40) = 1.64 , p = 0.0939 

 95%-Confidence Interval for ICC Population Values:
  -0.077 < ICC < 0.484

R> o$results["Single_raters_absolute", "ICC"]
[1] 0.1750224
R> o2$value
[1] 0.1750224

R> icc(anxiety, model="twoway", type = "consistency")
 Single Score Intraclass Correlation

   Model: twoway 
   Type : consistency 

   Subjects = 20 
     Raters = 3 
   ICC(C,1) = 0.216

 F-Test, H0: r0 = 0 ; H1: r0 > 0 
   F(19,38) = 1.83 , p = 0.0562 

 95%-Confidence Interval for ICC Population Values:
  -0.046 < ICC < 0.522
R> icc(anxiety, model="twoway", type = "agreement")
 Single Score Intraclass Correlation

   Model: twoway 
   Type : agreement 

   Subjects = 20 
     Raters = 3 
   ICC(A,1) = 0.198

 F-Test, H0: r0 = 0 ; H1: r0 > 0 
 F(19,39.7) = 1.83 , p = 0.0543 

 95%-Confidence Interval for ICC Population Values:
  -0.039 < ICC < 0.494

library(magrittr)
library(tidyr)
library(ggplot2)

set.seed(1)
r1 <- round(rnorm(20, 10, 4))
r2 <- round(r1 + 10 + rnorm(20, 0, 2))
r3 <- round(r1 + 20 + rnorm(20, 0, 2))
df <- data.frame(r1, r2, r3) %>% pivot_longer(cols=1:3)
df %>% ggplot(aes(x=name, y=value)) + geom_point()

df0 <- cbind(r1, r2, r3)
icc(df0, model="oneway")  #  ICC(1) = -0.262  --> Negative. 
                          #  Shift can mess up the ICC. See wikipedia.
icc(df0, model="twoway", type = "consistency")  # ICC(C,1) = 0.846 --> Make sense
icc(df0, model="twoway", type = "agreement")    # ICC(A,1) = 0.106 --> Why?

ICC(df0)
Call: ICC(x = df0, lmer = T)

Intraclass correlation coefficients 
                         type   ICC     F df1 df2       p lower bound upper bound
Single_raters_absolute   ICC1 -0.26  0.38  19  40 9.9e-01     -0.3613      -0.085
Single_random_raters     ICC2  0.11 17.43  19  38 2.9e-13      0.0020       0.293
Single_fixed_raters      ICC3  0.85 17.43  19  38 2.9e-13      0.7353       0.920
Average_raters_absolute ICC1k -1.65  0.38  19  40 9.9e-01     -3.9076      -0.307
Average_random_raters   ICC2k  0.26 17.43  19  38 2.9e-13      0.0061       0.555
Average_fixed_raters    ICC3k  0.94 17.43  19  38 2.9e-13      0.8929       0.972

 Number of subjects = 20     Number of Judges =  3

Wine rating

Intraclass Correlation: Multiple Approaches from David C. Howell. The data appeared on the paper by Shrout and Fleiss 1979.

Winerating.png 

library(magrittr)
library(psych); library(lme4)
rating <- matrix(c(9,    2,   5,    8,
                   6,    1,   3,    2,
                   8,    4,   6,    8,
                   7,    1,   2,    6,
                   10,   5,   6,    9,
                   6,   2,   4,    7), ncol=4, byrow=TRUE)
(o <- ICC(rating))
o$results[, 1:2]
#                         type       ICC
#Single_raters_absolute   ICC1 0.1657423  # match with icc(, "oneway")
#Single_random_raters     ICC2 0.2897642  # match with icc(, "twoway", "agreement")
#Single_fixed_raters      ICC3 0.7148415  # match with icc(, "twoway", "consistency")
#Average_raters_absolute ICC1k 0.4427981
#Average_random_raters   ICC2k 0.6200510
#Average_fixed_raters    ICC3k 0.9093159

# Plot
rating2 <- data.frame(rating) %>% 
  dplyr::bind_cols(data.frame(subj = paste0("s", 1:nrow(rating)))) %>% 
  tidyr::pivot_longer(1:4, names_to="group", values_to="y")

rating2 %>% ggplot(aes(x=group, y=y)) + geom_point()

library(irr)
icc(rating, "oneway")
# Single Score Intraclass Correlation
#
#   Model: oneway 
#   Type : consistency 
#
#   Subjects = 6 
#     Raters = 4 
#     ICC(1) = 0.166
#
# F-Test, H0: r0 = 0 ; H1: r0 > 0 
#    F(5,18) = 1.79 , p = 0.165 
#
# 95%-Confidence Interval for ICC Population Values:
#  -0.133 < ICC < 0.723

icc(rating, "twoway", "agreement")
# Single Score Intraclass Correlation
#
#   Model: twoway 
#   Type : agreement 
#
#   Subjects = 6 
#     Raters = 4 
#   ICC(A,1) = 0.29
#
# F-Test, H0: r0 = 0 ; H1: r0 > 0 
#  F(5,4.79) = 11 , p = 0.0113 
#
# 95%-Confidence Interval for ICC Population Values:
#  0.019 < ICC < 0.761

icc(rating, "twoway", "consistency")
# Single Score Intraclass Correlation
#
#   Model: twoway 
#   Type : consistency 
#
#   Subjects = 6 
#     Raters = 4 
#   ICC(C,1) = 0.715
#
# F-Test, H0: r0 = 0 ; H1: r0 > 0 
#    F(5,15) = 11 , p = 0.000135 
#
# 95%-Confidence Interval for ICC Population Values:
#  0.342 < ICC < 0.946

anova(aov(y ~ subj + group, rating2))
# Analysis of Variance Table
#
# Response: y
#           Df Sum Sq Mean Sq F value    Pr(>F)    
# subj       5 56.208  11.242  11.027 0.0001346 ***
# group      3 97.458  32.486  31.866 9.454e-07 ***
# Residuals 15 15.292   1.019                      
# ---
# Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(11.242 - (97.458+15.292)/18) / (11.242 + 3*(97.458+15.292)/18)
# [1] 0.165751   # ICC(1) = (BMS - WMS) / (BMS + (k-1)WMS)
                 # k = number of raters

(11.242 - 1.019) / (11.242 + 3*1.019 + 4*(32.486-1.019)/6)
# [1] 0.2897922  # ICC(2,1) = (BMS - EMS) / (BMS + (k-1)EMS + k(JMS-EMS)/n)
                 # n = number of subjects/targets

(11.242 - 1.019) / (11.242 + 3*1.019)
# [1] 0.7149451  # ICC(3,1)

Wine rating2

Intraclass correlation (from Real Statistics Using Excel) with a simple example. 

R> wine <- cbind(c(1,1,3,6,6,7,8,9), c(2,3,8,4,5,5,7,9), 
                 c(0,3,1,3,5,6,7,9), c(1,2,4,3,6,2,9,8))
R> icc(wine, model="oneway")
 Single Score Intraclass Correlation

   Model: oneway 
   Type : consistency 

   Subjects = 8 
     Raters = 4 
     ICC(1) = 0.728

 F-Test, H0: r0 = 0 ; H1: r0 > 0 
    F(7,24) = 11.7 , p = 2.18e-06 

 95%-Confidence Interval for ICC Population Values:
  0.434 < ICC < 0.927

# For one-way random model, the order of raters is not important
R> wine2 <- wine
R> for(j in 1:8) wine2[j, ] <- sample(wine[j,])
R> icc(wine2, model="oneway")
 Single Score Intraclass Correlation

   Model: oneway 
   Type : consistency 

   Subjects = 8 
     Raters = 4 
     ICC(1) = 0.728

 F-Test, H0: r0 = 0 ; H1: r0 > 0 
    F(7,24) = 11.7 , p = 2.18e-06 

 95%-Confidence Interval for ICC Population Values:
  0.434 < ICC < 0.927

R> icc(wine, model="twoway", type="agreement")
 Single Score Intraclass Correlation

   Model: twoway 
   Type : agreement 

   Subjects = 8 
     Raters = 4 
   ICC(A,1) = 0.728

 F-Test, H0: r0 = 0 ; H1: r0 > 0 
    F(7,24) = 11.8 , p = 2.02e-06 

 95%-Confidence Interval for ICC Population Values:
  0.434 < ICC < 0.927

R> icc(wine, model="twoway", type="consistency")
 Single Score Intraclass Correlation

   Model: twoway 
   Type : consistency 

   Subjects = 8 
     Raters = 4 
   ICC(C,1) = 0.729

 F-Test, H0: r0 = 0 ; H1: r0 > 0 
    F(7,21) = 11.8 , p = 5.03e-06 

 95%-Confidence Interval for ICC Population Values:
  0.426 < ICC < 0.928

Two-way fixed effects model 

R> wine3 <- data.frame(wine) %>% 
            dplyr::bind_cols(data.frame(subj = paste0("s", 1:8))) %>% 
            tidyr::pivot_longer(1:4, names_to="group", values_to="y")
R> wine3 %>% ggplot(aes(x=group, y=y)) + geom_point()

R> anova(aov(y ~ subj + group, data = wine3))
Analysis of Variance Table

Response: y
          Df  Sum Sq Mean Sq F value    Pr(>F)    
subj       7 188.219 26.8884 11.7867 5.026e-06 ***
group      3   7.344  2.4479  1.0731    0.3818    
Residuals 21  47.906  2.2813                      
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R> anova(aov(y ~ group + subj, data = wine3))
Analysis of Variance Table

Response: y
          Df  Sum Sq Mean Sq F value    Pr(>F)    
group      3   7.344  2.4479  1.0731    0.3818    
subj       7 188.219 26.8884 11.7867 5.026e-06 ***
Residuals 21  47.906  2.2812                      
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

R> library(car)
R> Anova(aov(y ~ subj + group, data = wine3))
Anova Table (Type II tests)

Response: y
           Sum Sq Df F value    Pr(>F)    
subj      188.219  7 11.7867 5.026e-06 ***
group       7.344  3  1.0731    0.3818    
Residuals  47.906 21                      
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Cohen's Kappa statistic

ICC and Kappa totally disagree

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