如何通過循環比較R中對象的所有可能組合

Question

假設我有二元向量，需要將它們與Kappa函數進行類似比較。

library(asbio) 
A <- c(0,1,1,1,1,1,0) 
B <- c(0,0,1,0,1,0,1) 
C <- c(1,0,0,1,1,0,0) 
D <- c(1,1,0,0,0,1,1) 
E <- c(1,0,0,1,1,0,1) 

Kappa(A,B)$ttl_agreement # 42% 

如何循環Kappa功能得到表中的所有可能比較？

我希望得到的東西是這樣的：

A B C D E 
A 100 42 - - - 
B 42 100 - - - 
C - - 100 - - 
D - - - 100 - 
E - - - - 100 

Answer 1

可以使用outer功能

library(asbio) 

A <- c(0,1,1,1,1,1,0) 
B <- c(0,0,1,0,1,0,1) 
C <- c(1,0,0,1,1,0,0) 
D <- c(1,1,0,0,0,1,1) 
E <- c(1,0,0,1,1,0,1) 


M <- rbind(A,B,C,D,E) 

res <- outer(1:nrow(M), 
      1:nrow(M), 
      FUN=function(i,j){ 
       # i and j are 2 vectors of same length containing 
       # the combinations of the row indexes. 
       # e.g. (i[1] = 1, j[1] = 1) (i[2] = 1, j[2] = 2)) etc... 
       sapply(1:length(i), 
         FUN=function(x) Kappa(M[i[x],],M[j[x],])$ttl_agreement) 
      }) 
row.names(res) <- c('A','B','C','D','E') 
colnames(res) <- c('A','B','C','D','E') 

#> res 
      A   B   C   D   E 
# A 100.00000 42.85714 42.85714 28.57143 28.57143 
# B 42.85714 100.00000 42.85714 28.57143 57.14286 
# C 42.85714 42.85714 100.00000 28.57143 85.71429 
# D 28.57143 28.57143 28.57143 100.00000 42.85714 
# E 28.57143 57.14286 85.71429 42.85714 100.00000 

編輯：

如果你喜歡一個for循環（I」 d建議運行一些測試以查看哪種方法更快），則可以使用expand.grid生成組合，然後重複在他們填寫矩陣

M <- rbind(A,B,C,D,E) 

res <- matrix(NA,nrow=5,ncol=5) # pre-allocate the matrix 
combs <- expand.grid(1:nrow(M),1:nrow(M)) 
for(i in 1:nrow(combs)){ 
    r <- combs[i,1] 
    c <- combs[i,2] 
    res[r,c] <- Kappa(M[r,],M[c,])$ttl_agreement 
} 
row.names(res) <- c('A','B','C','D','E') 
colnames(res) <- c('A','B','C','D','E')