你可以试试crossprod + xtabs + as.data.frame.table

> tbl <- crossprod(!!xtabs(QTY ~ ., df))
> tbl[upper.tri(tbl, TRUE)] <- NA
> na.omit(as.data.frame.table(tbl))
        SKU    SKU.1 Freq
2   Banana   Apple      2
3   Cherry   Apple      1
4   Grape    Apple      1
5   Pear     Apple      1
8   Cherry   Banana     1
9   Grape    Banana     1
10  Pear     Banana     2
14  Grape    Cherry     0
15  Pear     Cherry     1
20  Pear     Grape      0

或者，如果您想删除0同现，可以尝试

> tbl <- crossprod(!!xtabs(QTY ~ ., df))
> tbl[upper.tri(tbl, TRUE) | tbl < 1] <- NA
> na.omit(as.data.frame.table(tbl))
        SKU    SKU.1 Freq
2   Banana   Apple      2
3   Cherry   Apple      1
4   Grape    Apple      1
5   Pear     Apple      1
8   Cherry   Banana     1
9   Grape    Banana     1
10  Pear     Banana     2
15  Pear     Cherry     1

数据

df <- structure(list(Order = c(1, 1, 1, 1, 2, 2, 2, 3, 3), SKU = c(" Banana ",
" Apple  ", " Pear   ", " Cherry ", " Banana ", " Apple  ", " Grape  ", 
" Banana ", " Pear   "), QTY = c(1L, 2L, 1L, 2L, 4L, 1L, 1L,
2L, 1L)), class = "data.frame", row.names = c(NA, -9L))