Alex - 11 months ago 68

R Question

I have trouble solving the following problem concerning the (simplified by limiting number of columns) data frame 'annotations' below.

`require(irr)`

# data

annotations <- read.table(text = "Obj1 Obj2 Obj3

Rater1 a b c

Rater2 a b b

Rater3 a b c", header = TRUE, stringsAsFactors = FALSE)

I would like to apply the function agree from the irr package to all combinations (not permutations) of rows, resulting in the following.

`Agreement rater 1-2: 67%`

Agreement rater 1-3: 100%

Agreement rater 2-3: 67%

I need to run a function on all combinations of rows and the function would need to access a number of/all columns.

I have worked out parts of the answer to the problem; I have generated a list of combinations running

`combn(rownames(annotations), 2)`

I have tried apply, as in

`apply(annotations, 1, agree)`

Does anyone have an idea how to proceed?

UPDATE: The following solution, based on your suggestions, works. (I have used

`kappa2`

`agree`

`require(irr) #require the irr library for agreement calculations`

annotations <- read.table(text = "Obj1 Obj2 Obj3

Rater1 a b c

Rater2 a b b

Rater3 a b c

Rater4 c a a", header = TRUE, stringsAsFactors = FALSE)

annotations <- t(annotations) #transpose annotations (rows become columns and vice versa)

kappa_list <- combn(colnames(annotations), 2, FUN=function(x) kappa_list[[length(kappa_list)+1]] = kappa2(matrix(c(annotations[,x[1]], annotations[,x[2]]), ncol=2))$value) #fill kappa_list with all pairs of columns (combinations of 2 raters) in annotations and, per combination, add a value to kappa_list that consists of the value of kappa2 applied to the current combination of raters

kappa_list # display the list of values

Answer Source

You are close, you just need to `apply`

on the result of `combn`

instead. I have no idea what function you are referring to, but this should work the same if you plug in your function.

First, save the results as a list instead, because it is easier to add names (which I am adding my combining the two entries together):

```
toCheck <- combn(rownames(annotations), 2, simplify = FALSE)
names(toCheck) <-
sapply(toCheck, paste, collapse = " - ")
```

Then, use `sapply`

to work through your combinations. Here, I am using `mean`

to do the comparison, but use what you need here. If you are returning more than a single value, use `lapply`

then work with the result to print as desired

```
sapply(toCheck, function(x){
mean(annotations[x[1], ] == annotations[x[2], ])
})
```

Which returns:

```
Rater 1 - Rater 2 Rater 1 - Rater 3 Rater 2 - Rater 3
0.6666667 1.0000000 0.6666667
```