Adding Elements to List using For Loop in R

Question

I am trying to create a simple data frame that contains information about what authors and their respective papers. I have a matrix that contains the author IDs as the rows and the paper IDs as the columns. This matrix contains 1s and 0s, where a 1 indicates that the author worked on that paper. For example, if A2P[1,1] == 1, that means that the author with ID 1 worked on the paper with ID 1.

I am trying to convert this matrix into a simple data frame that contains all of these relationships, something that just contains the author IDs and the papers that they worked on. As in,

au_ID  P_ID
1      1
1      12        # Author 1 has worked on both paper 1 and 12
2      1         # Author 2 has also worked on paper 1, in addition to papers 2 and 3. 
2      2
2      3 
...

Here is what I am doing:

list1 <- list()
list2 <- list()
# Rows are Author IDs
# Columns are Paper IDs
for (row in 1:nrow(A2P)){
  for (col in 1:ncol(A2P)){
    if (A2P[row,col] == 1){
      list1 <- append(list1, row)
      list2 <- append(list2, col)
    }
  }
}
authorship["au_ID"] = list1
authorship["P_ID"] = list2

I am having difficulty getting this code to run quickly. It is taking forever to run, going on twenty minutes now. I think it has something to do with appending each row and column value to each of the lists, but I am unsure.

Any help would be greatly appreciated! Thank you so much!

Cole · Accepted Answer · 2020-04-29 00:25:41Z

3

You likely need which(A2P == 1L, arr.ind = TRUE)

mat <- matrix(c(1L, 0L, 0L, 0L, 1L, 1L, 1L, 0L, 1L), ncol = 3)

mat
#     [,1] [,2] [,3]
#[1,]    1    0    1
#[2,]    0    1    0
#[3,]    0    1    1

which(mat == 1L, arr.ind = TRUE)
#     row col
#[1,]   1   1
#[2,]   2   2
#[3,]   3   2
#[4,]   1   3
#[5,]   3   3

In this case, row would correspond to au_ID and col would correspond to P_ID. Then to get it in your format completely:

authorship <- which(mat == 1L, arr.ind = TRUE)
colnames(authorship) <- c('au_ID', 'P_ID')

as.data.frame(authorship)
##  au_ID P_ID
##1     1    1
##2     2    2
##3     3    2
##4     1    3
##5     3    3

answered Apr 29, 2020 at 0:25

Cole

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3 Comments

RyanFrost Over a year ago

Nice solution, love the simplicity

Tal Over a year ago

Thank you very much! My code actually did finish running, and I was able to create the data frame I wanted using the following: authorship <- do.call(rbind, Map(data.frame, au_ID=list1, P_ID=list2))

Tal Over a year ago

However, yours is so much more compact and does not use a loop. Thank you very much! I really appreciate it as I'm quite new to R - I was trying to use python syntax with the whole authorship["au_ID"] thing.

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