CODEWITHSUNDEEP
r
Mark Miller
Mark Miller

Reputation: 13103

R: combine rows of a matrix by group

I am attempting to reformat the data set my.data to obtain the output shown below the my.data2 statement. Specifically, I want to put the last 4 columns of my.data on one line per record.id, where the last four columns of my.data will occupy columns 2-5 of the new data matrix if group=1 and columns 6-9 if group=2.

I wrote the cumbersome code below, but the double for-loop is causing an error that I simply cannot locate. Even if the double for-loop worked, I suspect there is a much more efficient way of accomplishing the same thing - (maybe reshape?)

Thank you for any help correcting the double for-loop or with more efficient code.

my.data <-  "record.id group s1 s2 s3 s4
    1  1      2      0      1      3
    1  2      0      0      0     12
    2  1      0      0      0      0
    3  1     10      0      0      0
    4  1      1      0      0      0
    4  2      0      0      0      0
    8  2      0      2      2      0
    9  1      0      0      0      0
    9  2      0      0      0      0"    

my.data2 <- read.table(textConnection(my.data), header=T)

# desired output
#
# 1     2      0      1      3      0      0      0     12
# 2     0      0      0      0      0      0      0      0
# 3    10      0      0      0      0      0      0      0
# 4     1      0      0      0      0      0      0      0
# 8     0      0      0      0      0      2      2      0
# 9     0      0      0      0      0      0      0      0

Code:

dat_sorted <- sort(unique(my.data2[,1]))
my.seq <- match(my.data2[,1],dat_sorted)

my.data3 <- cbind(my.seq, my.data2)

group.min <- tapply(my.data3$group, my.data3$my.seq, min)
group.max <- tapply(my.data3$group, my.data3$my.seq, max)

# my.min <- group.min[my.data3[,1]]
# my.max <- group.max[my.data3[,1]]

my.records <- matrix(0, nrow=length(unique(my.data3$record.id)), ncol=9)

x <- 1

for(i in 1:max(my.data3$my.seq)) {

   for(j in group.min[i]:group.max[i]) {

      if(my.data3[x,1] == i) my.records[i,1]   = i

      # the two lines below seem to be causing an error
      if((my.data3[x,1] == i) & (my.data3[x,3] == 1)) (my.records[i,2:5] = my.data3[x,4:7])
      if((my.data3[x,1] == i) & (my.data3[x,3] == 2)) (my.records[i,6:9] = my.data3[x,4:7])

      x <- x + 1

   }
}

Upvotes: 1

Views: 3114

Answers (2)

Mark Miller
Mark Miller

Reputation: 13103

Julius' answer is better, but for completeness, I think I managed to get the following for-loop to work:

dat_x <- (unique(my.data2[,1]))
my.seq <- match(my.data2[,1],dat_x)

my.data3 <- as.data.frame(cbind(my.seq, my.data2))

my.records <- matrix(0, nrow=length(unique(my.data3$record.id)), ncol=9)
my.records <- as.data.frame(my.records)

my.records[,1] = unique(my.data3[,2])

for(i in 1:9) {

      if(my.data3[i,3] == 1) (my.records[my.data3[i,1],c(2:5)] = my.data3[i,c(4:7)])
      if(my.data3[i,3] == 2) (my.records[my.data3[i,1],c(6:9)] = my.data3[i,c(4:7)])

}

Upvotes: 1

Julius Vainora
Julius Vainora

Reputation: 48191

You are right, reshape helps here.

library(reshape2)
m <- melt(my.data2, id.var = c("record.id", "group"))
dcast(m, record.id ~ group + variable, fill = 0)
  record.id 1_s1 1_s2 1_s3 1_s4 2_s1 2_s2 2_s3 2_s4
1         1    2    0    1    3    0    0    0   12
2         2    0    0    0    0    0    0    0    0
3         3   10    0    0    0    0    0    0    0
4         4    1    0    0    0    0    0    0    0
5         8    0    0    0    0    0    2    2    0
6         9    0    0    0    0    0    0    0    0

Comparison:

dfTest <- data.frame(record.id = rep(1:10e5, each = 2), group = 1:2, 
s1 = sample(1:10, 10e5 * 2, replace = TRUE), 
s2 = sample(1:10, 10e5 * 2, replace = TRUE), 
s3 = sample(1:10, 10e5 * 2, replace = TRUE), 
s4 = sample(1:10, 10e5 * 2, replace = TRUE))


system.time({
...# Your code
})
Error in my.records[i, 1] = i : incorrect number of subscripts on matrix
Timing stopped at: 41.61 0.36 42.56 

system.time({m <- melt(dfTest, id.var = c("record.id", "group"))
              dcast(m, record.id ~ group + variable, fill = 0)})
   user  system elapsed 
  25.04    2.78   28.72

Upvotes: 2

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