Collapse all columns by an ID column

Question

I'm trying to do something similar to what's answered here, which gets me 80% of the way. I have a data frame with one ID column and multiple information columns. I'd like to roll up all of the other columns so that there's only one row for each ID, and multiple entries are separated by, for instance, a semicolon. Here's an example of what I have and what I want.

HAVE:

     ID  info1          info2
1 id101    one          first
2 id102   twoA second alias A
3 id102   twoB second alias B
4 id103 threeA  third alias A
5 id103 threeB  third alias B
6 id104   four         fourth
7 id105   five          fifth

WANT:

     ID          info1                          info2
1 id101            one                          first
2 id102     twoA; twoB second alias A; second alias B
3 id103 threeA; threeB   third alias A; third alias B
4 id104           four                         fourth
5 id105           five                          fifth

Here's the code used to generate those:

have <- data.frame(ID=paste0("id", c(101, 102, 102, 103, 103, 104, 105)),
                   info1=c("one", "twoA", "twoB", "threeA", "threeB", "four", "five"), 
                   info2=c("first", "second alias A", "second alias B", "third alias A", "third alias B", "fourth", "fifth"),
                   stringsAsFactors=FALSE)
want <- data_frame(ID=paste0("id", c(101:105)),
                   info1=c("one", "twoA; twoB", "threeA; threeB", "four", "five"), 
                   info2=c("first", "second alias A; second alias B", "third alias A; third alias B", "fourth", "fifth"),
                   stringsAsFactors=FALSE)

This question asked basically the same question, but only a single "info" column. I have multiple other columns and would like to do this for all of them.

Bonus points for doing this using dplyr.

Answer 1

Here's an option using summarise_each (which makes it easy to apply the changes to all columns except the grouping variables) and toString:

require(dplyr)

have %>%
  group_by(ID) %>%
  summarise_each(funs(toString))

#Source: local data frame [5 x 3]
#
#     ID          info1                          info2
#1 id101            one                          first
#2 id102     twoA, twoB second alias A, second alias B
#3 id103 threeA, threeB   third alias A, third alias B
#4 id104           four                         fourth
#5 id105           five                          fifth

Or, if you want it separated by semicolons, you can use:

have %>%
  group_by(ID) %>%
  summarise_each(funs(paste(., collapse = "; ")))

Answer 2

Good old aggregate does this just fine

aggregate(have[,2:3], by=list(have$ID), paste, collapse=";")

Question is: does it scale?

Answer 3

Here's a data.table solution.

library(data.table)
setDT(have)[, lapply(.SD, paste, collapse = "; "), by = ID]
#       ID          info1                          info2
# 1: id101            one                          first
# 2: id102     twoA; twoB second alias A; second alias B
# 3: id103 threeA; threeB   third alias A; third alias B
# 4: id104           four                         fourth
# 5: id105           five                          fifth

Answer 4

Here is SQL solution^1:

library(sqldf)
#Static solution
sqldf("
SELECT ID,
       GROUP_CONCAT(info1,';') as info1,
       GROUP_CONCAT(info2,';') as info2
FROM have
GROUP BY ID")

#Dynamic solution
concat_cols <- colnames(have)[2:ncol(have)]
group_concat <-
  paste(paste0("GROUP_CONCAT(",concat_cols,",';') as ", concat_cols),
        collapse = ",")
sqldf(
  paste("
      SELECT ID,",
      group_concat,"
      FROM have
      GROUP BY ID"))

# Same output for both static and dynamic solutions
#      ID         info1                         info2
# 1 id101           one                         first
# 2 id102     twoA;twoB second alias A;second alias B
# 3 id103 threeA;threeB   third alias A;third alias B
# 4 id104          four                        fourth
# 5 id105          five                         fifth

^1 - probably data.table solution would perform better with millions of rows, luckily we don't have that many genes yet :)

Answer 5

library(stringr)
library(dplyr)
have %>% tbl_df %>% group_by(ID) %>% summarise_each(funs(str_c(., collapse="; ")))

Edit 1: So tbl_df may not needed and instead of the str_c of the stringr package you could use paste (in base). And what the above does is to group by the ID column and then apply the str_c (or paste) function to each remaining column for each group.

Edit 2: Another solution using the data.table package:

library(data.table)
dtbl <- as.data.table(have)
dtbl[,lapply(.SD, function(x) paste(x,collapse=";")), by=ID]

The above may be faster, especially if you set the key:

setkey(dtbl, ID)

"Hybrid" solution: You can use the dplyr syntax for data.tables! For example:

dtbl %>% tbl_dt %>%
     group_by(ID) %>% 
     summarise_each(funs(paste(., collapse="; ")))