R Data.table for computing summary stats across multiple columns

Question

I have a similar question to: R: data.table : searching on multiple columns AND setting data type , but this question did not get fully answered. I have a pairwise table that looks conceptually like the one below. The table is the result of converting a very large distance matrix into a data.table (> 100,000,000 rows), such that the comparison a,b is the same as b,a. However a and b may appear in either column V1 or V2. I want to compute simple summary statistics using data.table's querying style, but i haven't quite figured out how to select keys in either column. Is this possible?

I've tried setting keys in either direction, but this returns just the data for that column. I also tried using list(), but that returns the intersection (understandably), i hoped for a by=key1|key2, but no such luck.

> set.seed(123)
> 
> #create pairwise data
> a<-data.table(t(combn(3,2)))
> #create column that is equal both ways, 1*2 == 2*1
> dat<-a[,data:=V1*V2]
> dat
   V1 V2 data
1:  1  2    2
2:  1  3    3
3:  2  3    6
#The id ==2 is the problem here, the mean should be 4 ((2+6)/2)

> #set keys
> setkey(dat,V1,V2)
> 
> #One way data
> dat[,c("MEAN","VAR"):=list(mean(data),var(data)),by=V1]
> dat
   V1 V2 data MEAN VAR
1:  1  2    2  2.5 0.5
2:  1  3    3  2.5 0.5
3:  2  3    6  6.0  NA

> #The other way
> dat[,c("MEAN","VAR"):=list(mean(data),var(data)),by=V2]
> dat
   V1 V2 data MEAN VAR
1:  1  2    2  2.0  NA
2:  1  3    3  4.5 4.5
3:  2  3    6  4.5 4.5
> 
> #The intersect just produces the original data
> dat[,c("MEAN","VAR"):=list(mean(data),var(data)),by=list(V1,V2)]
> dat
   V1 V2 data MEAN VAR
1:  1  2    2    2  NA
2:  1  3    3    3  NA
3:  2  3    6    6  NA
> 
> #Meaningless but hopefull attempt. 
> dat[,c("MEAN","VAR"):=list(mean(data),var(data)),by=V1|V2]
> dat
   V1 V2 data     MEAN      VAR
1:  1  2    2 3.666667 4.333333
2:  1  3    3 3.666667 4.333333
3:  2  3    6 3.666667 4.333333
#The goal is to create a table would look like this (using mean as an example)
ID MEAN
 1  2.5
 2  4.0
 3  4.5

My default ideas would be too loop through a dat[V1==x|V2==x] statement, but i don't think i'm harnessing the full power of data.table to return a single column of ids with mean the var as summary columns.

Thank you!

edited to reflect the hopeful result, which is a single column of ids with the mean and var for that ID. Thank you for helping clarify. — bw4sz
– bw4sz, Commented May 7, 2014 at 15:06

eddi · Accepted Answer · 2014-05-07 15:15:02Z

5

It'll be easiest to rearrange your data a little to achieve what you want (I'm using recycling of data below not to type c(data, data) in the first part):

dat[, list(c(V1, V2), data)][, list(MEAN = mean(data)), by = V1]
#   V1 MEAN
#1:  1  2.5
#2:  2  4.0
#3:  3  4.5

answered May 7, 2014 at 15:15

eddi

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