Handling missing combinations of factors in R

Question

So, I have a data frame with two factors and one numeric variable like so:

>D
f1 f2 v1 
1   A  23
2   A  45
2   B  27
     .
     .
     .

Answer 1

Using your data:

dat <- data.frame(f1 = factor(c(1,2,2)), f2 = factor(c("A","A","B")),
                  v1 = c(23,45,27))

one option is to create a lookup table with the combinations of levels, which is done using the expand.grid() function supplied with the levels of both factors, as shown below:

dat2 <- with(dat, expand.grid(f1 = levels(f1), f2 = levels(f2)))

A database-like join operation can then be performed using the merge() function in which we specify that all values from the lookup table are included in the join (all.y = TRUE)

newdat <- merge(dat, dat2, all.y = TRUE)

The above line produces:

> newdat
  f1 f2 v1
1  1  A 23
2  1  B NA
3  2  A 45
4  2  B 27

As you can see, the missing combinations are given the value NA indicating the missing-ness. It is realtively simple to then replace these NAs with 0s:

> newdat$v1[is.na(newdat$v1)] <- 0
> newdat
  f1 f2 v1
1  1  A 23
2  1  B  0
3  2  A 45
4  2  B 27

Answer 2

I add the tidyr solution, spreading with fill=0 and gathering.

library(tidyr)
df %>% spread(f2, v1, fill=0) %>% gather(f2, v1, -f1)

#  f1 f2 v1
#1  1  A 23
#2  2  A 45
#3  1  B  0
#4  2  B 27

You could equally do df %>% spread(f1, v1, fill=0) %>% gather(f1, v1, -f2).

Answer 3

Two years late, but I had the same problem and came up with this plyr solution:

dat <- data.frame(f1 = factor(c(1,2,2)), f2 = factor(c("A","A","B")), v1 = c(23,45,27))

newdat <- ddply(dat, .(f1,f2), numcolwise(function(x) {if(length(x)>0) x else 0.0}), .drop=F)

> newdat
  f1 f2 v1
1  1  A 23
2  1  B  0
3  2  A 45
4  2  B 27