How do I get a contingency table?

Question

I am trying to create a contingency table from a particular type of data. This would be doable with loops etc... but because my final table would contain more than 10E5 cell

Answer 1

xtabs in base R should work, for example:

dat <- data.frame(PLANT = c("p1", "p2", "p2", "p4", "p5", "p5", "p6"),
                  ANIMAL = c("a1", "a2", "a3", "a3", "a4", "a5", "a5"),
                  INTERACTIONS = c(1,3,2,1,4,3,1),
                  stringsAsFactors = FALSE)

(x2.table <- xtabs(dat$INTERACTIONS ~ dat$PLANT + dat$ANIMAL))

     dat$ANIMAL
dat$PLANT a1 a2 a3 a4 a5
       p1  1  0  0  0  0
       p2  0  3  2  0  0
       p4  0  0  1  0  0
       p5  0  0  0  4  3
       p6  0  0  0  0  1

chisq.test(x2.table, simulate.p.value = TRUE)

I think that should do what you're looking for fairly easily. I'm not sure how it scales up in terms of efficiency to a 10E5 contingency table, but that might be a separate issue statistically.