r - 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 cells, I am looking for a pre-existing function.

My initial data are as follow:

PLANT                  ANIMAL                          INTERACTIONS
---------------------- ------------------------------- ------------
Tragopogon_pratensis   Propylea_quatuordecimpunctata         1
Anthriscus_sylvestris  Rhagonycha_nigriventris               3
Anthriscus_sylvestris  Sarcophaga_carnaria                   2
Heracleum_sphondylium  Sarcophaga_carnaria                   1
Anthriscus_sylvestris  Sarcophaga_variegata                  4
Anthriscus_sylvestris  Sphaerophoria_interrupta_Gruppe       3
Cerastium_holosteoides Sphaerophoria_interrupta_Gruppe       1

I would like to create a table like this:

                       Propylea_quatuordecimpunctata Rhagonycha_nigriventris Sarcophaga_carnaria Sarcophaga_variegata Sphaerophoria_interrupta_Gruppe
---------------------- ----------------------------- ----------------------- ------------------- -------------------- -------------------------------
Tragopogon_pratensis   1                             0                       0                   0                    0
Anthriscus_sylvestris  0                             3                       2                   4                    3
Heracleum_sphondylium  0                             0                       1                   0                    0
Cerastium_holosteoides 0                             0                       0                   0                    1

That is, all plant species in row, all animal species in columns, and sometimes there are no interactions (while my initial data only list interactions that occur).

Answer 1

In base R, use table or xtabs:

with(warpbreaks, table(wool, tension))

    tension
wool L M H
   A 9 9 9
   B 9 9 9

xtabs(~wool+tension, data=warpbreaks)

    tension
wool L M H
   A 9 9 9
   B 9 9 9

The gmodels packages has a function CrossTable that gives output similar to what users of SPSS or SAS expects:

library(gmodels)
with(warpbreaks, CrossTable(wool, tension))


   Cell Contents
|-------------------------|
|                       N |
| Chi-square contribution |
|           N / Row Total |
|           N / Col Total |
|         N / Table Total |
|-------------------------|


Total Observations in Table:  54 


             | tension 
        wool |         L |         M |         H | Row Total | 
-------------|-----------|-----------|-----------|-----------|
           A |         9 |         9 |         9 |        27 | 
             |     0.000 |     0.000 |     0.000 |           | 
             |     0.333 |     0.333 |     0.333 |     0.500 | 
             |     0.500 |     0.500 |     0.500 |           | 
             |     0.167 |     0.167 |     0.167 |           | 
-------------|-----------|-----------|-----------|-----------|
           B |         9 |         9 |         9 |        27 | 
             |     0.000 |     0.000 |     0.000 |           | 
             |     0.333 |     0.333 |     0.333 |     0.500 | 
             |     0.500 |     0.500 |     0.500 |           | 
             |     0.167 |     0.167 |     0.167 |           | 
-------------|-----------|-----------|-----------|-----------|
Column Total |        18 |        18 |        18 |        54 | 
             |     0.333 |     0.333 |     0.333 |           | 
-------------|-----------|-----------|-----------|-----------|