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
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 | |
-------------|-----------|-----------|-----------|-----------|