How to find the number of variables in common between variables two by two in a column R compared to variables in another column?

Question

I'm working on R, I have a character data table like that :

Species<- c("lion", "tiger", "lion","tiger","donkey","lion","donkey")
Countries <- c("Tanzania", "Tanzania", "Kenya","Kenya","Italia","Niger","France")

df <- data.frame(Species, Countries)

Species	Countries
lion	Tanzania
tiger	Tanzania
lion	Kenya
tiger	Kenya
donkey	Italia
lion	Niger
donkey	France

With this table, I would like to have for each country of my dataframe the number of species in common for the countries 2 by 2, and have a final table like this one:

Countries1	Countries2	number_common_species
Kenya	Tanzania	2
Italia	Tanzania	0
Italia	Kenya	0
Niger	Kenya	1
Niger	Tanzania	1
Italia	Niger	0
Italia	France	1
Tanzania	France	0
Kenya	France	0
Niger	France	0

I have a really big dataset with a lot of species.

Does anyone know how I can do this?

Answer 1

First make a data frame of each pairwise combination of countries, then find the length of the set of species that each pair has in common:

counts <- data.frame(t(combn(unique(dat$Countries),2)))
counts$count <- apply(counts, 1, function(x) length(intersect( dat$Species[dat$Countries==x[1]], 
                                                               dat$Species[dat$Countries==x[2]])))
counts

         X1     X2 count
1  Tanzania  Kenya     2
2  Tanzania Italia     0
3  Tanzania  Niger     1
4  Tanzania France     0
5     Kenya Italia     0
6     Kenya  Niger     1
7     Kenya France     0
8    Italia  Niger     0
9    Italia France     1
10    Niger France     0