# Is there an R function for combining two replicate site columns in a table to show presence absence of species?

I have the following DF (example data, my actual data set is 96 columns):

``````   class   X1A X1B X2A X2B X3A X3B X4A X4B X5A X5B X6A X6B
1       A     0   1   0   0   0   0   0   1   1   1   1   1
2       B     1   1   1   1   0   0   0   1   1   1   0   1
3       C     0   0   0   1   1   0   0   0   1   1   0   0
4       D     0   0   0   1   1   0   1   0   1   0   0   0
5       A     0   1   1   1   0   0   0   1   1   1   1   1
6       B     0   0   1   1   0   0   0   1   1   1   0   1
7       C     0   0   0   1   1   0   0   0   1   1   0   0
8       D     0   0   0   1   1   0   1   0   1   0   0   0
9       A     0   1   1   1   0   0   0   1   1   1   1   1
10      B     1   1   1   1   0   0   0   1   1   1   0   1
11      C     0   0   0   1   1   0   0   0   1   1   0   0
12      D     0   1   0   1   1   0   1   0   1   0   0   0
``````

Class denotes the phylogenic class of the organism (each replicate of the letter is a different species but members of the same class). 1A and 1B are samples from the same site. I want to combine the two presence/absence data (1/0 respectively) from each two samples from every site and add up the number of "presences" for the class across that site. so that my df now looks something like this:

``````  Sample Class  Number of Species Present
1     A     3
1     B     2
1     C     0
1     D     1
2     A     2
2     B     3
2     C     3
2     D     3
``````

For example, in the original df you see that Class C species are not present in sample 2A at all but each species of class C is present in sample 2B. So the output df records Species C as present 3 times in sample 2. Furthermore, Class B has 3 different species occur in 2A and in 2B but because they are replicates of the output df records sample 2 as having 3 Class B species present.

Any help would be appreactiated as I'm stumped!

Cheers!!

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