How to convert a matrix into a list in R [closed]

Question

I'm looking to create a script to convert a matrix of species abundance e.g:

species abundance matrix

into two vectors e.g:

vectors

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If you feel there is no easy answer to this and that it would be easier to do in excel or open office calc (or another program), please let me know.

Answer 1

How about something like this:

 #I typed in some data to make sure it works:
 species1 = c(5,4,NA,NA)
 species2 = c(NA,NA,5,NA)
 species3 = c(4,4,NA,NA)
 species4 = c(NA,4,NA,6)

 data.matrix = rbind(species1,species2, species3, species4)



 #lets say your original dataframe is called data.matrix 
 #and your new data set is called data.list
 #the number of rows in your new data set is the number of values that are not NA:
 rows = length(data.matrix[!is.na(data.matrix)])
 data.list = matrix(nrow = rows, ncol = 2)
 k = 1 #an index variable for the new data set
 for(j in 1:ncol(data.matrix)){
   for(i in 1:nrow(data.matrix)){
     if(is.na(data.matrix[j,i]) == FALSE){
       #store the site number
       data.list[k,1] = i
       #store the species number
       data.list[k,2] = j
       k = k + 1
     }
   }
 }
 #sort the data by the first column
 data.list = data.list[order(data.list[,1]),]

Output:

data.list [,1] [,2]

 [1,]    1    1
 [2,]    1    3
 [3,]    2    1
 [4,]    2    3
 [5,]    2    4
 [6,]    3    2
 [7,]    4    4

I think this question is OK in the stats section of stack exchange. I've noticed that this is a really common data transform for people in Biology to prepare their data for statistical analysis.