How to calculate a table of pairwise counts from long-form data frame

Question

I have a \'long-form\' data frame with columns id (the primary key) and featureCode (categorical variable). Each record has between 1 and 9 values

Answer 1

Another solution, which is conceptually easy to follow, I think. You have a bipartite graph here, and simply need the projection of this graph onto the "featureCode" vertices. Here is how to do this with the igraph package:

dat <- read.table(header = TRUE, stringsAsFactors=FALSE,
                  text = "id  featureCode                                       
                          5         PPLC                                                  
                          5         PCLI                                                  
                          6         PPLC                                                  
                          6         PCLI                                                  
                          7          PPL                                                  
                          7         PPLC                                                  
                          7         PCLI                                                  
                          8         PPLC                                                  
                          9         PPLC                                                  
                         10         PPLC")

g <- graph.data.frame(dat, vertices=unique(data.frame(c(dat[,1], dat[,2]),
                          type=rep(c(TRUE, FALSE), each=nrow(dat)))))

get.adjacency(bipartite.projection(g)[[1]], attr="weight", sparse=FALSE)

#      PPLC PCLI PPL
# PPLC    0    3   1
# PCLI    3    0   1
# PPL     1    1   0