Creating co-occurrence matrix
matrix, r
Solution
I'd use a combination of the reshape2 package and matrix algebra:
#read in your data
dat <- read.table(text="TrxID Items Quant
Trx1 A 3
Trx1 B 1
Trx1 C 1
Trx2 E 3
Trx2 B 1
Trx3 B 1
Trx3 C 4
Trx4 D 1
Trx4 E 1
Trx4 A 1
Trx5 F 5
Trx5 B 3
Trx5 C 2
Trx5 D 1", header=T)
#making the boolean matrix
library(reshape2)
dat2 <- melt(dat)
w <- dcast(dat2, Items~TrxID)
x <- as.matrix(w[,-1])
x[is.na(x)] <- 0
x <- apply(x, 2, function(x) as.numeric(x > 0)) #recode as 0/1
v <- x %*% t(x) #the magic matrix
diag(v) <- 0 #repalce diagonal
dimnames(v) <- list(w[, 1], w[,1]) #name the dimensions
v
For the graphing maybe...
g <- graph.adjacency(v, weighted=TRUE, mode ='undirected')
g <- simplify(g)
# set labels and degrees of vertices
V(g)$label <- V(g)$name
V(g)$degree <- degree(g)
plot(g)
Problem
I'm trying to solve the problem of having a co-occurence matrix. I have a datafile of transactions and items, and I want to see a matrix of the number of transactions where items appear together. I'm a newbie in R programming and I'm having some fun finding out all the shortcuts that R has, rather than creating specific loops (I used to use C years ago and only sticking to Excel macros and SPSS now). I have checked the solutions here, but haven't found one that works (the closest is the solution given here: Co-occurrence matrix using SAC? - but it produced an error message when I used projecting_tm, I suspected that the cbind wasn't successful in my case. Essentially I have a table containing the following: ``` TrxID Items Quant Trx1 A 3 Trx1 B 1 Trx1 C 1 Trx2 E 3 Trx2 B 1 Trx3 B 1 Trx3 C 4 Trx4 D 1 Trx4 E 1 Trx4 A 1 Trx5 F 5 Trx5 B 3 Trx5 C 2 Trx5 D 1, etc. ``` I want to create something like: ``` A B C D E F A 0 1 1 0 1 1 B 1 0 3 1 1 0 C 1 3 0 1 0 0 D 1 1 1 0 1 1 E 1 1 0 1 0 0 F 0 1 1 1 0 0 ``` What I did was (and you'd probably laugh at my rookie R approach): ``` library(igraph) library(tnet) trx <- read.table("FileName.txt", header=TRUE) transID <- t(trx[1]) items <- t(trx[2]) id_item <- cbind(items,transID) item_item <- projecting_tm(id_item, method="sum") item_item <- tnet_igraph(item_item,type="weighted one-mode tnet") item_matrix <-get.adjacency(item_item,attr="weight") item_matrix ``` As mentioned above the cbind was probably unsuccessful, so the projecting_tm couldn't give me any result. Any alternative approach or a correction to my method? Your help would be much appreciated!