CODEWITHSUNDEEP
rsparse-matrix
Allen Wang
Allen Wang

Reputation: 2502

bind together sparse model matrices by row names

I am trying to construct a large sparse matrix with a split-apply-combine approach by separately calling sparse.model.matrix() from the package Matrix on subsets of columns of a dataframe and then binding them together into a full matrix. I have to do this because of memory limitations (I can't call sparse.model.matrix on the whole df at once). This process works fine, and I get a list of sparse matrices, but these have different dimensions and when I try to bind them together, I can't.

ex:

data(iris)
set.seed(100)
iris$v6 <- sample(c("a","b","c",NA), 150, replace=TRUE)
iris$v7 <- sample(c("x","y",NA), 150, replace = TRUE)

sparse_m1 <- sparse.model.matrix(~., iris[,1:5])
sparse_m2 <- sparse.model.matrix(~.-1, iris[, 6:7])

dim(sparse_m1)
[1] 150   7

dim(sparse_m2)
[1] 71  4

cbind2(sparse_m1, sparse_m2)
Error: Matrices must have same number of rows in cbind2(sparse_m1, sparse_m2)

cbind(sparse_m1, sparse_m2)
Error: Matrices must have same number of rows in cbind2(..1, r)

The matrices have the same row names, just some rows have been omitted from sparse_m2 because they had missing values in both columns. Is there any way to combine them?

I also tried using rbind.fill.matrix() from the plyr package, by first transposing and then calling it and then re-transposing, but then I lose column names since row names are ignored in rbind.fill.matrix.

Any ideas?

Upvotes: 1

Views: 1245

Answers (2)

malcook
malcook

Reputation: 1733

An old question still in need of an answer...

One approach is to create an empty Matrix of the required dimensions and then populate it:

m12.dimnames<-list(union(rownames(sparse_m1),rownames(sparse_m2)),c(colnames(sparse_m1),colnames(sparse_m2)))
m12<- Matrix(0,nrow=length(m12.dimnames[[1]]),ncol=length(m12.dimnames[[2]]),dimnames=m12.dimnames)
m12[rownames(sparse_m2),colnames(sparse_m2)]<-sparse_m1
m12[rownames(sparse_m2),colnames(sparse_m2)]<-sparse_m2

Upvotes: 1

coulminer
coulminer

Reputation: 368

recently bumped in the same issue, and nowadays you can 

install.packages("Matrix.utils")
library(Matrix.utils)
sparse_filled <- rBind.fill(sparse_m1, sparse_m2)

Upvotes: 0

Related Questions