converting a dgCMatrix to data frame

I would like to convert a sparse matrix into a data frame of the type (row,column, value). I have found questions such as http://r.789695.n4.nabble.com/Converting-sparse-matrix-to-data-frame-in-Matrix-package-td2332012.html that in the question start with row,column,value and create a sparse matrix. I want the inverse, and I cannot use the as.matrix function, because the matrix is too large. Here is a small example.

r = c(1,2,2,3,3)

c = c(4,1,2,3,5)

v = c(1,2,1,3,1)



a = sparseMatrix(i=r,j=c,x=v) 



3 x 5 sparse Matrix of class "dgCMatrix"



[1,] . . . 1 .

[2,] 2 1 . . .

[3,] . . 3 . 1

Can I get a data.frame

Thank you

asked Nov 26 '18 at 17:23

HowYaDoing

495311

for calculating inverse, as you mention, solve() doesn't work? (a %*% t(a)) %>% solve seems to return a sparseMatrix object. Unless you need generalized inverse?

– Nutle
Nov 26 '18 at 18:25

not a matrix inverse, the question I pointed to started with vectors to create a data frame, then created a dense matrix. I wanted to start with a sparse matrix, and get a data frame of (row,col,value). I want to invert his problem, not invert the matrix.

– HowYaDoing
Nov 26 '18 at 20:00

oh, I see. Still, it's an open question (for me) of how to use generic matrix methods (such as MASS::ginv, for example), with sparseMatrix objects without resolving to as.matrix. I thought you were after a similar thing, but sadly the accepted answer does not solve it.

– Nutle
Nov 26 '18 at 20:03

add a comment |

r = c(1,2,2,3,3)

c = c(4,1,2,3,5)

v = c(1,2,1,3,1)



a = sparseMatrix(i=r,j=c,x=v) 



3 x 5 sparse Matrix of class "dgCMatrix"



[1,] . . . 1 .

[2,] 2 1 . . .

[3,] . . 3 . 1

Can I get a data.frame

Thank you

asked Nov 26 '18 at 17:23

HowYaDoing

495311

for calculating inverse, as you mention, solve() doesn't work? (a %*% t(a)) %>% solve seems to return a sparseMatrix object. Unless you need generalized inverse?

– Nutle
Nov 26 '18 at 18:25

not a matrix inverse, the question I pointed to started with vectors to create a data frame, then created a dense matrix. I wanted to start with a sparse matrix, and get a data frame of (row,col,value). I want to invert his problem, not invert the matrix.

– HowYaDoing
Nov 26 '18 at 20:00

oh, I see. Still, it's an open question (for me) of how to use generic matrix methods (such as MASS::ginv, for example), with sparseMatrix objects without resolving to as.matrix. I thought you were after a similar thing, but sadly the accepted answer does not solve it.

– Nutle
Nov 26 '18 at 20:03

add a comment |

r = c(1,2,2,3,3)

c = c(4,1,2,3,5)

v = c(1,2,1,3,1)



a = sparseMatrix(i=r,j=c,x=v) 



3 x 5 sparse Matrix of class "dgCMatrix"



[1,] . . . 1 .

[2,] 2 1 . . .

[3,] . . 3 . 1

Can I get a data.frame

Thank you

asked Nov 26 '18 at 17:23

HowYaDoing

495311

r = c(1,2,2,3,3)

c = c(4,1,2,3,5)

v = c(1,2,1,3,1)



a = sparseMatrix(i=r,j=c,x=v) 



3 x 5 sparse Matrix of class "dgCMatrix"



[1,] . . . 1 .

[2,] 2 1 . . .

[3,] . . 3 . 1

Can I get a data.frame

Thank you

r sparse-matrix

asked Nov 26 '18 at 17:23

HowYaDoing

495311

asked Nov 26 '18 at 17:23

HowYaDoing

495311

asked Nov 26 '18 at 17:23

HowYaDoing

495311

asked Nov 26 '18 at 17:23

HowYaDoing

495311

asked Nov 26 '18 at 17:23

HowYaDoing

495311

for calculating inverse, as you mention, solve() doesn't work? (a %*% t(a)) %>% solve seems to return a sparseMatrix object. Unless you need generalized inverse?

– Nutle
Nov 26 '18 at 18:25

not a matrix inverse, the question I pointed to started with vectors to create a data frame, then created a dense matrix. I wanted to start with a sparse matrix, and get a data frame of (row,col,value). I want to invert his problem, not invert the matrix.

– HowYaDoing
Nov 26 '18 at 20:00

oh, I see. Still, it's an open question (for me) of how to use generic matrix methods (such as MASS::ginv, for example), with sparseMatrix objects without resolving to as.matrix. I thought you were after a similar thing, but sadly the accepted answer does not solve it.

– Nutle
Nov 26 '18 at 20:03

add a comment |

for calculating inverse, as you mention, solve() doesn't work? (a %*% t(a)) %>% solve seems to return a sparseMatrix object. Unless you need generalized inverse?

– Nutle
Nov 26 '18 at 18:25

not a matrix inverse, the question I pointed to started with vectors to create a data frame, then created a dense matrix. I wanted to start with a sparse matrix, and get a data frame of (row,col,value). I want to invert his problem, not invert the matrix.

– HowYaDoing
Nov 26 '18 at 20:00

oh, I see. Still, it's an open question (for me) of how to use generic matrix methods (such as MASS::ginv, for example), with sparseMatrix objects without resolving to as.matrix. I thought you were after a similar thing, but sadly the accepted answer does not solve it.

– Nutle
Nov 26 '18 at 20:03

for calculating inverse, as you mention, solve() doesn't work? (a %*% t(a)) %>% solve seems to return a sparseMatrix object. Unless you need generalized inverse?

– Nutle
Nov 26 '18 at 18:25

not a matrix inverse, the question I pointed to started with vectors to create a data frame, then created a dense matrix. I wanted to start with a sparse matrix, and get a data frame of (row,col,value). I want to invert his problem, not invert the matrix.

– HowYaDoing
Nov 26 '18 at 20:00

oh, I see. Still, it's an open question (for me) of how to use generic matrix methods (such as MASS::ginv, for example), with sparseMatrix objects without resolving to as.matrix. I thought you were after a similar thing, but sadly the accepted answer does not solve it.

– Nutle
Nov 26 '18 at 20:03

add a comment |

1 Answer
1

active

oldest

votes

You can use

b = as.data.frame(summary(a))

#   i j x

# 1 2 1 2

# 2 2 2 1

# 3 3 3 3

# 4 1 4 1

# 5 3 5 1

If you need the same order as in your example, you can use

b = b[order(b$i),]

#   i j x

# 4 1 4 1

# 1 2 1 2

# 2 2 2 1

# 3 3 3 3

# 5 3 5 1

Another alternative, though not quite as neat, is to use

b = as(a, "dgTMatrix")

cbind.data.frame(r = b@i + 1, c = b@j + 1, x = b@x)

edited Nov 26 '18 at 17:56

answered Nov 26 '18 at 17:45

dww

15.2k22656

Any idea whether this approach is indeed cheaper than as.matrix %>% as.data.frame approach? (colnames doesn't matter)

– Nutle
Nov 26 '18 at 18:17

also, in the first case b %*% t(b) returns the following error:requires numeric/complex matrix/vector arguments. I don't see how can we avoid as.matrix here

– Nutle
Nov 26 '18 at 18:21

Thanks. That is exactly what I was looking for!!!

– HowYaDoing
Nov 26 '18 at 19:54

@Nutle your comments are't really applicable here. As noted already by OP you seem to have mistaken that the question is about inverse matrices - it is not. Maybe consider deleting your comments in case they could inadvertently be misleading to other readers?

– dww
Nov 29 '18 at 15:15

I will cite the exact words from the OP's question: and I cannot use the as.matrix function, because the matrix is too large.

– Nutle
Nov 29 '18 at 15:30

|
show 3 more comments

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1 Answer
1

active

oldest

votes

1 Answer
1

active

oldest

votes

You can use

b = as.data.frame(summary(a))

#   i j x

# 1 2 1 2

# 2 2 2 1

# 3 3 3 3

# 4 1 4 1

# 5 3 5 1

If you need the same order as in your example, you can use

b = b[order(b$i),]

#   i j x

# 4 1 4 1

# 1 2 1 2

# 2 2 2 1

# 3 3 3 3

# 5 3 5 1

Another alternative, though not quite as neat, is to use

b = as(a, "dgTMatrix")

cbind.data.frame(r = b@i + 1, c = b@j + 1, x = b@x)

edited Nov 26 '18 at 17:56

answered Nov 26 '18 at 17:45

dww

15.2k22656

Any idea whether this approach is indeed cheaper than as.matrix %>% as.data.frame approach? (colnames doesn't matter)

– Nutle
Nov 26 '18 at 18:17

also, in the first case b %*% t(b) returns the following error:requires numeric/complex matrix/vector arguments. I don't see how can we avoid as.matrix here

– Nutle
Nov 26 '18 at 18:21

Thanks. That is exactly what I was looking for!!!

– HowYaDoing
Nov 26 '18 at 19:54

@Nutle your comments are't really applicable here. As noted already by OP you seem to have mistaken that the question is about inverse matrices - it is not. Maybe consider deleting your comments in case they could inadvertently be misleading to other readers?

– dww
Nov 29 '18 at 15:15

I will cite the exact words from the OP's question: and I cannot use the as.matrix function, because the matrix is too large.

– Nutle
Nov 29 '18 at 15:30

|
show 3 more comments

You can use

b = as.data.frame(summary(a))

#   i j x

# 1 2 1 2

# 2 2 2 1

# 3 3 3 3

# 4 1 4 1

# 5 3 5 1

If you need the same order as in your example, you can use

b = b[order(b$i),]

#   i j x

# 4 1 4 1

# 1 2 1 2

# 2 2 2 1

# 3 3 3 3

# 5 3 5 1

Another alternative, though not quite as neat, is to use

b = as(a, "dgTMatrix")

cbind.data.frame(r = b@i + 1, c = b@j + 1, x = b@x)

edited Nov 26 '18 at 17:56

answered Nov 26 '18 at 17:45

dww

15.2k22656

Any idea whether this approach is indeed cheaper than as.matrix %>% as.data.frame approach? (colnames doesn't matter)

– Nutle
Nov 26 '18 at 18:17

also, in the first case b %*% t(b) returns the following error:requires numeric/complex matrix/vector arguments. I don't see how can we avoid as.matrix here

– Nutle
Nov 26 '18 at 18:21

Thanks. That is exactly what I was looking for!!!

– HowYaDoing
Nov 26 '18 at 19:54

@Nutle your comments are't really applicable here. As noted already by OP you seem to have mistaken that the question is about inverse matrices - it is not. Maybe consider deleting your comments in case they could inadvertently be misleading to other readers?

– dww
Nov 29 '18 at 15:15

I will cite the exact words from the OP's question: and I cannot use the as.matrix function, because the matrix is too large.

– Nutle
Nov 29 '18 at 15:30

|
show 3 more comments

You can use

b = as.data.frame(summary(a))

#   i j x

# 1 2 1 2

# 2 2 2 1

# 3 3 3 3

# 4 1 4 1

# 5 3 5 1

If you need the same order as in your example, you can use

b = b[order(b$i),]

#   i j x

# 4 1 4 1

# 1 2 1 2

# 2 2 2 1

# 3 3 3 3

# 5 3 5 1

Another alternative, though not quite as neat, is to use

b = as(a, "dgTMatrix")

cbind.data.frame(r = b@i + 1, c = b@j + 1, x = b@x)

edited Nov 26 '18 at 17:56

answered Nov 26 '18 at 17:45

dww

15.2k22656

You can use

b = as.data.frame(summary(a))

#   i j x

# 1 2 1 2

# 2 2 2 1

# 3 3 3 3

# 4 1 4 1

# 5 3 5 1

If you need the same order as in your example, you can use

b = b[order(b$i),]

#   i j x

# 4 1 4 1

# 1 2 1 2

# 2 2 2 1

# 3 3 3 3

# 5 3 5 1

Another alternative, though not quite as neat, is to use

b = as(a, "dgTMatrix")

cbind.data.frame(r = b@i + 1, c = b@j + 1, x = b@x)

edited Nov 26 '18 at 17:56

answered Nov 26 '18 at 17:45

dww

15.2k22656

edited Nov 26 '18 at 17:56

answered Nov 26 '18 at 17:45

dww

15.2k22656

answered Nov 26 '18 at 17:45

dww

15.2k22656

answered Nov 26 '18 at 17:45

dww

15.2k22656

Any idea whether this approach is indeed cheaper than as.matrix %>% as.data.frame approach? (colnames doesn't matter)

– Nutle
Nov 26 '18 at 18:17

also, in the first case b %*% t(b) returns the following error:requires numeric/complex matrix/vector arguments. I don't see how can we avoid as.matrix here

– Nutle
Nov 26 '18 at 18:21

Thanks. That is exactly what I was looking for!!!

– HowYaDoing
Nov 26 '18 at 19:54

@Nutle your comments are't really applicable here. As noted already by OP you seem to have mistaken that the question is about inverse matrices - it is not. Maybe consider deleting your comments in case they could inadvertently be misleading to other readers?

– dww
Nov 29 '18 at 15:15

I will cite the exact words from the OP's question: and I cannot use the as.matrix function, because the matrix is too large.

– Nutle
Nov 29 '18 at 15:30

|
show 3 more comments

Any idea whether this approach is indeed cheaper than as.matrix %>% as.data.frame approach? (colnames doesn't matter)

– Nutle
Nov 26 '18 at 18:17

also, in the first case b %*% t(b) returns the following error:requires numeric/complex matrix/vector arguments. I don't see how can we avoid as.matrix here

– Nutle
Nov 26 '18 at 18:21

Thanks. That is exactly what I was looking for!!!

– HowYaDoing
Nov 26 '18 at 19:54

@Nutle your comments are't really applicable here. As noted already by OP you seem to have mistaken that the question is about inverse matrices - it is not. Maybe consider deleting your comments in case they could inadvertently be misleading to other readers?

– dww
Nov 29 '18 at 15:15

I will cite the exact words from the OP's question: and I cannot use the as.matrix function, because the matrix is too large.

– Nutle
Nov 29 '18 at 15:30

Any idea whether this approach is indeed cheaper than as.matrix %>% as.data.frame approach? (colnames doesn't matter)

– Nutle
Nov 26 '18 at 18:17

also, in the first case b %*% t(b) returns the following error:requires numeric/complex matrix/vector arguments. I don't see how can we avoid as.matrix here

– Nutle
Nov 26 '18 at 18:21

Thanks. That is exactly what I was looking for!!!

– HowYaDoing
Nov 26 '18 at 19:54

@Nutle your comments are't really applicable here. As noted already by OP you seem to have mistaken that the question is about inverse matrices - it is not. Maybe consider deleting your comments in case they could inadvertently be misleading to other readers?

– dww
Nov 29 '18 at 15:15

I will cite the exact words from the OP's question: and I cannot use the as.matrix function, because the matrix is too large.

– Nutle
Nov 29 '18 at 15:30

|
show 3 more comments

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