extract positions from matrix

Hi everyone, I tried to solve this problem but I could not find the
solution. I have about 105 matrices of equal size in the memory of**R, I
need to do is extract from these matrices some known positions and
create a new matrix with these columns. Show you an example with only
three matrices (but in my case I have hundreds of them).

A=matrix(1:15,5)

[,1] [,2] [,3]

[1,] 1 6 11

[2,] 2 7 12

[3,] 3 8 13

[4,] 4 9 14

[5,] 5 10 15

B=matrix(15:29,5)

[,1] [,2] [,3]

[1,] 15 20 25

[2,] 16 21 26

[3,] 17 22 27

[4,] 18 23 28

[5,] 19 24 29

C=matrix(30:44,5)

[,1] [,2] [,3]

[1,] 30 35 40

[2,] 31 36 41

[3,] 32 37 42

[4,] 33 38 43

[5,] 34 39 44

The positions I wish to extract are 1 and 5 of the first row of each
matrix (in my case are 25positions) and with this generate a new matrix
with the form

d=

[,1] [,2] [,3]

[1,] 1 15 30

[2,] 5 19 34

The ideais to builda loop toextract thisinformation from
hundredsmatrices, butI failed todo so.

Any helpwould be greatthank you very muchin advance

regards
.jpg


? ? ? ?[[alternative HTML version deleted]]

Here's one approach:

A=matrix(1:15,5)
B=matrix(15:29,5)
C=matrix(30:44,5)

do.call(cbind, lapply(c("A","B","C"),function(x) get(x)[c(1,5),1]))

for(i in 1:3) assign(LETTERS[i], 15*(i-1)+seq_len(15)) ## toy data
rm(i)  ## want only the matrices in the global workspace

ar <-  array( sapply(ls(), get), dim=c(5,3,3))  ## the dim argument could also be specified programatically

ar[c(1,5),1,]

On Nov 19, 2011, at 9:32 AM, R. Michael Weylandt wrote:

Here's one approach:

A=matrix(1:15,5)
B=matrix(15:29,5)
C=matrix(30:44,5)

do.call(cbind, lapply(c("A","B","C"),function(x) get(x)[c(1,5),1]))

Also:

sapply( list(A,B,C), function(x) do.call("[", list(x, c(1,5))) ?)

Notice that this actually was extracting using what might be called the
"vector positions". If you wanted to use the i,j version of "[" then you
would need an extra column (this example pulling the second columns in the
rows selected:

sapply(list(A,B,C),function(x) do.call("[", list(x, c(1,5), 2)) )

? ? [,1] [,2] [,3]
[1,] ? ?6 ? 20 ? 35
[2,] ? 10 ? 24 ? 39


Comments on the differences: Michaels version used cbind to get the ruslt in
a matrix, whereas mine used sapply. His used the get function to extract the
objects from a character vector, whereas mine never constructed a character
vector. Which one you deploy will depend on your data setup. If you already
have these in a list, mine might be easier, but if they constitute an easily
constructed set of names you might use LETTERS[] numbers and paste() to
build your list of object names.

--
david.

Michael

On Thu, Nov 17, 2011 at 9:44 PM, .Jpg <jporobicg at gmail.com> wrote:

Hi everyone, I tried to solve this problem but I could not find the
solution. I have about 105 matrices of equal size in the memory of**R, I
need to do is extract from these matrices some known positions and
create a new matrix with these columns. Show you an example with only
three matrices (but in my case I have hundreds of them).

A=matrix(1:15,5)

[,1] [,2] [,3]

[1,] 1 6 11

[2,] 2 7 12

[3,] 3 8 13

[4,] 4 9 14

[5,] 5 10 15

B=matrix(15:29,5)

[,1] [,2] [,3]

[1,] 15 20 25

[2,] 16 21 26

[3,] 17 22 27

[4,] 18 23 28

[5,] 19 24 29

C=matrix(30:44,5)

[,1] [,2] [,3]

[1,] 30 35 40

[2,] 31 36 41

[3,] 32 37 42

[4,] 33 38 43

[5,] 34 39 44

The positions I wish to extract are 1 and 5 of the first row of each
matrix (in my case are 25positions) and with this generate a new matrix
with the form

d=

[,1] [,2] [,3]

[1,] 1 15 30

[2,] 5 19 34

The ideais to builda loop toextract thisinformation from
hundredsmatrices, butI failed todo so.

Any helpwould be greatthank you very muchin advance

regards
.jpg


? ? ? [[alternative HTML version deleted]]

David Winsemius, MD
West Hartford, CT

Folks:

David: I believe your approach needs to be modified to accommodate
hundreds of matrices per the OP's specification.

However, I would say that this is exactly the situation in which
arrays should be used. Not only does it appear simpler, but it also
could be faster since once the array is created, (vectorized) indexing
is used. The key is to take advantage of column major ordering of
arrays in R as follows:

1. The OP's example specification is wrong -- he wants positions 1 and
5 of the first COLUMN of each matrix (which both solutions gave, but
just didn't mention).

2. The code below creates the array assuming that the global workspace
has only the matrices in it. Subscript ls() appropriately if this is
not the case.

for(i in 1:3) assign(LETTERS[i], 15*(i-1)+seq_len(15)) ## toy data
rm(i)  ## want only the matrices in the global workspace

ar <-  array( sapply(ls(), get), dim=c(5,3,3))  ## the dim argument  
could also be specified programatically

On Nov 19, 2011, at 1:15 PM, Bert Gunter wrote:

Folks:

David: I believe your approach needs to be modified to accommodate
hundreds of matrices per the OP's specification.

I suggested that my approach was most applicable if the questioner had his
matrices already in a list. (He didn't say, so neither of us knows yet what
his/her use case is.)

However, I would say that this is exactly the situation in which
arrays should be used. Not only does it appear simpler, but it also
could be faster since once the array is created, (vectorized) indexing
is used. The key is to take advantage of column major ordering of
arrays in R as follows:

1. The OP's example specification is wrong -- he wants positions 1 and
5 of the first COLUMN of each matrix (which both solutions gave, but
just didn't mention).

2. The code below creates the array assuming that the global workspace
has only the matrices in it. Subscript ls() appropriately if this is
not the case.

for(i in 1:3) assign(LETTERS[i], 15*(i-1)+seq_len(15)) ## toy data
rm(i) ?## want only the matrices in the global workspace

ar <- ?array( sapply(ls(), get), dim=c(5,3,3)) ?## the dim argument could
also be specified programatically

I wonder if you are doing ".jpg" a favor by putting ls() at the center of
your strategy unless you offer the tools to isolate these objects from the
rest of the global environment. Who works with no other objects in the
workspace?

Perhaps this would add the extra level of encapsulation needed for the
sapply(ls() method of access the created matrices in a probably less
disruptive fashion:

e <- new.env()
with(e, { for(i in 1:3) assign( LETTERS[i], 15*(i-1)+seq_len(15) )
rm(i)
ar <- ?array( sapply(ls(), get), dim=c(5,3,3)) })

# ----------------
e$ar[c(1,5),1, ]

? ? [,1] [,2] [,3]
[1,] ? ?1 ? 16 ? 31
[2,] ? ?5 ? 20 ? 35

--
David.

ar[c(1,5),1,]

? ?[,1] [,2] [,3]
[1,] ? ?1 ? 16 ? 31
[2,] ? ?5 ? 20 ? 35


Cheers,
Bert

On Sat, Nov 19, 2011 at 9:19 AM, David Winsemius <dwinsemius at comcast.net>
wrote:

On Nov 19, 2011, at 9:32 AM, R. Michael Weylandt wrote:

Here's one approach:

A=matrix(1:15,5)
B=matrix(15:29,5)
C=matrix(30:44,5)

do.call(cbind, lapply(c("A","B","C"),function(x) get(x)[c(1,5),1]))

Also:

sapply( list(A,B,C), function(x) do.call("[", list(x, c(1,5))) ?)

Notice that this actually was extracting using what might be called the
"vector positions". If you wanted to use the i,j version of "[" then you
would need an extra column (this example pulling the second columns in
the
rows selected:

sapply(list(A,B,C),function(x) do.call("[", list(x, c(1,5), 2)) )

? ?[,1] [,2] [,3]
[1,] ? ?6 ? 20 ? 35
[2,] ? 10 ? 24 ? 39


Comments on the differences: Michaels version used cbind to get the ruslt
in
a matrix, whereas mine used sapply. His used the get function to extract
the
objects from a character vector, whereas mine never constructed a
character
vector. Which one you deploy will depend on your data setup. If you
already
have these in a list, mine might be easier, but if they constitute an
easily
constructed set of names you might use LETTERS[] numbers and paste() to
build your list of object names.

--
david.

Michael

On Thu, Nov 17, 2011 at 9:44 PM, .Jpg <jporobicg at gmail.com> wrote:

Hi everyone, I tried to solve this problem but I could not find the
solution. I have about 105 matrices of equal size in the memory of**R,
I
need to do is extract from these matrices some known positions and
create a new matrix with these columns. Show you an example with only
three matrices (but in my case I have hundreds of them).

A=matrix(1:15,5)

[,1] [,2] [,3]
[1,] 1 6 11
[2,] 2 7 12
[3,] 3 8 13
[4,] 4 9 14
[5,] 5 10 15

B=matrix(15:29,5)
[,1] [,2] [,3]
[1,] 15 20 25
[2,] 16 21 26
[3,] 17 22 27
[4,] 18 23 28
[5,] 19 24 29

C=matrix(30:44,5)
[,1] [,2] [,3]
[1,] 30 35 40
[2,] 31 36 41
[3,] 32 37 42
[4,] 33 38 43
[5,] 34 39 44

The positions I wish to extract are 1 and 5 of the first row of each
matrix (in my case are 25positions) and with this generate a new matrix
with the form

d=

[,1] [,2] [,3]
[1,] 1 15 30
[2,] 5 19 34

The ideais to builda loop toextract thisinformation from
hundredsmatrices, butI failed todo so.

Any helpwould be greatthank you very muchin advance

regards
.jpg

--

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:

http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

David Winsemius, MD
West Hartford, CT