====== MATLAB data in R ======

March 13, 2018

===== Reading MATLAB sparse matrix =====

FB100 networks: ZIP dowloaded from https://archive.org/details/oxford-2005-facebook-matrix 
<code>
> install.packages("R.matlab")
> library(R.matlab)
> help(readMat)
> A <- readMat("Amherst41.mat")
> str(A)
List of 2
 $ A         :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. ..@ i       : int [1:181908] 253 357 384 759 778 841 1120 1184 1307 1310 ...
  .. ..@ p       : int [1:2236] 0 25 104 297 396 610 631 644 749 783 ...
  .. ..@ Dim     : int [1:2] 2235 2235
  .. ..@ Dimnames:List of 2
  .. .. ..$ : NULL
  .. .. ..$ : NULL
  .. ..@ x       : num [1:181908] 1 1 1 1 1 1 1 1 1 1 ...
  .. ..@ factors : list()
 $ local.info: num [1:2235, 1:7] 1 1 1 1 1 1 1 1 1 1 ...
 - attr(*, "header")=List of 3
  ..$ description: chr "MATLAB 5.0 MAT-file, Platform: MACI64, Created on: Fri Feb 11 20:09:04 2011"
  ..$ version    : chr "5"
  ..$ endian     : chr "little"
> head(A$local.info)
     [,1] [,2] [,3] [,4] [,5] [,6]  [,7]
[1,]    1    2    0    0  359 2008 50112
[2,]    1    1  106  103  340 2007 11279
[3,]    1    1  114    0    0 2007 16202
[4,]    1    1   99    0    0 2006  9076
[5,]    1    2  111  109  347 2007 17773
[6,]    1    1    0    0    0 2009  3576
</code>

===== Converting to Pajek =====

==== Toy example ====

<code>
> M0 <- matrix(0, nrow = 4, ncol = 5)
> M0[1,1] <- 5
> M0[3,1] <- 7
> M0[4,2] <- 4
> M0[2,3] <- 1
> M0[3,5] <- 1
> M0[4,5] <- 1
> M0
     [,1] [,2] [,3] [,4] [,5]
[1,]    5    0    0    0    0
[2,]    0    0    1    0    0
[3,]    7    0    0    0    1
[4,]    0    4    0    0    1
> library(Matrix)
> M <- as(M0, "sparseMatrix")
> M
4 x 5 sparse Matrix of class "dgCMatrix"

[1,] 5 . . . .
[2,] . . 1 . .
[3,] 7 . . . 1
[4,] . 4 . . 1
> M@x
[1] 5 7 4 1 1 1
> M@i
[1] 0 2 3 1 2 3
> M@p
[1] 0 2 3 4 4 6
> M@Dim
[1] 4 5
> diff(M@p)
[1] 2 1 1 0 2
> T <- as(M,'dgTMatrix')
> str(T)
Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
  ..@ i       : int [1:6] 0 2 3 1 2 3
  ..@ j       : int [1:6] 0 0 1 2 4 4
  ..@ Dim     : int [1:2] 4 5
  ..@ Dimnames:List of 2
  .. ..$ : NULL
  .. ..$ : NULL
  ..@ x       : num [1:6] 5 7 4 1 1 1
  ..@ factors : list()
> cat("*arcs\n "); cat(paste(T@i+1,T@j+1,T@x,"\n"))
*arcs
 1 1 5 
 3 1 7 
 4 2 4 
 2 3 1 
 3 5 1 
 4 5 1 
</code>

==== Conversion from "dgCMatrix" to Pajek ====

<code>
mat2Pajek <- function(A,file,twomode=FALSE){
  library(Matrix)
  tit <- attr(A,"header")$description; net <- file(file,"w")
  cat("MATLAB to Pajek\n",tit,"\nTransformed: ",date(),"\n",sep="")
  cat("% MATLAB to Pajek\n% ",tit,"\n% Transformed: ",date(),"\n",sep="",file=net)
  M <- A$A; T <- as(M,'dgTMatrix'); D <- A$local.info
  nr <- T@Dim[1]; nc <- T@Dim[2]
  cat("*network fromMATLAB\n",file=net)
  if(twomode){
    cat("*vertices",nr+nc,nr,"\n",file=net)
    if(!is.null(T@Dimnames[[1]])){N <- T@Dimnames[[1]]
      for(i in seq_along(N)) cat(i,' "',N[i],'"\n',sep="",file=net)}
    if(!is.null(T@Dimnames[[2]])){N <- T@Dimnames[[2]]
      for(i in seq_along(N)) cat(i+nr,' "',N[i],'"\n',sep="",file=net)}
  } else {
    cat("*vertices",nr,"\n",file=net)
    if(!is.null(T@Dimnames[[1]])){N <- T@Dimnames[[1]]
      for(i in seq_along(N)) cat(i,' "',N[i],'"\n',sep="",file=net)}
  }
  cat("*arcs\n ",file=net)
  if(twomode) cat(paste(T@i+1,nr+T@j+1,T@x,"\n"),file=net) else
    cat(paste(T@i+1,T@j+1,T@x,"\n"),file=net)
  if(!is.null(D)){
    nr <- nrow(D); nc <- ncol(D)
    for(j in 1:nc){
      cat("\n*vector V",j,"\n*vertices ",nr,"\n ",sep="",file=net)
      cat(paste(D[,j],"\n"),file=net)
    }
  }
  close(net)
}
</code>

=== Converting the toy example ===


<code>
> M0 <- matrix(0, nrow = 4, ncol = 5)
> M0[1,1] <- 5
> M0[3,1] <- 7
> M0[4,2] <- 4
> M0[2,3] <- 1
> M0[3,5] <- 1
> M0[4,5] <- 1
> library(Matrix)
> rownames(M0) <- c("a","b","c","d")
> colnames(M0) <- c("A","B","C","D","E")
> M <- as(M0, "sparseMatrix")
> M
4 x 5 sparse Matrix of class "dgCMatrix"
  A B C D E
a 5 . . . .
b . . 1 . .
c 7 . . . 1
d . 4 . . 1
> B <- list(A=M,local.info=NULL)
> attr(B,"header") <- list(description="Hand made example")
> str(B)
List of 2
 $ A         :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
  .. ..@ i       : int [1:6] 0 2 3 1 2 3
  .. ..@ p       : int [1:6] 0 2 3 4 4 6
  .. ..@ Dim     : int [1:2] 4 5
  .. ..@ Dimnames:List of 2
  .. .. ..$ : chr [1:4] "a" "b" "c" "d"
  .. .. ..$ : chr [1:5] "A" "B" "C" "D" ...
  .. ..@ x       : num [1:6] 5 7 4 1 1 1
  .. ..@ factors : list()
 $ local.info: NULL
 - attr(*, "header")=List of 1
  ..$ description: chr "Hand made example"
> mat2Pajek(B,file="B.paj",twomode=TRUE)
MATLAB to Pajek
Hand made example
Transformed: Wed Mar 14 00:03:49 2018
</code>

<code>
% MATLAB to Pajek
% Hand made example
% Transformed: Wed Mar 14 00:03:49 2018
*network fromMATLAB
*vertices 9 4 
1 "a"
2 "b"
3 "c"
4 "d"
5 "A"
6 "B"
7 "C"
8 "D"
9 "E"
*arcs
 1 5 5 
 3 5 7 
 4 6 4 
 2 7 1 
 3 9 1 
 4 9 1 

</code>

=== Converting a FB100 network ===

<code>
> mat2Pajek(A,file="A.paj")
MATLAB to Pajek
MATLAB 5.0 MAT-file, Platform: MACI64, Created on: Fri Feb 11 20:09:04 2011 
Transformed: Wed Mar 14 00:04:07 2018 
</code>

<code>
% MATLAB to Pajek
% MATLAB 5.0 MAT-file, Platform: MACI64, Created on: Fri Feb 11 20:09:04 2011 
% Transformed: Wed Mar 14 00:04:07 2018
*network fromMATLAB
*vertices 2235 
*arcs
 254 1 1 
 358 1 1 
 385 1 1 
...
 1963 2235 1 
 1999 2235 1 
 2041 2235 1 

*vector V1
*vertices 2235
 1 
 1 
...
 2005 
 2004 
 2009 

*vector V7
*vertices 2235
 50112 
 11279 
...
 18233 
 9492 
 60686 
</code>