search for: dscmatrix

...; calculate the relatedness-matrix based on the pedigree for > our ornamental plants. I was wondering if you could give > me some advice, for which I would like to thank you in > advance! > The output of the relatedness matrix I get from > the nadiv package is a dsCMatrix. I would like to save it > in some way, so I could query a subset of this matrix > later on, as in most cases, the full matrix is not > needed. Do you know what kind of format is ideal for > data-storage (either in file or in a database) for a > sparse matrix? Th...

I have library in development with a function that works when called from the top level, but fails under R CMD check. The paricular line of failure is rsum <- rowSums(kmat>0) where kmat is a dsCMatrix object. I'm currently stumped and looking for some ideas. I've created a stripped down library "ktest" that has only 3 functions: pedigree.R to create a pedigree or pedigreeList object, kinship.R with "kinship" methods for the two objects one small comput...

I have been playing around with sparse matrices in the Matrix package, in particularly with the Cholesky factorization of matrices of class dsCMatrix. And BTW, what a fantastic package. My problem is that I have to carry out repeated Cholesky factorization of a spares symmetric matrices, say Q_1, Q_2, ...,Q_n, where the Q's have the same non-zero pattern. I know in this case one does only need to carry out the symbolic factorization _onc...

Friends I'm not seeing why the following occurs: > T1 <- (A1 - A2) %*% D > T2 <- (A1 %*% D) - (A2 %*% D) > identical(T1, T2) [1] FALSE Harold > dput(A1) new("dsCMatrix" , i = c(0L, 1L, 2L, 3L, 0L, 1L, 4L, 2L, 3L, 5L) , p = c(0L, 1L, 2L, 3L, 4L, 7L, 10L) , Dim = c(6L, 6L) , Dimnames = list(NULL, NULL) , x = c(5, 5, 5, 5, 5, 5, 10, 5, 5, 10) , uplo = "U" , factors = list() ) > dput(A2) new("dgeMatrix" , x...

Reasonably easy to avoid, but maybe an edge case that should be handled? Haven't looked yet to see how easy it would be to fix ... Am I missing something? > library(Matrix) > m <- Matrix(0,nrow=3,ncol=3) > m 3 x 3 sparse Matrix of class "dsCMatrix" [1,] . . . [2,] . . . [3,] . . . > image(m) Error in seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 'from' must be a finite number In addition: Warning messages: 1: In min(xx, na.rm = TRUE) : no non-missing arguments to min; returning Inf 2: In min(x) : no non-missing...

...want to create a sparse matrix of type "dgCMatrix" using the Matrix package (and the matrix must be of this type even if other more compact representations may exist). I do > library(Matrix) > m1<-Matrix(rep(1,4),nrow=2,ncol=2,sparse=T) > m1 2 x 2 sparse Matrix of class "dsCMatrix" [1,] 1 1 [2,] 1 1 To convert m1, I do > as(m1, "dgCMatrix") 2 x 2 sparse Matrix of class "dgCMatrix" [1,] 1 1 [2,] 1 1 Is it possible to construct a dgCMatrix "directly" i.e. without going through the additional as() step above? Best regar...

...make[1]: Leaving directory `/tmp/R.INSTALL.TW3399/Matrix/src/AMD' pgCC -L/usr/lib64 -L/usr/X11R6/lib64 -pgf90libs -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o SPQR.a CHOLMOD.a COLAMD.a AMD.a -L/usr/local/apps/R/R-2.8.1/lib64/R/lib -lRlapack -lRblas -lpgf90 -lpgf90_rpm1 -lpgf902 -lpgf90rtl -lpgftnrtl -lnspgc -lpgc -lrt -lpthread...

...tion failed with the following messages, ....... CC -library=stlport4 -G -L/opt/csw/lib/sparcv9 -L/opt/solstudio12.2/prod/lib/v9 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a -L/apps/sparcv9/R-2.12.0/lib/R/lib -lRlapack -L/apps/sparcv9/R-2.12.0/lib/R/lib -lRblas -lifai -lsunimath -lfai -lfai2 -lfsumai -lfprodai -lf...

...ing of the recommended packages and also if Matrix is compiled separately: [...] CC -G -lCstd -L/opt/sun/sunstudio12/lib/amd64 -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o CHOLMOD.a COLAMD.a AMD.a -L/home/user/R/R-devel/lib -lRlapack -L/home/user/R/R-devel/lib -lRblas -R/opt/sun/sunstudio12/lib/amd64:/opt/sun/sunstudio12/lib/amd64:/opt/sun/lib/rt...

Hi everyone: I try to use r to do the Cholesky Decomposition,which is A=LDL',so far I only found how to decomposite A in to LL' by using chol(A),the function Cholesky(A) doesnt work,any one know other command to decomposte A in to LDL' My r code is: library(Matrix) A=matrix(c(1,1,1,1,5,5,1,5,14),nrow=3) > chol(A) [,1] [,2] [,3] [1,] 1 1 1 [2,] 0 2 2

...Dim = c(8L, 10L), Dimnames = list( | > NULL, NULL), factors = list()) | > --> checking list(*): Ok | > --=--=--=--=-- | 961a1154,1156 | > perm: c(2L, 3L, 6L, 4L, 1L, 7L, 5L) | > --> checking list(*): Ok | > --=--=--=--=-- | 1010a1206,1211 | > sA: new("dsCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, | > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(10L, 10L), Dimnames = list( | > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), uplo = "U", | > factors = list()) | > --> checking list(*): Ok | > --=--=...

Hi all, I am new to R and learning the same. I would like to create a sparse matrix from an existing file whose contents are in the format "rowIndex,columnIndex,value" for ex: 1,2,14 2,4,15 I would like to create a sparse matrix by taking the above as input. However, I couldn't find an example where the data was being read from a file. I tried searching in R tutorial and

...col, ncell) resolution : 100.0049, 99.98945 (x, y) extent : 1460708, 1625516, 4947383, 5165460 (xmin, xmax, ymin, ymax) coord. ref. : +proj=tmerc +lat_0=0 +lon_0=9 +k=0.9996 +x_0=1500000 +y_0=0 +ellps=intl +towgs84=-225,-65,9,0,0,0,0 +units=m +no_defs values : conductance matrix class: dsCMatrix I applied two different geocorrections to this same transition: > MY_correction<-geoCorrection(MY_transition,"c",F,scl=T) > MY_Rcorrection<-geoCorrection(MY_transition,"r",F,scl=T) My coords are 44 points where samples were taken (some further genetic analyses ar...

...e a Cholesky of a pseudovariance that is reasonably close to the original matrix. I know that there are R packages that contain code for Gill-Murray and Schnabel-Eskow algorithms for standard, dense, base-R matrices. But my Matrix is large (k=30000), and sparse (block-arrow structure, stored as a dsCMatrix class from the Matrix package). Is anyone aware of existing code (or perhaps an algorithm that is easy to adapt) that would perform a modified Cholesky decomposition on a large, sparse indefinite matrix, preferably working on sparseMatrix classes? Alternatively, is there a way I could compute a...

...nclude -I/usr/include -I/usr/sfw/include -KPIC -O -I/opt/SUNWspro/prod/include -c dppMatrix.c -o dppMatrix.o cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include -I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O -I/opt/SUNWspro/prod/include -c dsCMatrix.c -o dsCMatrix.o cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/local/include -I/opt/SUNWspro/prod/include -I/usr/include -I/usr/sfw/include -KPIC -O -I/opt/SUNWspro/prod/include -c dsyMatrix.c -o dsyMatrix.o cc -m64 -I/home/choid/bin/R281/lib/R/include -I./UFconfig -I/usr/loc...

...NULL, NULL), factors = list()) > | > --> checking list(*): Ok > | > --=--=--=--=-- > | 961a1154,1156 > | > perm: c(2L, 3L, 6L, 4L, 1L, 7L, 5L) > | > --> checking list(*): Ok > | > --=--=--=--=-- > | 1010a1206,1211 > | > sA: new("dsCMatrix", i = c(0L, 3L, 4L, 5L, 2L, 6L, 7L), p = c(0L, > | > 0L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 6L, 7L), Dim = c(10L, 10L), Dimnames = list( > | > NULL, NULL), x = c(7, 21, 28, 35, 14, 42, 49), uplo = "U", > | > factors = list()) > | > --> checking li...

Hello everyone Could anybody tell me how to set the following matrix? n2<-matrix(nrow=10185,ncol=10185,seq(0,0,length=103734225)) R answer was Error: cannot allocate vector of size 810423 Kb Are there any solution? I tried to increase the memory size but it didn't work G This message has been scanned for viruses by TRENDMICRO,\ an...{{dropped}}

Hi, I have been having a tedious issue with lmer models with lots of factors and lots of levels. In order to get the basic information at the beginning of the print out I also have to generate these enormous tables as well. Is there a method command to leave off all of the effects and correlations? Or, do I have to go to string commands?

I am developing a new R package and am now checking it for submission to CRAN. The some functions in the package make use of the sparse matrix routines in the package 'Matrix'. When these are loaded in R, they create no problems. However, when running R CMD check, I run into the following error in executing the examples in a .rd file: > DD = Matrix(diag(1,200),sparse=TRUE) >

The bulk is on my forums - the final post for today is: Results to date: A. It looks like I am going to need a newer compiler for C - xlc/xlC V11 apparently does not understand this code: "/data/prj/cran/R-3.2.3/src/main/memory.c", line 2149.31: 1506-046 (S) Syntax error. I will have to check if R-devel has different code before asking for assistence. +2139 #ifdef