search for: dsymatrix

Hi, I'd like to store large covariance matrices using Matrix classes. dsyMatrix seems like the right one, but I want to specify just the upper/lower triangle and diagonal and not have to instantiate a huge n^2 vector just for the sake of having half of it ignored: Dumb example: M <- new("dsyMatrix", uplo="U", x=rnorm(1e4), Dim=as.integer(c(100, 100))) d...

Dear UseRs, here is an example scenario presenting my problem: Multiplying a dsyMatrix with a numeric vector results in an error (unfortunately in German due to my locale): > (M1 <- Matrix( c( 1, 2, 2, 2, 1, 2, 2, 2, 1), nrow = 3)) 3 x 3 Matrix of class "dsyMatrix" [,1] [,2] [,3] [1,] 1 2 2 [2,] 2 1 2 [3,] 2 2 1 > M1 %*% 1:3 Fehl...

...is materialized through a call to 'load'. That's a mouthful, so I've put together a relatively small reproducible example online here: https://github.com/kevinushey/s4inherits This package, 's4inherits', defines an S4 class, 'SubMatrix', that inherits from the 'dsyMatrix' class defined in the Matrix package. After installing the package, I run some simple tests: $ R -f test-save.R > library(s4inherits) > data <- SubMatrix(1) > > is(data, "SubMatrix") [1] TRUE > inherits(data, "SubMatrix") [1] TRUE > > is(data, &quot...

...at's a mouthful, so I've put together a relatively small >> reproducible example online here: >> >> https://github.com/kevinushey/s4inherits >> >> This package, 's4inherits', defines an S4 class, 'SubMatrix', that >> inherits from the 'dsyMatrix' class defined in the Matrix package. >> After installing the package, I run some simple tests: >> >> $ R -f test-save.R >> >>> library(s4inherits) >>> data <- SubMatrix(1) >>> >>> is(data, "SubMatrix") >> [1] TRUE &...

...> 'load'. That's a mouthful, so I've put together a relatively small > reproducible example online here: > > https://github.com/kevinushey/s4inherits > > This package, 's4inherits', defines an S4 class, 'SubMatrix', that > inherits from the 'dsyMatrix' class defined in the Matrix package. > After installing the package, I run some simple tests: > > $ R -f test-save.R > >> library(s4inherits) >> data <- SubMatrix(1) >> >> is(data, "SubMatrix") > [1] TRUE >> inherits(data, "SubMatr...

...t;>>> relatively small reproducible example online here: >>>> >>>> https://github.com/kevinushey/s4inherits >>>> >>>> This package, 's4inherits', defines an S4 class, >>>> 'SubMatrix', that inherits from the 'dsyMatrix' class >>>> defined in the Matrix package. After installing the >>>> package, I run some simple tests: >>>> >>>> $ R -f test-save.R >>>> >>>>> library(s4inherits) data <- SubMatrix(1) >>>>> >>...

...>>> relatively small reproducible example online here: >>> >>> https://github.com/kevinushey/s4inherits >>> >>> This package, 's4inherits', defines an S4 class, >>> 'SubMatrix', that inherits from the 'dsyMatrix' class >>> defined in the Matrix package. After installing the >>> package, I run some simple tests: >>> >>> $ R -f test-save.R >>> >>>> library(s4inherits) data <- SubMatrix(1) >>>> >...

...(193.55.70.206) There appears to be a conflict between the chol functions from the Matrix and the SparseM packages. chol() can only be applied to a matrix of class dspMatrix if SparseM is not in the path. with gratitude David > library(Matrix) > sm <- as(as(Matrix(diag(5) + 1), "dsyMatrix"), "dspMatrix") > chol(sm) 5 x 5 Matrix of class "pCholesky" [,1] [,2] [,3] [,4] [,5] [1,] 1.4142136 0.7071068 0.7071068 0.7071068 0.7071068 [2,] . 1.2247449 0.4082483 0.4082483 0.4082483 [3,] . . 1.1547005 0.2886751...

...atively small reproducible example online here: >>>>> >>>>> https://github.com/kevinushey/s4inherits >>>>> >>>>> This package, 's4inherits', defines an S4 class, >>>>> 'SubMatrix', that inherits from the 'dsyMatrix' class >>>>> defined in the Matrix package. After installing the >>>>> package, I run some simple tests: >>>>> >>>>> $ R -f test-save.R >>>>> >>>>>> library(s4inherits) data <- SubMatrix(1) >>...

...eaving 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 -lm -pgf90li...

...rix> Matrix(0, 2, 2, sparse=FALSE)# diagonal ! | > 2 x 2 diagonal matrix of class "ddiMatrix" | > [,1] [,2] | > [1,] 0 . | > [2,] . 0 | > | > Matrix> Matrix(0, 2, 2, sparse=FALSE, doDiag=FALSE)# -> dense | > 2 x 2 Matrix of class "dsyMatrix" | > [,1] [,2] | > [1,] 0 0 | > [2,] 0 0 | > | > Matrix> Matrix(1:6, 3, 2) # a 3 by 2 matrix (+ integer warning) | > 3 x 2 Matrix of class "dgeMatrix" | > [,1] [,2] | > [1,] 1 4 | > [2,] 2 5 | > [3...

...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 -lfminlai -lfma...

...gonal ! > | > 2 x 2 diagonal matrix of class "ddiMatrix" > | > [,1] [,2] > | > [1,] 0 . > | > [2,] . 0 > | > > | > Matrix> Matrix(0, 2, 2, sparse=FALSE, doDiag=FALSE)# -> dense > | > 2 x 2 Matrix of class "dsyMatrix" > | > [,1] [,2] > | > [1,] 0 0 > | > [2,] 0 0 > | > > | > Matrix> Matrix(1:6, 3, 2) # a 3 by 2 matrix (+ integer warning) > | > 3 x 2 Matrix of class "dgeMatrix" > | > [,1] [,2] > | >...

...ecommended 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/rtlibs/amd64:/...

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

After loading the package "Matrix" (version 0.995-12), using the summary function with an lme (package nlme version 3.1-75) object results in an error message saying Fehler in dim(x) : kein Slot des Namens "Dim" f?r dieses Objekt der Klasse "correlation" (translated: 'Error in dim(x) : no slot of the name "Dim" for this object of class

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