search for: dmatrix

Dear all, I am trying (without much success) to use the fuction 'silhouette'. Would anyone encountered that before (or would know where I am wrong ?) Please find below the R ouput. Thanks in advance, L. > s <- silhouette(ct, as.dist(metric)) Error in "[<-"(*tmp*, iC, "sil_width", value = s.i) : number of items to replace is not a multiple of replacement

...of the clustering programs I use (snob) assigns more or less arbitrary integer ids to clusters starting from 3! (clusters 1 and 2 have special meaning in snob). the modified code fixing both problems is included below, changes are commented. best Murad silhouette.default <- function (x, dist, dmatrix, ...) { cll <- match.call() if (!is.null(cl <- x$clustering)) x <- cl n <- length(x) if (!all(x == round(x))) stop("`x' must only have integer codes") k <- length(clid <- sort(unique(x))) if (k <= 1 || k >= n)...

...ne character is not recognized, because R prints a newline, but puts the '+' continuation symbol on the next line, and does so for each subsequent line, as follows ... ... 0.673485477583901, 0.492934866805126, 0.67+ 97955088067, 0.359755098747052, 0.734365384276714, 0.776102576892879, 1) + Dmatrix <- matrix (mydata, byrow=TRUE, nrow=11, ncol=11 ) + result<-eigen(Dmatrix) + varEig<-var(result$values) + cat (c('variance of the eigenvalues:', varEig), fill=TRUE) When the list is shorter, I don't get this problem. Anyone have any ideas as to what is going on? The reason...

...R: > dyn.load("tryit.so") Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library "/export/home/gpetris/tryit.so": ld.so.1: /export/home/share/R/R-1.4.0/lib/R/bin/R.bin: fatal: relocation error: file /export/home/gpetris/tryit.so: symbol dmatrix: referenced symbol not found The function dmatrix is contained in the object file nrutil.o in the library /export/home/gpetris/lib/SUN/32bit/libutil.a I was hoping that the flags given to R SHLIB could take care of that, but apparently I was wrong... What am I missing? Any help will be greatly app...

Hi, I have a S3 package with namespace called "myS3Pkg". Inside my package I would like to create a S4 class which extends (adds 2 slots) another S4 class from some other package. The class should be created in "myPkg" environment (and not global environment). Using: setClass("myS4class", representation("otherS4class", mydata = "numeric"),

...al/lib -o survival.so agexact.o agfit2.o agfit3.o agfit5.o agfit_null.o agmart2.o agmart.o agscore.o agsurv1.o agsurv2.o agsurv3.o char_date.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o coxdetail.o coxfit2.o coxfit5.o coxmart.o coxph_wtest.o cox_Rcallback.o coxscho.o coxscore.o dmatrix.o doloop.o pyears1.o pyears2.o pyears3.o pystep.o surv_callback.o survdiff2.o survfit2.o survfit3.o survindex2.o survindex3.o survreg2.o survreg3.o survreg4.o survreg5.o /usr/bin/ld: unrecognized option '--as-needed' /usr/bin/ld: use the --help option for usage information collect2: ld retu...

This is a Request For Comment, also BCCed to 390 package maintainers of reverse dependencies of the Matrix package. Most users and package authors working with our 'Matrix' package will be using it for numerical computations, and so will be using "dMatrix" (d : double precision) matrix objects M, and indirectly, e.g., for M >= c will also use "lMatrix" (l: logical i.e. TRUE/FALSE/NA). All the following is **not** affecting those numerical / logical computations. A few others will know that we also have "pattern" ma...

Hello. This question concerns the Methods package. I have created a new class and am trying to set a method for it for S4 group generic "Summary". I have run into some signature problems. An example: > setClass("track", representation(x="numeric", y="character")) [1] "track" > setGeneric("max", group="Summary")

..."dgRMatrix") : > no method or default for coercing "dgTMatrix" to "dgRMatrix" The general philosophy in 'Matrix' with all the class hierarchies and the many specific classes has been to allow and foster coercing to abstract super classes, i.e, to "dMatrix" or "generalMatrix", "triangularMatrix", or then "denseMatrix", "sparseMatrix", "CsparseMatrix" or "RsparseMatrix", etc So in the above as(*, "RsparseMatrix") should work always. As a summary, in other words, for wha...

Using the Matrix package, how can I create a row-oriented sparse Matrix from scratch populated with some data? By default a column-oriented one is created and I'm aware of the note that the package is optimized for column-oriented ones, but I'm only interested in using it for holding my sparse row-oriented data and doing basic subsetting by rows (even using drop=FALSE). Here is what I

Dear all, I need to re-define some mathematical operators (+, *, /, etc) for an S4 class based on array. All references I have found (S Programming, Green Book) show how to define S3 methods for this (like in page 89 of S Programming for "-.polynomial"). What is the preferred S4 way for doing this? I hope I haven't missed some obvious piece of documentation. Many thanks, Iago

...ib -o surv ival.sl agexact.o agfit2.o agfit3.o agfit5.o agfit_null.o agmart.o agmart2.o ags core.o agsurv1.o agsurv2.o agsurv3.o char_date.o chinv2.o chinv3.o cholesky2.o c holesky3.o chsolve2.o chsolve3.o cox_Rcallback.o coxdetail.o coxfit2.o coxfit5.o coxmart.o coxph_wtest.o coxscho.o coxscore.o dmatrix.o doloop.o pyears1.o pyear s2.o pyears3.o pystep.o surv_callback.o survdiff2.o survfit2.o survfit3.o survin dex2.o survindex3.o survreg2.o survreg3.o survreg4.o survreg5.o ** R ** data ** moving datasets to lazyload DB ** inst ** preparing package for lazy loading /bi/common/src/R-2.1.1/bin/INS...

...al/lib -o survival.so agexact.o agfit2.o agfit3.o agfit5.o agfit_null.o agmart2.o agmart.o agscore.o agsurv1.o agsurv2.o agsurv3.o char_date.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o coxdetail.o coxfit2.o coxfit5.o coxmart.o coxph_wtest.o cox_Rcallback.o coxscho.o coxscore.o dmatrix.o doloop.o pyears1.o pyears2.o pyears3.o pystep.o surv_callback.o survdiff2.o survfit2.o survfit3.o survindex2.o survindex3.o survreg2.o survreg3.o survreg4.o survreg5.o > /usr/bin/ld: unrecognized option '--as-needed' > /usr/bin/ld: use the --help option for usage information > co...

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

It seems that it is possible to pass a matrix to C++ by using .C() The R part of the interface should be something like: ('C++function', matrix, numberRows, numberColumns ) ...I guess. The C++ part of the interface could be something like void C++( double matrix[][], int numberRows, numberColumns ) but C++ requires to indicate the number of columns, that is, instead of matrix[][], it

...: > > This is a Request For Comment, also BCCed to 390 package maintainers > of reverse dependencies of the Matrix package. > > Most users and package authors working with our 'Matrix' package will > be using it for numerical computations, and so will be using > "dMatrix" (d : double precision) matrix objects M, and indirectly, e.g., for > M >= c will also use "lMatrix" (l: logical i.e. TRUE/FALSE/NA). > All the following is **not** affecting those numerical / logical > computations. > > A few others will know that we also ha...

...r wrote: > This is a Request For Comment, also BCCed to 390 package maintainers > of reverse dependencies of the Matrix package. > > Most users and package authors working with our 'Matrix' package will > be using it for numerical computations, and so will be using > "dMatrix" (d : double precision) matrix objects M, and indirectly, e.g., for > M >= c will also use "lMatrix" (l: logical i.e. TRUE/FALSE/NA). > All the following is **not** affecting those numerical / logical > computations. > > A few others will know that we also hav...

...al/lib -o survival.so agexact.o agfit2.o agfit3.o agfit5.o agfit_null.o agmart.o agmart2.o agscore.o agsurv1.o agsurv2.o agsurv3.o char_date.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o cox_Rcallback.o coxdetail.o coxfit2.o coxfit5.o coxmart.o coxph_wtest.o coxscho.o coxscore.o dmatrix.o doloop.o pyears1.o pyears2.o pyears3.o pystep.o surv_callback.o survdiff2.o survfit2.o survfit3.o survindex2.o survindex3.o survreg2.o survreg3.o survreg4.o survreg5.o -lm gmake[3]: Leaving directory `/ltmp/R.INSTALL.5603432/survival/src' ** R ** data ** moving datasets to lazyload DB ** i...

...eof(double)); } /* end of accelerator() */ void gradient(DVECTOR w,int n_w,double Penalty,DVECTOR d,int n_d,IVECTOR pos) { /* NOTE: FIXED_h=1,VARIABLE_h=2 */ int h_TYPE=2; num_gradient(h_TYPE,w,n_w,Penalty,d,n_d,pos); } /* end of gradient */ void hessian(DVECTOR w,int n_w,double Penalty,DMATRIX G,int n_G,IVECTOR pos) { /* NOTE: FIXED_h=1,VARIABLE_h=2 */ int h_TYPE=2; num_hessian(h_TYPE,w,n_w,Penalty,G,n_G,pos); } /* end of hessian() */ void pre_processor (struct SOLUTION *START) { int PHASE = INT_STATUS[17]; if((PHASE EQ 1) AND (*(TASK.ACTIVE_SYSTEM) EQ 0) AND (*ALLOCATION_SW...

...eof(double)); } /* end of accelerator() */ void gradient(DVECTOR w,int n_w,double Penalty,DVECTOR d,int n_d,IVECTOR pos) { /* NOTE: FIXED_h=1,VARIABLE_h=2 */ int h_TYPE=2; num_gradient(h_TYPE,w,n_w,Penalty,d,n_d,pos); } /* end of gradient */ void hessian(DVECTOR w,int n_w,double Penalty,DMATRIX G,int n_G,IVECTOR pos) { /* NOTE: FIXED_h=1,VARIABLE_h=2 */ int h_TYPE=2; num_hessian(h_TYPE,w,n_w,Penalty,G,n_G,pos); } /* end of hessian() */ void pre_processor (struct SOLUTION *START) { int PHASE = INT_STATUS[17]; if((PHASE EQ 1) AND (*(TASK.ACTIVE_SYSTEM) EQ 0) AND (*ALLOCATION_SW...