SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 726, Thu May 12 14:59:04 2005 UTC revision 1398, Sun Aug 20 03:26:06 2006 UTC
# Line 1  Line 1 
1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-08-19  Douglas Bates  <bates@R-project.org>
2    
3            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
4            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
5            and qr.fitted.
6            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
7            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
8    
9    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
12            the base version has no "..." argument.
13    
14            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
15    
16            * R/Matrix.R: define and
17            * NAMESPACE: export as.numeric() and as.logical() methods.
18                    Let's hope these do not badly slow down something...
19            Finally export the zapsmall() method.
20    
21    2006-08-17  Douglas Bates  <bates@R-project.org>
22    
23            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
24            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
25            * src/dtCMatrix.c :Remove code that is no longer used
26            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
27    
28    2006-08-14  Douglas Bates  <bates@R-project.org>
29    
30            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
31            Csparse_to_logical and Csparse_symmetric_to_general.
32            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
33            coercion methods between CsparseMatrix and TsparseMatrix.
34    
35    2006-08-14  Douglas Bates  <bates@R-project.org>
36    
37            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
38            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
39            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
40            possible.
41    
42    2006-08-12  Douglas Bates  <bates@R-project.org>
43    
44            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
45              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
46              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
47              generalize conversions between TsparseMatrix, CsparseMatrix,
48              denseMatrix and matrix.  Preserve triangularity property and
49              propagate Dimnames in the easy cases.
50    
51    2006-08-10  Douglas Bates  <bates@R-project.org>
52    
53            * src/lmer.c: adjust checks in glmer_init for S4SXP
54            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
55            before S4SXP but for the wrong reasons.
56    
57    2006-08-08  Douglas Bates  <bates@R-project.org>
58    
59            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
60            Later modified to return the upper triangle only.
61            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
62    
63    2006-08-07  Douglas Bates  <bates@R-project.org>
64    
65            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
66            R-level conversion to a sparse symmetric class.
67            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
68            Remove conversion to sparse symmetric classes (now done in C code).
69    
70    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
73            * man/band.Rd:  adapt the \dontshow{} unit test.
74    
75    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * DESCRIPTION (Version): 0.995-14  for CRAN
78    
79            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
80    
81            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
82            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
83    
84            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
85            * R/Tsparse.R (tril, triu, band): methods
86            * R/dgRMatrix.R (tril, ...):    ditto
87            * man/band.Rd:                  ditto
88    
89    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/Matrix.R (head, tail): directly use utils:::head.matrix
92                    to be up-to-date automatically.
93    
94    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
97    
98            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
99            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
100            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
101            such that the S4 objects are always created by the current version
102            of R and 'Matrix' class definitions.
103    
104    2006-08-01  Douglas Bates  <bates@R-project.org>
105    
106            * R/lmer.R (LMEoptimize method), tests/lmer.R,
107            inst/external/test3comp.rda: Added warnings for convergence on
108            boundary and test cases.
109    
110            * src/lmer.c (mer_postVar): Modified to return the variances that
111            are marginal to the fixed effects, not conditional on them (which
112            is what the bVar slot contents represent).
113    
114    2006-07-31  Douglas Bates  <bates@R-project.org>
115    
116            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
117            function which calls the C function mer_hat_trace2.
118    
119            * man/ranef.Rd: Include description of "postVar" argument and
120            producing a caterpillar plot.
121    
122    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * NAMESPACE:    change  "correlation" to "corMatrix"
125            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
126            * R/dpoMatrix.R: ditto
127            * R/lmer.R:      ditto
128    
129    2006-07-28  Douglas Bates  <bates@R-project.org>
130    
131            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
132            RZXinv slot's contents into a separate internal function that can
133            be used in mer_hat_trace.
134    
135    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
138            via new smart
139            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
140            utility functions.
141    
142    
143    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/Csparse.R (tril, triu, band): do return *triangular* classed
146            matrices when appropriate; band() even symmetric ones.
147            (replCmat): extend to potentially all "CsparseMatrix"
148            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
149            allow subassignment for special sparse matrices.
150    
151            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
152    
153            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
154            argument; in glmer_*(): print only if(verbose).
155    
156            speed-optimize a few places by moving REAL(.) out of loops.
157    
158            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
159    
160    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
163                    since that wrongly triggers also for M[ logi , ]
164    
165            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
166            a symmetric matrix that results in a non-symmetric one.
167            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
168    
169            * R/dMatrix.R: make round(M) work as round(M, 0)
170    
171            * R/dgTMatrix.R (image): coordinate system and axis now use
172            1-based indices, not 0-based ones.
173    
174            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
175            * tests/indexing.R: test it.
176    
177            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
178            * man/isSymmetric-methods.Rd: and document it.
179    
180            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
181            * man/SparseM-conv.Rd: docu them
182    
183            * tests/other-pkgs.R: renamed from tests/graph.R and add example
184                    for 'SparseM' conversions
185    
186    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
187    
188            * R/Matrix.R (head): added head() and tail() methods.
189    
190    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * DESCRIPTION (Version): 0.995-12 released to CRAN
193    
194    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * tests/simple.R: add check for correct dsT -> dgT coercion;
197                    add check for correct printing of symmetric sparse matrices.
198    
199            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
200            for sparse symmetric matrices.
201    
202            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
203            diagonal twice.
204    
205    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
206    
207            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
208            being applied to the x slot (detected by Brian Ripley).
209    
210    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
213    
214            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
215    
216    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * src/lgCMatrix.c (lgCMatrix_diag): new function
219            * R/lgCMatrix.R (diag): for new method
220    
221            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
222                 ==> construction of illegal "*gTMatrix" via new() should
223                 now be much less easy:
224            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
225    
226            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
227                    directly.
228            * man/Matrix.Rd: documents it.
229    
230    2006-07-06  Douglas Bates  <bates@R-project.org>
231    
232            * src/pedigree.c (pedigree_inbreeding): Correction in
233            initialization.  This function is not currently being used and is
234            not fully tested.
235    
236            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
237            Introduced the glmer class.  Added code for mcmcmsamp on glmer
238            objects.  Modified validity check on pedigree objects to account
239            for nonparallel patterns of missingness of parents.
240    
241            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
242            class.
243    
244    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/pMatrix.R: coercion pMatrix -> Tsparse
247    
248    2006-06-12  Douglas Bates  <bates@R-project.org>
249    
250            * DESCRIPTION (Version): 0.995-11 released to CRAN
251    
252            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
253            the output from mcmcsamp.
254    
255    2006-06-10  Douglas Bates  <bates@R-project.org>
256    
257            * R/lmer.R (simulestimate): added C code for calculating the trace
258            of the hat matrix.
259    
260    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
263            classes.
264            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
265    
266    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * R/dgTMatrix.R (colSums): etc. All four of
269            colSums(), rowSums(), colMeans(), rowMeans() now should work for
270            all "Matrices".
271    
272    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
273    
274            * R/lmer.R (panel.ci): Add a reference line at zero and a
275            background grid to the qqmath plot of ranef.lmer.
276    
277    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
278    
279            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
280            grouping factors to be specified in the formula as (1|foo/bar).
281    
282    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
283    
284            * R/lmer.R (findbars and others): Change check of is.numeric to
285            !is.language to resolve the bug reported by Jacob Wegelin.
286    
287            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
288            code to evaluate inbreeding coefficients without calculating T,
289            based on code in Sargolzaei and Iwaisaki's paper.
290    
291    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
292    
293            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
294            generic and mer methods for isNested and denomDF. This denomDF was
295            an attempt to emulate that in lme but I don't think that makes
296            sense.  Use the trace of the hat matrix instead.
297    
298    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
301            the C code depending on a slot structure that's no longer valid.
302            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
303    
304    
305    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
306    
307            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
308            of lowerTriMatrix generic and methods to tril (also upper to triu)
309            and added a general band extractor.
310    
311    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
312    
313            * R/pedigree.R (pedigree): Replace sire and dam values outside the
314            allowable range with NAs. Added a corresponding check in the
315            validity check for the pedigree class.
316    
317            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
318            crossprod methods now inherits from symmetricMatrix.
319    
320    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
321    
322            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
323            generics lowerTriMatrix and upperTriMatrix along with methods for
324            the Csparse virtual class.  Also added a C function Csparse_band
325            that implements these methods by calling cholmod_band.
326    
327    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
330            erased when it was NULL.  This led to invalid subselections!
331    
332    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
333    
334            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
335            in method for "t" so as not to lose the unit diagonal property.
336    
337    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
338    
339            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
340            and methods.  This is now an option to the ranef method for the
341            mer class.
342    
343            * src/cs_utils.c: Ensure that the nz component is -1 for a
344            compressed column-oriented matrix.  Minor formatting cleanup.
345    
346            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
347            objects.
348    
349    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
352            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
353    
354    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
355    
356            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
357            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
358    
359            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
360            for the dtCMatrix class.
361    
362    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
363    
364            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
365            and methods for it.
366    
367    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
370            arguments, such that M %*% 1:6 now works
371            * Tests/matprod.R: test the above
372    
373    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
374    
375            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
376            the ranef.lmer class.
377    
378            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
379            methods to extract the posterior variances from the bVar slot.
380    
381    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
384            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
385    
386            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
387            * tests/simple: (extended)
388    
389            * R/sparseMatrix.R (isTriangular): now using much improved
390            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
391    
392    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
393    
394            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
395            (problem report from Franklin Parlamis).  This should be done
396            generally.
397    
398    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
399    
400            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
401            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
402            update the plot methods.
403    
404    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
405    
406            * R/lmer.R (resid and ranef methods):  Added methods for the
407            "residuals" and "resid" generic but only for linear mixed model
408            fits.  Changed the ranef method to return a list of data frames so
409            that the plot methods now work.
410    
411    2006-03-16  Douglas Bates  <bates@bates2>
412    
413            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
414            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
415    
416            * DESCRIPTION (Date): New release
417    
418    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
421    
422            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
423            * man/KNex.Rd: and other help files
424            * tests/*.R: several ones needed adaption
425            * inst/doc/Comparisons.Rnw: ditto
426    
427    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
430    
431            * tests/indexing.R: tests for new [<- methods for sparse matrices.
432    
433    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
436    
437            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
438    
439    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/dMatrix.R: enable things like  M [ M < 10 ]
442            * R/dgeMatrix.R: implement it
443    
444    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/AllClass.R: define "summary.mer" and "*.lmer"
447            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
448            * R/lmer.R (show): now works with summary()
449    
450    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
453            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
454                    support the above
455    
456    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
457    
458            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
459            Use glmFit$prior.weights for weights in a glmm.
460            Allow an option usePQL = FALSE to skip the PQL steps for the
461            Laplace method (and, in time, the AGQ method).
462    
463            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
464            into a separate function internal_mer_Xfactor to be able to call
465            it from internal_bhat.
466    
467    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * tests/Class+Meth.R (tstMatrixClass): function for much better
470            testing; now again of all actual classes.
471    
472            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
473                    use macros and define make_d_matrix_* and make_i_matrix_*
474                    where _i_ is for the ldense routines:
475    
476            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
477            * src/ldense.c (lsyMatrix_as_lgeMatrix):
478    
479            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
480    
481    
482    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
485                    many different kinds of matrices.
486            * R/*.R: quite a few new methods were needed for R CMD check with
487                    new Matrix().  Very good for users playing around.
488    
489    
490    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * src/dgeMatrix.c (dMatrix_validate): new
493            * src/Mutils.c (dense_nonpacked_validate): new
494    
495            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
496    
497    
498    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
499    
500            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
501    
502    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
503    
504            * DESCRIPTION (Version): 0.99-6 released to CRAN
505    
506            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
507            segfault in cases with multiple non-nested grouping factors.
508    
509    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
512                    (Depends): also on 'utils'
513    
514            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
515            * R/diagMatrix.R (Diagonal): constructor and methods for
516            diagonal matrices
517    
518            * R/ltTMatrix.R: new "minimal methods"
519    
520    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
523            all methods (and help files).
524    
525    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
528                    for case (dimn.  op  no_dimn.)
529    
530    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
531    
532            * DESCRIPTION (Version): 0.99-2  released to CRAN
533    
534    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
535    
536            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
537            by Julian Faraway.
538    
539    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Auxiliaries.R (try_as): new utility
542            * R/sparseMatrix.R: use try_as() in coercion to original class
543    
544    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
547    
548    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/Auxiliaries.R (dimNamesCheck): added
551    
552            * R/Matrix.R (as.array), (as.vector): new
553    
554    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
555    
556            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
557                    default.
558            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
559                    "pMatrix" now contains "sparseMatrix"
560    
561    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * tests/Class+Meth.R: new tests; t(t(m)) == m
564    
565            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
566    
567            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
568            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
569    
570            * R/dspMatrix.R: typo in "t" method
571    
572    2005-09-18  Douglas Bates  <bates@wisc.edu>
573    
574            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
575            * R/Tsparse.R: instead of R/gTMatrix.R
576            * R/Csparse.R: new
577            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
578            * src/Tsparse.c: new; many trivial methods calling cholmod_()
579            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
580                            via cholmod
581    
582    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/Auxiliaries.R (non0ind): new function using new C code
585            * src/dgCMatrix.c (compressed_non_0_ij): new utility
586    
587    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
588    
589            * src/chm_common.h: header file required by all C sources that
590            call CHOLMOD functions.  It defines a cholmod_common structure
591            called 'c' whose address is passed as the last argument to
592            (virtually) every CHOLMOD function.
593    
594            * src/Pattern.c: Simple example of the use of CHOLMOD.
595    
596            * src/init.c: initialize and finalize the cholmod_common structure.
597    
598            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
599            LDL and CCOLAMD from the U. of Florida sparse matrix library.
600    
601    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * inst/test-tools.R: new file collecting the utility functions used
604                    in ./tests/*.R
605    
606            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
607            * R/Matrix.R (cbind2): methods for NULL and missing
608    
609    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/AllClass.R: new "index" class for "[" and "[<-":
612                    First cut at "symmetricMatrix" and "triangularMatrix"
613            * R/gTMatrix.R (.ind.prep): new function;
614                    Logical and character indexing now work too.
615            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
616            * tests/indexing.R: new, including *.Rout.save
617            * tests/dgTMatrix.R: new
618    
619    2005-08-29  Douglas Bates  <bates@wisc.edu>
620    
621            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
622            indicator pos not being updated.  Also enforced upper triangular
623            for symmetric case.  Need to coerce edges component of elements of
624            edge list - grr! (Why don't they define their classes cleanly?)
625    
626    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/Matrix.R:  added first "[<-" methods; not yet functional
629            * R/denseMatrix.R: ditto
630            * man/Subassign-methods.Rd: new help file for these
631    
632    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * DESCRIPTION (Version): 0.98-6
635    
636            * R/denseMatrix.R: new file for "[" fallback methods for all dense
637            matrices.
638    
639    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
642                    as( <logical>, "matrix")
643    
644            * R/pMatrix.R: coercion to "lgTMatrix"
645    
646            * R/gTMatrix.R: new virtual class to define "[" methods for.
647            * man/gTMatrix-class.Rd:
648            * General slight re-organization of where "[" methods are defined.
649              more to come.
650    
651    2005-08-18  Douglas Bates  <bates@wisc.edu>
652    
653            * DESCRIPTION (Version): 0.98-5  released to CRAN
654    
655            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
656            * .....
657    
658    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
659    
660            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
661            or glmer objects.
662    
663    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
666    
667    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
668    
669            * R/HBMM.R: finish re-writing R-only code.
670    
671    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
672    
673            * man/externalFormats.Rd: move documentation for writeHB and
674            writeMM here.
675    
676            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
677            (suggested by Paul Roecker).
678    
679            * tests/validObj.R (assertError): Comment out test that is failing
680            after recent changes in r-devel.
681    
682    
683    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/AllClass.R: intermediate virtual class "denseMatrix"
686            * man/denseMatrix-class.Rd
687            * NAMESPACE: export it, and also export
688            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
689    
690    2005-08-10  Douglas Bates  <bates@wisc.edu>
691    
692            * DESCRIPTION (Version): 0.98-3 to CRAN
693    
694            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
695            matrix_solve code (which was really, really wrong).
696    
697    2005-08-07  Douglas Bates  <bates@wisc.edu>
698    
699            * DESCRIPTION (Version): 0.98-2
700    
701            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
702    
703            * R/lmer.R (abbrvNms): new
704            * R/lmer.R (mcmcsamp): allow transformed parameters
705            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
706            for the Harwell-Boeing and the MatrixMarket formats.
707    
708    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * man/dtrMatrix-class.Rd: add examples
711            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
712    
713            * TODO: note the dtpMatrix (docu) bug
714    
715            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
716            in order to ensure that new as.matrix() is used by old functions,
717            e.g., svd(), qr(), eigen(), dist(),..;
718                  apply(), also matplot() or pairs().
719    
720    
721    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
722    
723            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
724              add comments about 'control' / lmerControl() arguments
725    
726    2005-07-27  Douglas Bates  <bates@wisc.edu>
727    
728            * man/sleepstudy.Rd: Added the sleep data set.
729            * DESCRIPTION (Version): 0.98-1  released to CRAN
730    
731    2005-07-12  Douglas Bates  <bates@wisc.edu>
732            * man/sleepstudy.Rd: Added the sleep data set.
733    
734            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
735            .Call calls that were producing spurious output.
736    
737    2005-07-05  Douglas Bates  <bates@wisc.edu>
738    
739            * R/lmer.R (lmer): stored updated variance component estimates in
740            mer object for the generalized model.  (Bug reported by Renaud
741            Lancelot).
742    
743    2005-07-03  Douglas Bates  <bates@wisc.edu>
744    
745            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
746            unidimensional case.
747    
748    2005-06-08  Douglas Bates  <bates@wisc.edu>
749    
750            * DESCRIPTION (Version): 0.96-1
751    
752            * moved  lmer-class' R and C code moved from lme4 to here
753    
754    2005-06-04  Douglas Bates  <bates@wisc.edu>
755    
756            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
757            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
758    
759    2005-06-02  Douglas Bates  <bates@wisc.edu>
760    
761            * src/Makefile.win: Forgot to update this when Makefile changed.
762    
763    2005-05-11  Douglas Bates  <bates@wisc.edu>
764    
765          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
766          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
767    
768  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
769    
770          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
771          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 774 
774          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
775          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
776    
777  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
778    
779          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
780          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
781    
782  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
783    
784          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
785          multiplication operation.          multiplication operation.
# Line 30  Line 792 
792    
793          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
794    
795  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
796    
797          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
798    
799          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
800    
801    
802  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
803    
804          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
805    
# Line 46  Line 808 
808          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
809          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
810    
811  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
812    
813          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
814    
# Line 72  Line 834 
834          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
835            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
836    
837  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
838    
839          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
840          * ....          * ....
841    
842  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
843    
844          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
845    
# Line 92  Line 854 
854            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
855          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
856    
857  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
858    
859          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
860    
861  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
862    
863          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
864    
865  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
866    
867          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
868          the package.          the package.
# Line 148  Line 910 
910    
911          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
912    
913  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
914    
915          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
916          for the geMatrix class.          for the geMatrix class.
917    
918  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
919    
920          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
921    
922          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
923    
924  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
925    
926          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
927          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
928    
929  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
930    
931          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
932    
933  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
934    
935          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
936          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
937    
938  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
939    
940          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
941    
942          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
943          for tripletMatrix to matrix.          for tripletMatrix to matrix.
944    
945  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
946    
947          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
948          no longer used.          no longer used.
# Line 192  Line 954 
954          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
955          Fixes part but not all of #15.          Fixes part but not all of #15.
956    
957  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
958    
959          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
960          scalar grouping factors corrected.          scalar grouping factors corrected.
961    
962  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
963    
964          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
965    
966  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
967    
968          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
969          .h file can be included.          .h file can be included.
970    
971  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
972    
973          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
974          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
975    
976          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
977    
978  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
979    
980          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
981    
982  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
983    
984          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
985    
986  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
987    
988          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
989    
990  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
991    
992          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
993    
994  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
995    
996          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
997          routines.          routines.
998    
999  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1000    
1001          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1002    
1003  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1004    
1005          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1006    

Legend:
Removed from v.726  
changed lines
  Added in v.1398

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge