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revision 392, Tue Dec 14 20:01:16 2004 UTC revision 1423, Tue Aug 22 22:51:56 2006 UTC
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1  2004-12-14  Douglas Bates  <bates@bates1-home>  2006-08-22  Douglas Bates  <bates@R-project.org>
2    
3            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
4            types of classed Matrices, matrices or numeric or logical vectors.
5            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
6            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
7            to Mutils.h (as an inline) and change name to Matrix_check_class;
8            fixes in as_cholmod_factor and chm_factor_to_SEXP.
9            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
10            dsCMatrix_matrix_solve.  Comment out vestigial functions.
11            * src/Csparse.c: use diag_P and uplo_P macros.
12    
13    2006-08-21  Douglas Bates  <bates@R-project.org>
14    
15            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
16            valgrind.
17            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
18            inverses.
19            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
20            -Wall warnings.
21            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
22            Use dup_mMatrix_as_dgeMatrix.
23    
24    2006-08-20  Douglas Bates  <bates@R-project.org>
25    
26            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
27            * tests/sparseQR.R: Added
28            * man/sparseQR-class.Rd: Document methods for qr.* generics
29            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
30    
31    2006-08-19  Douglas Bates  <bates@R-project.org>
32    
33            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
34            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
35            and qr.fitted.
36            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
37            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
38    
39    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
42            the base version has no "..." argument.
43    
44            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
45    
46            * R/Matrix.R: define and
47            * NAMESPACE: export as.numeric() and as.logical() methods.
48                    Let's hope these do not badly slow down something...
49            Finally export the zapsmall() method.
50    
51    2006-08-17  Douglas Bates  <bates@R-project.org>
52    
53            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
54            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
55            * src/dtCMatrix.c :Remove code that is no longer used
56            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
57    
58    2006-08-14  Douglas Bates  <bates@R-project.org>
59    
60            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
61            Csparse_to_logical and Csparse_symmetric_to_general.
62            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
63            coercion methods between CsparseMatrix and TsparseMatrix.
64    
65    2006-08-14  Douglas Bates  <bates@R-project.org>
66    
67            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
68            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
69            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
70            possible.
71    
72    2006-08-12  Douglas Bates  <bates@R-project.org>
73    
74            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
75              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
76              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
77              generalize conversions between TsparseMatrix, CsparseMatrix,
78              denseMatrix and matrix.  Preserve triangularity property and
79              propagate Dimnames in the easy cases.
80    
81    2006-08-10  Douglas Bates  <bates@R-project.org>
82    
83            * src/lmer.c: adjust checks in glmer_init for S4SXP
84            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
85            before S4SXP but for the wrong reasons.
86    
87    2006-08-08  Douglas Bates  <bates@R-project.org>
88    
89            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
90            Later modified to return the upper triangle only.
91            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
92    
93    2006-08-07  Douglas Bates  <bates@R-project.org>
94    
95            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
96            R-level conversion to a sparse symmetric class.
97            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
98            Remove conversion to sparse symmetric classes (now done in C code).
99    
100    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
103            * man/band.Rd:  adapt the \dontshow{} unit test.
104    
105    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * DESCRIPTION (Version): 0.995-14  for CRAN
108    
109            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
110    
111            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
112            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
113    
114            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
115            * R/Tsparse.R (tril, triu, band): methods
116            * R/dgRMatrix.R (tril, ...):    ditto
117            * man/band.Rd:                  ditto
118    
119    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/Matrix.R (head, tail): directly use utils:::head.matrix
122                    to be up-to-date automatically.
123    
124    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
127    
128            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
129            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
130            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
131            such that the S4 objects are always created by the current version
132            of R and 'Matrix' class definitions.
133    
134    2006-08-01  Douglas Bates  <bates@R-project.org>
135    
136            * R/lmer.R (LMEoptimize method), tests/lmer.R,
137            inst/external/test3comp.rda: Added warnings for convergence on
138            boundary and test cases.
139    
140            * src/lmer.c (mer_postVar): Modified to return the variances that
141            are marginal to the fixed effects, not conditional on them (which
142            is what the bVar slot contents represent).
143    
144    2006-07-31  Douglas Bates  <bates@R-project.org>
145    
146            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
147            function which calls the C function mer_hat_trace2.
148    
149            * man/ranef.Rd: Include description of "postVar" argument and
150            producing a caterpillar plot.
151    
152    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * NAMESPACE:    change  "correlation" to "corMatrix"
155            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
156            * R/dpoMatrix.R: ditto
157            * R/lmer.R:      ditto
158    
159    2006-07-28  Douglas Bates  <bates@R-project.org>
160    
161            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
162            RZXinv slot's contents into a separate internal function that can
163            be used in mer_hat_trace.
164    
165    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
168            via new smart
169            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
170            utility functions.
171    
172    
173    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/Csparse.R (tril, triu, band): do return *triangular* classed
176            matrices when appropriate; band() even symmetric ones.
177            (replCmat): extend to potentially all "CsparseMatrix"
178            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
179            allow subassignment for special sparse matrices.
180    
181            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
182    
183            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
184            argument; in glmer_*(): print only if(verbose).
185    
186            speed-optimize a few places by moving REAL(.) out of loops.
187    
188            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
189    
190    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
193                    since that wrongly triggers also for M[ logi , ]
194    
195            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
196            a symmetric matrix that results in a non-symmetric one.
197            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
198    
199            * R/dMatrix.R: make round(M) work as round(M, 0)
200    
201            * R/dgTMatrix.R (image): coordinate system and axis now use
202            1-based indices, not 0-based ones.
203    
204            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
205            * tests/indexing.R: test it.
206    
207            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
208            * man/isSymmetric-methods.Rd: and document it.
209    
210            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
211            * man/SparseM-conv.Rd: docu them
212    
213            * tests/other-pkgs.R: renamed from tests/graph.R and add example
214                    for 'SparseM' conversions
215    
216    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
217    
218            * R/Matrix.R (head): added head() and tail() methods.
219    
220    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * DESCRIPTION (Version): 0.995-12 released to CRAN
223    
224    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * tests/simple.R: add check for correct dsT -> dgT coercion;
227                    add check for correct printing of symmetric sparse matrices.
228    
229            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
230            for sparse symmetric matrices.
231    
232            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
233            diagonal twice.
234    
235    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
236    
237            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
238            being applied to the x slot (detected by Brian Ripley).
239    
240    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
243    
244            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
245    
246    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * src/lgCMatrix.c (lgCMatrix_diag): new function
249            * R/lgCMatrix.R (diag): for new method
250    
251            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
252                 ==> construction of illegal "*gTMatrix" via new() should
253                 now be much less easy:
254            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
255    
256            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
257                    directly.
258            * man/Matrix.Rd: documents it.
259    
260    2006-07-06  Douglas Bates  <bates@R-project.org>
261    
262            * src/pedigree.c (pedigree_inbreeding): Correction in
263            initialization.  This function is not currently being used and is
264            not fully tested.
265    
266            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
267            Introduced the glmer class.  Added code for mcmcmsamp on glmer
268            objects.  Modified validity check on pedigree objects to account
269            for nonparallel patterns of missingness of parents.
270    
271            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
272            class.
273    
274    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/pMatrix.R: coercion pMatrix -> Tsparse
277    
278    2006-06-12  Douglas Bates  <bates@R-project.org>
279    
280            * DESCRIPTION (Version): 0.995-11 released to CRAN
281    
282            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
283            the output from mcmcsamp.
284    
285    2006-06-10  Douglas Bates  <bates@R-project.org>
286    
287            * R/lmer.R (simulestimate): added C code for calculating the trace
288            of the hat matrix.
289    
290    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
293            classes.
294            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
295    
296    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/dgTMatrix.R (colSums): etc. All four of
299            colSums(), rowSums(), colMeans(), rowMeans() now should work for
300            all "Matrices".
301    
302    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
303    
304            * R/lmer.R (panel.ci): Add a reference line at zero and a
305            background grid to the qqmath plot of ranef.lmer.
306    
307    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
308    
309            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
310            grouping factors to be specified in the formula as (1|foo/bar).
311    
312    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
313    
314            * R/lmer.R (findbars and others): Change check of is.numeric to
315            !is.language to resolve the bug reported by Jacob Wegelin.
316    
317            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
318            code to evaluate inbreeding coefficients without calculating T,
319            based on code in Sargolzaei and Iwaisaki's paper.
320    
321    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
322    
323            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
324            generic and mer methods for isNested and denomDF. This denomDF was
325            an attempt to emulate that in lme but I don't think that makes
326            sense.  Use the trace of the hat matrix instead.
327    
328    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
331            the C code depending on a slot structure that's no longer valid.
332            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
333    
334    
335    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
336    
337            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
338            of lowerTriMatrix generic and methods to tril (also upper to triu)
339            and added a general band extractor.
340    
341    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
342    
343            * R/pedigree.R (pedigree): Replace sire and dam values outside the
344            allowable range with NAs. Added a corresponding check in the
345            validity check for the pedigree class.
346    
347            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
348            crossprod methods now inherits from symmetricMatrix.
349    
350    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
351    
352            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
353            generics lowerTriMatrix and upperTriMatrix along with methods for
354            the Csparse virtual class.  Also added a C function Csparse_band
355            that implements these methods by calling cholmod_band.
356    
357    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
360            erased when it was NULL.  This led to invalid subselections!
361    
362    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
363    
364            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
365            in method for "t" so as not to lose the unit diagonal property.
366    
367    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
368    
369            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
370            and methods.  This is now an option to the ranef method for the
371            mer class.
372    
373            * src/cs_utils.c: Ensure that the nz component is -1 for a
374            compressed column-oriented matrix.  Minor formatting cleanup.
375    
376            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
377            objects.
378    
379    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
382            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
383    
384    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
385    
386            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
387            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
388    
389            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
390            for the dtCMatrix class.
391    
392    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
393    
394            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
395            and methods for it.
396    
397    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
400            arguments, such that M %*% 1:6 now works
401            * Tests/matprod.R: test the above
402    
403    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
404    
405            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
406            the ranef.lmer class.
407    
408            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
409            methods to extract the posterior variances from the bVar slot.
410    
411    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
414            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
415    
416            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
417            * tests/simple: (extended)
418    
419            * R/sparseMatrix.R (isTriangular): now using much improved
420            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
421    
422    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
423    
424            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
425            (problem report from Franklin Parlamis).  This should be done
426            generally.
427    
428    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
429    
430            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
431            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
432            update the plot methods.
433    
434    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
435    
436            * R/lmer.R (resid and ranef methods):  Added methods for the
437            "residuals" and "resid" generic but only for linear mixed model
438            fits.  Changed the ranef method to return a list of data frames so
439            that the plot methods now work.
440    
441    2006-03-16  Douglas Bates  <bates@bates2>
442    
443            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
444            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
445    
446            * DESCRIPTION (Date): New release
447    
448    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
451    
452            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
453            * man/KNex.Rd: and other help files
454            * tests/*.R: several ones needed adaption
455            * inst/doc/Comparisons.Rnw: ditto
456    
457    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
460    
461            * tests/indexing.R: tests for new [<- methods for sparse matrices.
462    
463    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
466    
467            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
468    
469    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * R/dMatrix.R: enable things like  M [ M < 10 ]
472            * R/dgeMatrix.R: implement it
473    
474    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/AllClass.R: define "summary.mer" and "*.lmer"
477            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
478            * R/lmer.R (show): now works with summary()
479    
480    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
483            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
484                    support the above
485    
486    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
487    
488            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
489            Use glmFit$prior.weights for weights in a glmm.
490            Allow an option usePQL = FALSE to skip the PQL steps for the
491            Laplace method (and, in time, the AGQ method).
492    
493            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
494            into a separate function internal_mer_Xfactor to be able to call
495            it from internal_bhat.
496    
497    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * tests/Class+Meth.R (tstMatrixClass): function for much better
500            testing; now again of all actual classes.
501    
502            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
503                    use macros and define make_d_matrix_* and make_i_matrix_*
504                    where _i_ is for the ldense routines:
505    
506            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
507            * src/ldense.c (lsyMatrix_as_lgeMatrix):
508    
509            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
510    
511    
512    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
515                    many different kinds of matrices.
516            * R/*.R: quite a few new methods were needed for R CMD check with
517                    new Matrix().  Very good for users playing around.
518    
519    
520    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * src/dgeMatrix.c (dMatrix_validate): new
523            * src/Mutils.c (dense_nonpacked_validate): new
524    
525            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
526    
527    
528    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
529    
530            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
531    
532    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
533    
534            * DESCRIPTION (Version): 0.99-6 released to CRAN
535    
536            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
537            segfault in cases with multiple non-nested grouping factors.
538    
539    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
542                    (Depends): also on 'utils'
543    
544            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
545            * R/diagMatrix.R (Diagonal): constructor and methods for
546            diagonal matrices
547    
548            * R/ltTMatrix.R: new "minimal methods"
549    
550    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
553            all methods (and help files).
554    
555    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
558                    for case (dimn.  op  no_dimn.)
559    
560    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
561    
562            * DESCRIPTION (Version): 0.99-2  released to CRAN
563    
564    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
565    
566            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
567            by Julian Faraway.
568    
569    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/Auxiliaries.R (try_as): new utility
572            * R/sparseMatrix.R: use try_as() in coercion to original class
573    
574    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
577    
578    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * R/Auxiliaries.R (dimNamesCheck): added
581    
582            * R/Matrix.R (as.array), (as.vector): new
583    
584    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
587                    default.
588            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
589                    "pMatrix" now contains "sparseMatrix"
590    
591    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * tests/Class+Meth.R: new tests; t(t(m)) == m
594    
595            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
596    
597            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
598            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
599    
600            * R/dspMatrix.R: typo in "t" method
601    
602    2005-09-18  Douglas Bates  <bates@wisc.edu>
603    
604            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
605            * R/Tsparse.R: instead of R/gTMatrix.R
606            * R/Csparse.R: new
607            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
608            * src/Tsparse.c: new; many trivial methods calling cholmod_()
609            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
610                            via cholmod
611    
612    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/Auxiliaries.R (non0ind): new function using new C code
615            * src/dgCMatrix.c (compressed_non_0_ij): new utility
616    
617    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
618    
619            * src/chm_common.h: header file required by all C sources that
620            call CHOLMOD functions.  It defines a cholmod_common structure
621            called 'c' whose address is passed as the last argument to
622            (virtually) every CHOLMOD function.
623    
624            * src/Pattern.c: Simple example of the use of CHOLMOD.
625    
626            * src/init.c: initialize and finalize the cholmod_common structure.
627    
628            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
629            LDL and CCOLAMD from the U. of Florida sparse matrix library.
630    
631    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * inst/test-tools.R: new file collecting the utility functions used
634                    in ./tests/*.R
635    
636            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
637            * R/Matrix.R (cbind2): methods for NULL and missing
638    
639    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * R/AllClass.R: new "index" class for "[" and "[<-":
642                    First cut at "symmetricMatrix" and "triangularMatrix"
643            * R/gTMatrix.R (.ind.prep): new function;
644                    Logical and character indexing now work too.
645            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
646            * tests/indexing.R: new, including *.Rout.save
647            * tests/dgTMatrix.R: new
648    
649    2005-08-29  Douglas Bates  <bates@wisc.edu>
650    
651            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
652            indicator pos not being updated.  Also enforced upper triangular
653            for symmetric case.  Need to coerce edges component of elements of
654            edge list - grr! (Why don't they define their classes cleanly?)
655    
656    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/Matrix.R:  added first "[<-" methods; not yet functional
659            * R/denseMatrix.R: ditto
660            * man/Subassign-methods.Rd: new help file for these
661    
662    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * DESCRIPTION (Version): 0.98-6
665    
666            * R/denseMatrix.R: new file for "[" fallback methods for all dense
667            matrices.
668    
669    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
670    
671            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
672                    as( <logical>, "matrix")
673    
674            * R/pMatrix.R: coercion to "lgTMatrix"
675    
676            * R/gTMatrix.R: new virtual class to define "[" methods for.
677            * man/gTMatrix-class.Rd:
678            * General slight re-organization of where "[" methods are defined.
679              more to come.
680    
681    2005-08-18  Douglas Bates  <bates@wisc.edu>
682    
683            * DESCRIPTION (Version): 0.98-5  released to CRAN
684    
685            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
686            * .....
687    
688    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
689    
690            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
691            or glmer objects.
692    
693    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
696    
697    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
698    
699            * R/HBMM.R: finish re-writing R-only code.
700    
701    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
702    
703            * man/externalFormats.Rd: move documentation for writeHB and
704            writeMM here.
705    
706            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
707            (suggested by Paul Roecker).
708    
709            * tests/validObj.R (assertError): Comment out test that is failing
710            after recent changes in r-devel.
711    
712    
713    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/AllClass.R: intermediate virtual class "denseMatrix"
716            * man/denseMatrix-class.Rd
717            * NAMESPACE: export it, and also export
718            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
719    
720    2005-08-10  Douglas Bates  <bates@wisc.edu>
721    
722            * DESCRIPTION (Version): 0.98-3 to CRAN
723    
724            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
725            matrix_solve code (which was really, really wrong).
726    
727    2005-08-07  Douglas Bates  <bates@wisc.edu>
728    
729            * DESCRIPTION (Version): 0.98-2
730    
731            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
732    
733            * R/lmer.R (abbrvNms): new
734            * R/lmer.R (mcmcsamp): allow transformed parameters
735            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
736            for the Harwell-Boeing and the MatrixMarket formats.
737    
738    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * man/dtrMatrix-class.Rd: add examples
741            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
742    
743            * TODO: note the dtpMatrix (docu) bug
744    
745            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
746            in order to ensure that new as.matrix() is used by old functions,
747            e.g., svd(), qr(), eigen(), dist(),..;
748                  apply(), also matplot() or pairs().
749    
750    
751    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
754              add comments about 'control' / lmerControl() arguments
755    
756    2005-07-27  Douglas Bates  <bates@wisc.edu>
757    
758            * man/sleepstudy.Rd: Added the sleep data set.
759            * DESCRIPTION (Version): 0.98-1  released to CRAN
760    
761    2005-07-12  Douglas Bates  <bates@wisc.edu>
762            * man/sleepstudy.Rd: Added the sleep data set.
763    
764            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
765            .Call calls that were producing spurious output.
766    
767    2005-07-05  Douglas Bates  <bates@wisc.edu>
768    
769            * R/lmer.R (lmer): stored updated variance component estimates in
770            mer object for the generalized model.  (Bug reported by Renaud
771            Lancelot).
772    
773    2005-07-03  Douglas Bates  <bates@wisc.edu>
774    
775            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
776            unidimensional case.
777    
778    2005-06-08  Douglas Bates  <bates@wisc.edu>
779    
780            * DESCRIPTION (Version): 0.96-1
781    
782            * moved  lmer-class' R and C code moved from lme4 to here
783    
784    2005-06-04  Douglas Bates  <bates@wisc.edu>
785    
786            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
787            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
788    
789    2005-06-02  Douglas Bates  <bates@wisc.edu>
790    
791            * src/Makefile.win: Forgot to update this when Makefile changed.
792    
793    2005-05-11  Douglas Bates  <bates@wisc.edu>
794    
795            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
796            bug reported by Kurt Hornik and Michael Hahsler.
797    
798    2005-05-10  Douglas Bates  <bates@wisc.edu>
799    
800            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
801            logical sparse matrices.  These will also be used in the symbolic
802            analysis for lmer objects.
803    
804            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
805            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
806    
807    2005-05-06  Douglas Bates  <bates@wisc.edu>
808    
809            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
810            colMeans, colSums, rowMeans and rowSums.
811    
812    2005-04-18  Douglas Bates  <bates@wisc.edu>
813    
814            * src/lgCMatrix.[ch]: code for _validate method and stub for
815            multiplication operation.
816    
817            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
818            to dgetrs.
819    
820            * src/init.c: Fix cut-and-paste error in definition of
821            dgeMatrix_matrix_solve
822    
823            * src/{many files}: Tighten code by using ALLOC_SLOT.
824    
825    2005-04-15  Douglas Bates  <bates@wisc.edu>
826    
827            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
828    
829            * DESCRIPTION: Eliminate import of stats.
830    
831    
832    2005-04-06  Douglas Bates  <bates@wisc.edu>
833    
834            * R/AllClass.R : add logical sparse matrix classes
835    
836    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/dgTMatrix.R: add "[" method for triplet matrices
839            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
840    
841    2005-03-31  Douglas Bates  <bates@wisc.edu>
842    
843            * DESCRIPTION (Version): release 0.95-5 to CRAN
844    
845            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
846            * R/sparseMatrix.R: %*%, crossprod()
847            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
848            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
849            * src/lmer.c (lmer_fitted): fix thinko
850    
851    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/AllClass.R: add two virtual sparse classes ``on top''
854    
855    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
858                    correspondingly fix examples and tests/ since new()
859                    doesn't work for virtual classes.
860    
861    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * R/Matrix.R (as.matrix): method and one for unname()
864            * tests/dpoMatrix.R: tests should now be less platform dependent;
865              also run for R 2.1.0; using as.matrix()
866    
867    2005-03-15  Douglas Bates  <bates@wisc.edu>
868    
869            * R/pMatrix.R: "pMatrix" class added
870            * ....
871    
872    2005-03-14  Douglas Bates  <bates@wisc.edu>
873    
874            * R/dtpMatrix.R: Add unpack method and an example.
875    
876            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
877            of general symmetric matrices and associated S4 methods.
878    
879    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
880            +
881    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
882    
883            * R/dgeMatrix.R (setAs): and many other files: more coercion,
884              crossprod() and "%*%" methods added; tests, too.
885            * tests/matprod.R: new, for testing these
886    
887    2005-03-03  Douglas Bates  <bates@wisc.edu>
888    
889            * src/lmer.c (lmer_fitted): Added.
890    
891    2005-03-02  Douglas Bates  <bates@wisc.edu>
892    
893            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
894    
895    2005-02-28  Douglas Bates  <bates@wisc.edu>
896    
897            * src/*.c,po/,inst/po: Internationalization and localization of
898            the package.
899    
900            * src/ldl.[ch]: Removed these as their contents are referenced in the
901            R_ldl.c file.
902    
903            * src/flame.[ch]: Removed these source files.
904    
905            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
906    
907            * src/LU.[ch],src/init.c: absorb in factorizations
908    
909            * src/Mutils.h: prepare for internationalization
910    
911            * src/cblas.h: move the enum definitions to Mutils.h and remove
912            this file
913    
914    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
917    
918            * R/dtrMatrix.R: fix t() method
919    
920            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
921            * NAMESPACE: export them (and import generics from "methods")
922            * tests/group-methods.R : and test them.
923    
924            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
925            border case
926    
927    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
928    
929            * DESCRIPTION (Version): 0.95-2  released to CRAN
930    
931            * src/dgBCMatrix.c:
932            * src/lmer.c: many changes
933            * ...
934    
935    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
936    
937            * R/Matrix.R: add more sophisticated show() method.
938    
939    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
940    
941            * */* : almost complete reorganization of classes.
942    
943    2005-01-26  Douglas Bates  <bates@wisc.edu>
944    
945            * R/AllGeneric.R: Added matrix exponential generic expm and a method
946            for the geMatrix class.
947    
948    2005-01-24  Douglas Bates  <bates@wisc.edu>
949    
950            * src/Makefile (clean): Remove *.a and *.so
951    
952            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
953    
954    2005-01-23  Douglas Bates  <bates@wisc.edu>
955    
956            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
957            had an effect in cases with more than 2 grouping factors.
958    
959    2005-01-03  Douglas Bates  <bates@wisc.edu>
960    
961            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
962    
963    2004-12-23  Douglas Bates  <bates@wisc.edu>
964    
965            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
966            and R_useDynamicSymbols (suggested by B.D.Ripley).
967    
968    2004-12-14  Douglas Bates  <bates@wisc.edu>
969    
970          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
971    
972          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
973          for tripletMatrix to matrix.          for tripletMatrix to matrix.
974    
975  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
976    
977          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
978          no longer used.          no longer used.
# Line 17  Line 984 
984          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
985          Fixes part but not all of #15.          Fixes part but not all of #15.
986    
987  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
988    
989          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
990          scalar grouping factors corrected.          scalar grouping factors corrected.
991    
992  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
993    
994          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
995    
996  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
997    
998          * 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
999          .h file can be included.          .h file can be included.
1000    
1001  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1002    
1003          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1004          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1005    
1006          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1007    
1008  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1009    
1010          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1011    
1012  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1013    
1014          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1015    
1016  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1017    
1018          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1019    
1020  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1021    
1022          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1023    
1024  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1025    
1026          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1027          routines.          routines.
1028    
1029  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1030    
1031          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1032    
1033  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1034    
1035          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1036    

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