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revision 726, Thu May 12 14:59:04 2005 UTC revision 1414, Tue Aug 22 17:25:43 2006 UTC
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1  2005-05-11  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    
7    2006-08-21  Douglas Bates  <bates@R-project.org>
8    
9            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
10            valgrind.
11            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
12            inverses.
13            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
14            -Wall warnings.
15            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
16            Use dup_mMatrix_as_dgeMatrix.
17    
18    2006-08-20  Douglas Bates  <bates@R-project.org>
19    
20            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
21            * tests/sparseQR.R: Added
22            * man/sparseQR-class.Rd: Document methods for qr.* generics
23            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
24    
25    2006-08-19  Douglas Bates  <bates@R-project.org>
26    
27            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
28            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
29            and qr.fitted.
30            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
31            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
32    
33    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
36            the base version has no "..." argument.
37    
38            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
39    
40            * R/Matrix.R: define and
41            * NAMESPACE: export as.numeric() and as.logical() methods.
42                    Let's hope these do not badly slow down something...
43            Finally export the zapsmall() method.
44    
45    2006-08-17  Douglas Bates  <bates@R-project.org>
46    
47            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
48            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
49            * src/dtCMatrix.c :Remove code that is no longer used
50            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
51    
52    2006-08-14  Douglas Bates  <bates@R-project.org>
53    
54            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
55            Csparse_to_logical and Csparse_symmetric_to_general.
56            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
57            coercion methods between CsparseMatrix and TsparseMatrix.
58    
59    2006-08-14  Douglas Bates  <bates@R-project.org>
60    
61            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
62            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
63            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
64            possible.
65    
66    2006-08-12  Douglas Bates  <bates@R-project.org>
67    
68            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
69              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
70              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
71              generalize conversions between TsparseMatrix, CsparseMatrix,
72              denseMatrix and matrix.  Preserve triangularity property and
73              propagate Dimnames in the easy cases.
74    
75    2006-08-10  Douglas Bates  <bates@R-project.org>
76    
77            * src/lmer.c: adjust checks in glmer_init for S4SXP
78            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
79            before S4SXP but for the wrong reasons.
80    
81    2006-08-08  Douglas Bates  <bates@R-project.org>
82    
83            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
84            Later modified to return the upper triangle only.
85            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
86    
87    2006-08-07  Douglas Bates  <bates@R-project.org>
88    
89            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
90            R-level conversion to a sparse symmetric class.
91            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
92            Remove conversion to sparse symmetric classes (now done in C code).
93    
94    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
97            * man/band.Rd:  adapt the \dontshow{} unit test.
98    
99    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * DESCRIPTION (Version): 0.995-14  for CRAN
102    
103            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
104    
105            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
106            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
107    
108            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
109            * R/Tsparse.R (tril, triu, band): methods
110            * R/dgRMatrix.R (tril, ...):    ditto
111            * man/band.Rd:                  ditto
112    
113    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/Matrix.R (head, tail): directly use utils:::head.matrix
116                    to be up-to-date automatically.
117    
118    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
121    
122            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
123            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
124            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
125            such that the S4 objects are always created by the current version
126            of R and 'Matrix' class definitions.
127    
128    2006-08-01  Douglas Bates  <bates@R-project.org>
129    
130            * R/lmer.R (LMEoptimize method), tests/lmer.R,
131            inst/external/test3comp.rda: Added warnings for convergence on
132            boundary and test cases.
133    
134            * src/lmer.c (mer_postVar): Modified to return the variances that
135            are marginal to the fixed effects, not conditional on them (which
136            is what the bVar slot contents represent).
137    
138    2006-07-31  Douglas Bates  <bates@R-project.org>
139    
140            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
141            function which calls the C function mer_hat_trace2.
142    
143            * man/ranef.Rd: Include description of "postVar" argument and
144            producing a caterpillar plot.
145    
146    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * NAMESPACE:    change  "correlation" to "corMatrix"
149            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
150            * R/dpoMatrix.R: ditto
151            * R/lmer.R:      ditto
152    
153    2006-07-28  Douglas Bates  <bates@R-project.org>
154    
155            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
156            RZXinv slot's contents into a separate internal function that can
157            be used in mer_hat_trace.
158    
159    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
162            via new smart
163            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
164            utility functions.
165    
166    
167    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/Csparse.R (tril, triu, band): do return *triangular* classed
170            matrices when appropriate; band() even symmetric ones.
171            (replCmat): extend to potentially all "CsparseMatrix"
172            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
173            allow subassignment for special sparse matrices.
174    
175            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
176    
177            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
178            argument; in glmer_*(): print only if(verbose).
179    
180            speed-optimize a few places by moving REAL(.) out of loops.
181    
182            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
183    
184    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
187                    since that wrongly triggers also for M[ logi , ]
188    
189            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
190            a symmetric matrix that results in a non-symmetric one.
191            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
192    
193            * R/dMatrix.R: make round(M) work as round(M, 0)
194    
195            * R/dgTMatrix.R (image): coordinate system and axis now use
196            1-based indices, not 0-based ones.
197    
198            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
199            * tests/indexing.R: test it.
200    
201            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
202            * man/isSymmetric-methods.Rd: and document it.
203    
204            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
205            * man/SparseM-conv.Rd: docu them
206    
207            * tests/other-pkgs.R: renamed from tests/graph.R and add example
208                    for 'SparseM' conversions
209    
210    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
211    
212            * R/Matrix.R (head): added head() and tail() methods.
213    
214    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * DESCRIPTION (Version): 0.995-12 released to CRAN
217    
218    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * tests/simple.R: add check for correct dsT -> dgT coercion;
221                    add check for correct printing of symmetric sparse matrices.
222    
223            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
224            for sparse symmetric matrices.
225    
226            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
227            diagonal twice.
228    
229    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
230    
231            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
232            being applied to the x slot (detected by Brian Ripley).
233    
234    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
237    
238            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
239    
240    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * src/lgCMatrix.c (lgCMatrix_diag): new function
243            * R/lgCMatrix.R (diag): for new method
244    
245            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
246                 ==> construction of illegal "*gTMatrix" via new() should
247                 now be much less easy:
248            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
249    
250            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
251                    directly.
252            * man/Matrix.Rd: documents it.
253    
254    2006-07-06  Douglas Bates  <bates@R-project.org>
255    
256            * src/pedigree.c (pedigree_inbreeding): Correction in
257            initialization.  This function is not currently being used and is
258            not fully tested.
259    
260            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
261            Introduced the glmer class.  Added code for mcmcmsamp on glmer
262            objects.  Modified validity check on pedigree objects to account
263            for nonparallel patterns of missingness of parents.
264    
265            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
266            class.
267    
268    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/pMatrix.R: coercion pMatrix -> Tsparse
271    
272    2006-06-12  Douglas Bates  <bates@R-project.org>
273    
274            * DESCRIPTION (Version): 0.995-11 released to CRAN
275    
276            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
277            the output from mcmcsamp.
278    
279    2006-06-10  Douglas Bates  <bates@R-project.org>
280    
281            * R/lmer.R (simulestimate): added C code for calculating the trace
282            of the hat matrix.
283    
284    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
287            classes.
288            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
289    
290    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/dgTMatrix.R (colSums): etc. All four of
293            colSums(), rowSums(), colMeans(), rowMeans() now should work for
294            all "Matrices".
295    
296    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
297    
298            * R/lmer.R (panel.ci): Add a reference line at zero and a
299            background grid to the qqmath plot of ranef.lmer.
300    
301    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
302    
303            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
304            grouping factors to be specified in the formula as (1|foo/bar).
305    
306    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
307    
308            * R/lmer.R (findbars and others): Change check of is.numeric to
309            !is.language to resolve the bug reported by Jacob Wegelin.
310    
311            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
312            code to evaluate inbreeding coefficients without calculating T,
313            based on code in Sargolzaei and Iwaisaki's paper.
314    
315    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
316    
317            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
318            generic and mer methods for isNested and denomDF. This denomDF was
319            an attempt to emulate that in lme but I don't think that makes
320            sense.  Use the trace of the hat matrix instead.
321    
322    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
325            the C code depending on a slot structure that's no longer valid.
326            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
327    
328    
329    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
330    
331            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
332            of lowerTriMatrix generic and methods to tril (also upper to triu)
333            and added a general band extractor.
334    
335    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * R/pedigree.R (pedigree): Replace sire and dam values outside the
338            allowable range with NAs. Added a corresponding check in the
339            validity check for the pedigree class.
340    
341            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
342            crossprod methods now inherits from symmetricMatrix.
343    
344    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
345    
346            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
347            generics lowerTriMatrix and upperTriMatrix along with methods for
348            the Csparse virtual class.  Also added a C function Csparse_band
349            that implements these methods by calling cholmod_band.
350    
351    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
354            erased when it was NULL.  This led to invalid subselections!
355    
356    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
357    
358            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
359            in method for "t" so as not to lose the unit diagonal property.
360    
361    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
362    
363            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
364            and methods.  This is now an option to the ranef method for the
365            mer class.
366    
367            * src/cs_utils.c: Ensure that the nz component is -1 for a
368            compressed column-oriented matrix.  Minor formatting cleanup.
369    
370            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
371            objects.
372    
373    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
376            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
377    
378    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
379    
380            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
381            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
382    
383            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
384            for the dtCMatrix class.
385    
386    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
389            and methods for it.
390    
391    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
394            arguments, such that M %*% 1:6 now works
395            * Tests/matprod.R: test the above
396    
397    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
398    
399            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
400            the ranef.lmer class.
401    
402            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
403            methods to extract the posterior variances from the bVar slot.
404    
405    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
408            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
409    
410            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
411            * tests/simple: (extended)
412    
413            * R/sparseMatrix.R (isTriangular): now using much improved
414            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
415    
416    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
419            (problem report from Franklin Parlamis).  This should be done
420            generally.
421    
422    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
423    
424            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
425            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
426            update the plot methods.
427    
428    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
429    
430            * R/lmer.R (resid and ranef methods):  Added methods for the
431            "residuals" and "resid" generic but only for linear mixed model
432            fits.  Changed the ranef method to return a list of data frames so
433            that the plot methods now work.
434    
435    2006-03-16  Douglas Bates  <bates@bates2>
436    
437            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
438            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
439    
440            * DESCRIPTION (Date): New release
441    
442    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
445    
446            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
447            * man/KNex.Rd: and other help files
448            * tests/*.R: several ones needed adaption
449            * inst/doc/Comparisons.Rnw: ditto
450    
451    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
454    
455            * tests/indexing.R: tests for new [<- methods for sparse matrices.
456    
457    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
460    
461            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
462    
463    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * R/dMatrix.R: enable things like  M [ M < 10 ]
466            * R/dgeMatrix.R: implement it
467    
468    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * R/AllClass.R: define "summary.mer" and "*.lmer"
471            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
472            * R/lmer.R (show): now works with summary()
473    
474    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
477            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
478                    support the above
479    
480    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
481    
482            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
483            Use glmFit$prior.weights for weights in a glmm.
484            Allow an option usePQL = FALSE to skip the PQL steps for the
485            Laplace method (and, in time, the AGQ method).
486    
487            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
488            into a separate function internal_mer_Xfactor to be able to call
489            it from internal_bhat.
490    
491    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * tests/Class+Meth.R (tstMatrixClass): function for much better
494            testing; now again of all actual classes.
495    
496            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
497                    use macros and define make_d_matrix_* and make_i_matrix_*
498                    where _i_ is for the ldense routines:
499    
500            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
501            * src/ldense.c (lsyMatrix_as_lgeMatrix):
502    
503            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
504    
505    
506    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
509                    many different kinds of matrices.
510            * R/*.R: quite a few new methods were needed for R CMD check with
511                    new Matrix().  Very good for users playing around.
512    
513    
514    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * src/dgeMatrix.c (dMatrix_validate): new
517            * src/Mutils.c (dense_nonpacked_validate): new
518    
519            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
520    
521    
522    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
523    
524            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
525    
526    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
527    
528            * DESCRIPTION (Version): 0.99-6 released to CRAN
529    
530            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
531            segfault in cases with multiple non-nested grouping factors.
532    
533    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
536                    (Depends): also on 'utils'
537    
538            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
539            * R/diagMatrix.R (Diagonal): constructor and methods for
540            diagonal matrices
541    
542            * R/ltTMatrix.R: new "minimal methods"
543    
544    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
547            all methods (and help files).
548    
549    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
550    
551            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
552                    for case (dimn.  op  no_dimn.)
553    
554    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
555    
556            * DESCRIPTION (Version): 0.99-2  released to CRAN
557    
558    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
559    
560            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
561            by Julian Faraway.
562    
563    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/Auxiliaries.R (try_as): new utility
566            * R/sparseMatrix.R: use try_as() in coercion to original class
567    
568    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
571    
572    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/Auxiliaries.R (dimNamesCheck): added
575    
576            * R/Matrix.R (as.array), (as.vector): new
577    
578    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
581                    default.
582            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
583                    "pMatrix" now contains "sparseMatrix"
584    
585    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * tests/Class+Meth.R: new tests; t(t(m)) == m
588    
589            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
590    
591            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
592            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
593    
594            * R/dspMatrix.R: typo in "t" method
595    
596    2005-09-18  Douglas Bates  <bates@wisc.edu>
597    
598            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
599            * R/Tsparse.R: instead of R/gTMatrix.R
600            * R/Csparse.R: new
601            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
602            * src/Tsparse.c: new; many trivial methods calling cholmod_()
603            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
604                            via cholmod
605    
606    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/Auxiliaries.R (non0ind): new function using new C code
609            * src/dgCMatrix.c (compressed_non_0_ij): new utility
610    
611    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
612    
613            * src/chm_common.h: header file required by all C sources that
614            call CHOLMOD functions.  It defines a cholmod_common structure
615            called 'c' whose address is passed as the last argument to
616            (virtually) every CHOLMOD function.
617    
618            * src/Pattern.c: Simple example of the use of CHOLMOD.
619    
620            * src/init.c: initialize and finalize the cholmod_common structure.
621    
622            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
623            LDL and CCOLAMD from the U. of Florida sparse matrix library.
624    
625    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * inst/test-tools.R: new file collecting the utility functions used
628                    in ./tests/*.R
629    
630            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
631            * R/Matrix.R (cbind2): methods for NULL and missing
632    
633    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/AllClass.R: new "index" class for "[" and "[<-":
636                    First cut at "symmetricMatrix" and "triangularMatrix"
637            * R/gTMatrix.R (.ind.prep): new function;
638                    Logical and character indexing now work too.
639            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
640            * tests/indexing.R: new, including *.Rout.save
641            * tests/dgTMatrix.R: new
642    
643    2005-08-29  Douglas Bates  <bates@wisc.edu>
644    
645            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
646            indicator pos not being updated.  Also enforced upper triangular
647            for symmetric case.  Need to coerce edges component of elements of
648            edge list - grr! (Why don't they define their classes cleanly?)
649    
650    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/Matrix.R:  added first "[<-" methods; not yet functional
653            * R/denseMatrix.R: ditto
654            * man/Subassign-methods.Rd: new help file for these
655    
656    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * DESCRIPTION (Version): 0.98-6
659    
660            * R/denseMatrix.R: new file for "[" fallback methods for all dense
661            matrices.
662    
663    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
666                    as( <logical>, "matrix")
667    
668            * R/pMatrix.R: coercion to "lgTMatrix"
669    
670            * R/gTMatrix.R: new virtual class to define "[" methods for.
671            * man/gTMatrix-class.Rd:
672            * General slight re-organization of where "[" methods are defined.
673              more to come.
674    
675    2005-08-18  Douglas Bates  <bates@wisc.edu>
676    
677            * DESCRIPTION (Version): 0.98-5  released to CRAN
678    
679            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
680            * .....
681    
682    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
683    
684            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
685            or glmer objects.
686    
687    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
690    
691    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
692    
693            * R/HBMM.R: finish re-writing R-only code.
694    
695    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
696    
697            * man/externalFormats.Rd: move documentation for writeHB and
698            writeMM here.
699    
700            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
701            (suggested by Paul Roecker).
702    
703            * tests/validObj.R (assertError): Comment out test that is failing
704            after recent changes in r-devel.
705    
706    
707    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * R/AllClass.R: intermediate virtual class "denseMatrix"
710            * man/denseMatrix-class.Rd
711            * NAMESPACE: export it, and also export
712            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
713    
714    2005-08-10  Douglas Bates  <bates@wisc.edu>
715    
716            * DESCRIPTION (Version): 0.98-3 to CRAN
717    
718            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
719            matrix_solve code (which was really, really wrong).
720    
721    2005-08-07  Douglas Bates  <bates@wisc.edu>
722    
723            * DESCRIPTION (Version): 0.98-2
724    
725            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
726    
727            * R/lmer.R (abbrvNms): new
728            * R/lmer.R (mcmcsamp): allow transformed parameters
729            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
730            for the Harwell-Boeing and the MatrixMarket formats.
731    
732    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * man/dtrMatrix-class.Rd: add examples
735            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
736    
737            * TODO: note the dtpMatrix (docu) bug
738    
739            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
740            in order to ensure that new as.matrix() is used by old functions,
741            e.g., svd(), qr(), eigen(), dist(),..;
742                  apply(), also matplot() or pairs().
743    
744    
745    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
748              add comments about 'control' / lmerControl() arguments
749    
750    2005-07-27  Douglas Bates  <bates@wisc.edu>
751    
752            * man/sleepstudy.Rd: Added the sleep data set.
753            * DESCRIPTION (Version): 0.98-1  released to CRAN
754    
755    2005-07-12  Douglas Bates  <bates@wisc.edu>
756            * man/sleepstudy.Rd: Added the sleep data set.
757    
758            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
759            .Call calls that were producing spurious output.
760    
761    2005-07-05  Douglas Bates  <bates@wisc.edu>
762    
763            * R/lmer.R (lmer): stored updated variance component estimates in
764            mer object for the generalized model.  (Bug reported by Renaud
765            Lancelot).
766    
767    2005-07-03  Douglas Bates  <bates@wisc.edu>
768    
769            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
770            unidimensional case.
771    
772    2005-06-08  Douglas Bates  <bates@wisc.edu>
773    
774            * DESCRIPTION (Version): 0.96-1
775    
776            * moved  lmer-class' R and C code moved from lme4 to here
777    
778    2005-06-04  Douglas Bates  <bates@wisc.edu>
779    
780            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
781            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
782    
783    2005-06-02  Douglas Bates  <bates@wisc.edu>
784    
785            * src/Makefile.win: Forgot to update this when Makefile changed.
786    
787    2005-05-11  Douglas Bates  <bates@wisc.edu>
788    
789          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
790          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
791    
792  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
793    
794          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
795          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 798 
798          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
799          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
800    
801  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
802    
803          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
804          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
805    
806  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
807    
808          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
809          multiplication operation.          multiplication operation.
# Line 30  Line 816 
816    
817          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
818    
819  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
820    
821          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
822    
823          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
824    
825    
826  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
827    
828          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
829    
# Line 46  Line 832 
832          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
833          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
834    
835  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
836    
837          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
838    
# Line 72  Line 858 
858          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
859            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
860    
861  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
862    
863          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
864          * ....          * ....
865    
866  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
867    
868          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
869    
# Line 92  Line 878 
878            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
879          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
880    
881  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
882    
883          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
884    
885  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
886    
887          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
888    
889  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
890    
891          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
892          the package.          the package.
# Line 148  Line 934 
934    
935          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
936    
937  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
938    
939          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
940          for the geMatrix class.          for the geMatrix class.
941    
942  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
943    
944          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
945    
946          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
947    
948  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
949    
950          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
951          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
952    
953  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
954    
955          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
956    
957  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
958    
959          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
960          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
961    
962  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
963    
964          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
965    
966          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
967          for tripletMatrix to matrix.          for tripletMatrix to matrix.
968    
969  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
970    
971          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
972          no longer used.          no longer used.
# Line 192  Line 978 
978          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
979          Fixes part but not all of #15.          Fixes part but not all of #15.
980    
981  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
982    
983          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
984          scalar grouping factors corrected.          scalar grouping factors corrected.
985    
986  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
987    
988          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
989    
990  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
991    
992          * 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
993          .h file can be included.          .h file can be included.
994    
995  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
996    
997          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
998          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
999    
1000          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1001    
1002  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1003    
1004          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1005    
1006  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1007    
1008          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1009    
1010  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1011    
1012          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1013    
1014  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1015    
1016          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1017    
1018  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1019    
1020          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1021          routines.          routines.
1022    
1023  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1024    
1025          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1026    
1027  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1028    
1029          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1030    

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