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revision 645, Tue Mar 15 00:51:42 2005 UTC revision 1405, Mon Aug 21 14:43:00 2006 UTC
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1  2005-03-14  Douglas Bates  <bates@bates1-home>  2006-08-21  Douglas Bates  <bates@R-project.org>
2    
3            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
4            valgrind.
5    
6    2006-08-20  Douglas Bates  <bates@R-project.org>
7    
8            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
9            * tests/sparseQR.R: Added
10            * man/sparseQR-class.Rd: Document methods for qr.* generics
11            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
12    
13    2006-08-19  Douglas Bates  <bates@R-project.org>
14    
15            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
16            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
17            and qr.fitted.
18            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
19            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
20    
21    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
24            the base version has no "..." argument.
25    
26            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
27    
28            * R/Matrix.R: define and
29            * NAMESPACE: export as.numeric() and as.logical() methods.
30                    Let's hope these do not badly slow down something...
31            Finally export the zapsmall() method.
32    
33    2006-08-17  Douglas Bates  <bates@R-project.org>
34    
35            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
36            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
37            * src/dtCMatrix.c :Remove code that is no longer used
38            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
39    
40    2006-08-14  Douglas Bates  <bates@R-project.org>
41    
42            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
43            Csparse_to_logical and Csparse_symmetric_to_general.
44            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
45            coercion methods between CsparseMatrix and TsparseMatrix.
46    
47    2006-08-14  Douglas Bates  <bates@R-project.org>
48    
49            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
50            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
51            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
52            possible.
53    
54    2006-08-12  Douglas Bates  <bates@R-project.org>
55    
56            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
57              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
58              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
59              generalize conversions between TsparseMatrix, CsparseMatrix,
60              denseMatrix and matrix.  Preserve triangularity property and
61              propagate Dimnames in the easy cases.
62    
63    2006-08-10  Douglas Bates  <bates@R-project.org>
64    
65            * src/lmer.c: adjust checks in glmer_init for S4SXP
66            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
67            before S4SXP but for the wrong reasons.
68    
69    2006-08-08  Douglas Bates  <bates@R-project.org>
70    
71            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
72            Later modified to return the upper triangle only.
73            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
74    
75    2006-08-07  Douglas Bates  <bates@R-project.org>
76    
77            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
78            R-level conversion to a sparse symmetric class.
79            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
80            Remove conversion to sparse symmetric classes (now done in C code).
81    
82    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
85            * man/band.Rd:  adapt the \dontshow{} unit test.
86    
87    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * DESCRIPTION (Version): 0.995-14  for CRAN
90    
91            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
92    
93            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
94            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
95    
96            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
97            * R/Tsparse.R (tril, triu, band): methods
98            * R/dgRMatrix.R (tril, ...):    ditto
99            * man/band.Rd:                  ditto
100    
101    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Matrix.R (head, tail): directly use utils:::head.matrix
104                    to be up-to-date automatically.
105    
106    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
109    
110            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
111            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
112            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
113            such that the S4 objects are always created by the current version
114            of R and 'Matrix' class definitions.
115    
116    2006-08-01  Douglas Bates  <bates@R-project.org>
117    
118            * R/lmer.R (LMEoptimize method), tests/lmer.R,
119            inst/external/test3comp.rda: Added warnings for convergence on
120            boundary and test cases.
121    
122            * src/lmer.c (mer_postVar): Modified to return the variances that
123            are marginal to the fixed effects, not conditional on them (which
124            is what the bVar slot contents represent).
125    
126    2006-07-31  Douglas Bates  <bates@R-project.org>
127    
128            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
129            function which calls the C function mer_hat_trace2.
130    
131            * man/ranef.Rd: Include description of "postVar" argument and
132            producing a caterpillar plot.
133    
134    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * NAMESPACE:    change  "correlation" to "corMatrix"
137            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
138            * R/dpoMatrix.R: ditto
139            * R/lmer.R:      ditto
140    
141    2006-07-28  Douglas Bates  <bates@R-project.org>
142    
143            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
144            RZXinv slot's contents into a separate internal function that can
145            be used in mer_hat_trace.
146    
147    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
150            via new smart
151            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
152            utility functions.
153    
154    
155    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/Csparse.R (tril, triu, band): do return *triangular* classed
158            matrices when appropriate; band() even symmetric ones.
159            (replCmat): extend to potentially all "CsparseMatrix"
160            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
161            allow subassignment for special sparse matrices.
162    
163            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
164    
165            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
166            argument; in glmer_*(): print only if(verbose).
167    
168            speed-optimize a few places by moving REAL(.) out of loops.
169    
170            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
171    
172    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
175                    since that wrongly triggers also for M[ logi , ]
176    
177            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
178            a symmetric matrix that results in a non-symmetric one.
179            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
180    
181            * R/dMatrix.R: make round(M) work as round(M, 0)
182    
183            * R/dgTMatrix.R (image): coordinate system and axis now use
184            1-based indices, not 0-based ones.
185    
186            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
187            * tests/indexing.R: test it.
188    
189            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
190            * man/isSymmetric-methods.Rd: and document it.
191    
192            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
193            * man/SparseM-conv.Rd: docu them
194    
195            * tests/other-pkgs.R: renamed from tests/graph.R and add example
196                    for 'SparseM' conversions
197    
198    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
199    
200            * R/Matrix.R (head): added head() and tail() methods.
201    
202    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * DESCRIPTION (Version): 0.995-12 released to CRAN
205    
206    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * tests/simple.R: add check for correct dsT -> dgT coercion;
209                    add check for correct printing of symmetric sparse matrices.
210    
211            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
212            for sparse symmetric matrices.
213    
214            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
215            diagonal twice.
216    
217    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
218    
219            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
220            being applied to the x slot (detected by Brian Ripley).
221    
222    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
225    
226            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
227    
228    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * src/lgCMatrix.c (lgCMatrix_diag): new function
231            * R/lgCMatrix.R (diag): for new method
232    
233            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
234                 ==> construction of illegal "*gTMatrix" via new() should
235                 now be much less easy:
236            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
237    
238            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
239                    directly.
240            * man/Matrix.Rd: documents it.
241    
242    2006-07-06  Douglas Bates  <bates@R-project.org>
243    
244            * src/pedigree.c (pedigree_inbreeding): Correction in
245            initialization.  This function is not currently being used and is
246            not fully tested.
247    
248            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
249            Introduced the glmer class.  Added code for mcmcmsamp on glmer
250            objects.  Modified validity check on pedigree objects to account
251            for nonparallel patterns of missingness of parents.
252    
253            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
254            class.
255    
256    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/pMatrix.R: coercion pMatrix -> Tsparse
259    
260    2006-06-12  Douglas Bates  <bates@R-project.org>
261    
262            * DESCRIPTION (Version): 0.995-11 released to CRAN
263    
264            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
265            the output from mcmcsamp.
266    
267    2006-06-10  Douglas Bates  <bates@R-project.org>
268    
269            * R/lmer.R (simulestimate): added C code for calculating the trace
270            of the hat matrix.
271    
272    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
275            classes.
276            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
277    
278    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/dgTMatrix.R (colSums): etc. All four of
281            colSums(), rowSums(), colMeans(), rowMeans() now should work for
282            all "Matrices".
283    
284    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * R/lmer.R (panel.ci): Add a reference line at zero and a
287            background grid to the qqmath plot of ranef.lmer.
288    
289    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
290    
291            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
292            grouping factors to be specified in the formula as (1|foo/bar).
293    
294    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
295    
296            * R/lmer.R (findbars and others): Change check of is.numeric to
297            !is.language to resolve the bug reported by Jacob Wegelin.
298    
299            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
300            code to evaluate inbreeding coefficients without calculating T,
301            based on code in Sargolzaei and Iwaisaki's paper.
302    
303    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
304    
305            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
306            generic and mer methods for isNested and denomDF. This denomDF was
307            an attempt to emulate that in lme but I don't think that makes
308            sense.  Use the trace of the hat matrix instead.
309    
310    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
313            the C code depending on a slot structure that's no longer valid.
314            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
315    
316    
317    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
318    
319            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
320            of lowerTriMatrix generic and methods to tril (also upper to triu)
321            and added a general band extractor.
322    
323    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * R/pedigree.R (pedigree): Replace sire and dam values outside the
326            allowable range with NAs. Added a corresponding check in the
327            validity check for the pedigree class.
328    
329            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
330            crossprod methods now inherits from symmetricMatrix.
331    
332    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
333    
334            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
335            generics lowerTriMatrix and upperTriMatrix along with methods for
336            the Csparse virtual class.  Also added a C function Csparse_band
337            that implements these methods by calling cholmod_band.
338    
339    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
342            erased when it was NULL.  This led to invalid subselections!
343    
344    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
345    
346            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
347            in method for "t" so as not to lose the unit diagonal property.
348    
349    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
350    
351            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
352            and methods.  This is now an option to the ranef method for the
353            mer class.
354    
355            * src/cs_utils.c: Ensure that the nz component is -1 for a
356            compressed column-oriented matrix.  Minor formatting cleanup.
357    
358            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
359            objects.
360    
361    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
364            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
365    
366    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
367    
368            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
369            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
370    
371            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
372            for the dtCMatrix class.
373    
374    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
375    
376            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
377            and methods for it.
378    
379    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
382            arguments, such that M %*% 1:6 now works
383            * Tests/matprod.R: test the above
384    
385    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
386    
387            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
388            the ranef.lmer class.
389    
390            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
391            methods to extract the posterior variances from the bVar slot.
392    
393    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
396            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
397    
398            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
399            * tests/simple: (extended)
400    
401            * R/sparseMatrix.R (isTriangular): now using much improved
402            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
403    
404    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
405    
406            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
407            (problem report from Franklin Parlamis).  This should be done
408            generally.
409    
410    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
411    
412            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
413            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
414            update the plot methods.
415    
416    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * R/lmer.R (resid and ranef methods):  Added methods for the
419            "residuals" and "resid" generic but only for linear mixed model
420            fits.  Changed the ranef method to return a list of data frames so
421            that the plot methods now work.
422    
423    2006-03-16  Douglas Bates  <bates@bates2>
424    
425            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
426            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
427    
428            * DESCRIPTION (Date): New release
429    
430    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
433    
434            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
435            * man/KNex.Rd: and other help files
436            * tests/*.R: several ones needed adaption
437            * inst/doc/Comparisons.Rnw: ditto
438    
439    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
442    
443            * tests/indexing.R: tests for new [<- methods for sparse matrices.
444    
445    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
448    
449            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
450    
451    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/dMatrix.R: enable things like  M [ M < 10 ]
454            * R/dgeMatrix.R: implement it
455    
456    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/AllClass.R: define "summary.mer" and "*.lmer"
459            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
460            * R/lmer.R (show): now works with summary()
461    
462    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
465            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
466                    support the above
467    
468    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
469    
470            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
471            Use glmFit$prior.weights for weights in a glmm.
472            Allow an option usePQL = FALSE to skip the PQL steps for the
473            Laplace method (and, in time, the AGQ method).
474    
475            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
476            into a separate function internal_mer_Xfactor to be able to call
477            it from internal_bhat.
478    
479    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * tests/Class+Meth.R (tstMatrixClass): function for much better
482            testing; now again of all actual classes.
483    
484            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
485                    use macros and define make_d_matrix_* and make_i_matrix_*
486                    where _i_ is for the ldense routines:
487    
488            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
489            * src/ldense.c (lsyMatrix_as_lgeMatrix):
490    
491            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
492    
493    
494    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
497                    many different kinds of matrices.
498            * R/*.R: quite a few new methods were needed for R CMD check with
499                    new Matrix().  Very good for users playing around.
500    
501    
502    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * src/dgeMatrix.c (dMatrix_validate): new
505            * src/Mutils.c (dense_nonpacked_validate): new
506    
507            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
508    
509    
510    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
511    
512            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
513    
514    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
515    
516            * DESCRIPTION (Version): 0.99-6 released to CRAN
517    
518            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
519            segfault in cases with multiple non-nested grouping factors.
520    
521    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
524                    (Depends): also on 'utils'
525    
526            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
527            * R/diagMatrix.R (Diagonal): constructor and methods for
528            diagonal matrices
529    
530            * R/ltTMatrix.R: new "minimal methods"
531    
532    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
535            all methods (and help files).
536    
537    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
540                    for case (dimn.  op  no_dimn.)
541    
542    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
543    
544            * DESCRIPTION (Version): 0.99-2  released to CRAN
545    
546    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
547    
548            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
549            by Julian Faraway.
550    
551    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/Auxiliaries.R (try_as): new utility
554            * R/sparseMatrix.R: use try_as() in coercion to original class
555    
556    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
559    
560    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/Auxiliaries.R (dimNamesCheck): added
563    
564            * R/Matrix.R (as.array), (as.vector): new
565    
566    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
569                    default.
570            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
571                    "pMatrix" now contains "sparseMatrix"
572    
573    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * tests/Class+Meth.R: new tests; t(t(m)) == m
576    
577            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
578    
579            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
580            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
581    
582            * R/dspMatrix.R: typo in "t" method
583    
584    2005-09-18  Douglas Bates  <bates@wisc.edu>
585    
586            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
587            * R/Tsparse.R: instead of R/gTMatrix.R
588            * R/Csparse.R: new
589            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
590            * src/Tsparse.c: new; many trivial methods calling cholmod_()
591            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
592                            via cholmod
593    
594    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/Auxiliaries.R (non0ind): new function using new C code
597            * src/dgCMatrix.c (compressed_non_0_ij): new utility
598    
599    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
600    
601            * src/chm_common.h: header file required by all C sources that
602            call CHOLMOD functions.  It defines a cholmod_common structure
603            called 'c' whose address is passed as the last argument to
604            (virtually) every CHOLMOD function.
605    
606            * src/Pattern.c: Simple example of the use of CHOLMOD.
607    
608            * src/init.c: initialize and finalize the cholmod_common structure.
609    
610            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
611            LDL and CCOLAMD from the U. of Florida sparse matrix library.
612    
613    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * inst/test-tools.R: new file collecting the utility functions used
616                    in ./tests/*.R
617    
618            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
619            * R/Matrix.R (cbind2): methods for NULL and missing
620    
621    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
622    
623            * R/AllClass.R: new "index" class for "[" and "[<-":
624                    First cut at "symmetricMatrix" and "triangularMatrix"
625            * R/gTMatrix.R (.ind.prep): new function;
626                    Logical and character indexing now work too.
627            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
628            * tests/indexing.R: new, including *.Rout.save
629            * tests/dgTMatrix.R: new
630    
631    2005-08-29  Douglas Bates  <bates@wisc.edu>
632    
633            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
634            indicator pos not being updated.  Also enforced upper triangular
635            for symmetric case.  Need to coerce edges component of elements of
636            edge list - grr! (Why don't they define their classes cleanly?)
637    
638    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640            * R/Matrix.R:  added first "[<-" methods; not yet functional
641            * R/denseMatrix.R: ditto
642            * man/Subassign-methods.Rd: new help file for these
643    
644    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * DESCRIPTION (Version): 0.98-6
647    
648            * R/denseMatrix.R: new file for "[" fallback methods for all dense
649            matrices.
650    
651    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
654                    as( <logical>, "matrix")
655    
656            * R/pMatrix.R: coercion to "lgTMatrix"
657    
658            * R/gTMatrix.R: new virtual class to define "[" methods for.
659            * man/gTMatrix-class.Rd:
660            * General slight re-organization of where "[" methods are defined.
661              more to come.
662    
663    2005-08-18  Douglas Bates  <bates@wisc.edu>
664    
665            * DESCRIPTION (Version): 0.98-5  released to CRAN
666    
667            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
668            * .....
669    
670    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
671    
672            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
673            or glmer objects.
674    
675    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
678    
679    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
680    
681            * R/HBMM.R: finish re-writing R-only code.
682    
683    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
684    
685            * man/externalFormats.Rd: move documentation for writeHB and
686            writeMM here.
687    
688            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
689            (suggested by Paul Roecker).
690    
691            * tests/validObj.R (assertError): Comment out test that is failing
692            after recent changes in r-devel.
693    
694    
695    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/AllClass.R: intermediate virtual class "denseMatrix"
698            * man/denseMatrix-class.Rd
699            * NAMESPACE: export it, and also export
700            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
701    
702    2005-08-10  Douglas Bates  <bates@wisc.edu>
703    
704            * DESCRIPTION (Version): 0.98-3 to CRAN
705    
706            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
707            matrix_solve code (which was really, really wrong).
708    
709    2005-08-07  Douglas Bates  <bates@wisc.edu>
710    
711            * DESCRIPTION (Version): 0.98-2
712    
713            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
714    
715            * R/lmer.R (abbrvNms): new
716            * R/lmer.R (mcmcsamp): allow transformed parameters
717            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
718            for the Harwell-Boeing and the MatrixMarket formats.
719    
720    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * man/dtrMatrix-class.Rd: add examples
723            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
724    
725            * TODO: note the dtpMatrix (docu) bug
726    
727            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
728            in order to ensure that new as.matrix() is used by old functions,
729            e.g., svd(), qr(), eigen(), dist(),..;
730                  apply(), also matplot() or pairs().
731    
732    
733    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
736              add comments about 'control' / lmerControl() arguments
737    
738    2005-07-27  Douglas Bates  <bates@wisc.edu>
739    
740            * man/sleepstudy.Rd: Added the sleep data set.
741            * DESCRIPTION (Version): 0.98-1  released to CRAN
742    
743    2005-07-12  Douglas Bates  <bates@wisc.edu>
744            * man/sleepstudy.Rd: Added the sleep data set.
745    
746            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
747            .Call calls that were producing spurious output.
748    
749    2005-07-05  Douglas Bates  <bates@wisc.edu>
750    
751            * R/lmer.R (lmer): stored updated variance component estimates in
752            mer object for the generalized model.  (Bug reported by Renaud
753            Lancelot).
754    
755    2005-07-03  Douglas Bates  <bates@wisc.edu>
756    
757            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
758            unidimensional case.
759    
760    2005-06-08  Douglas Bates  <bates@wisc.edu>
761    
762            * DESCRIPTION (Version): 0.96-1
763    
764            * moved  lmer-class' R and C code moved from lme4 to here
765    
766    2005-06-04  Douglas Bates  <bates@wisc.edu>
767    
768            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
769            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
770    
771    2005-06-02  Douglas Bates  <bates@wisc.edu>
772    
773            * src/Makefile.win: Forgot to update this when Makefile changed.
774    
775    2005-05-11  Douglas Bates  <bates@wisc.edu>
776    
777            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
778            bug reported by Kurt Hornik and Michael Hahsler.
779    
780    2005-05-10  Douglas Bates  <bates@wisc.edu>
781    
782            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
783            logical sparse matrices.  These will also be used in the symbolic
784            analysis for lmer objects.
785    
786            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
787            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
788    
789    2005-05-06  Douglas Bates  <bates@wisc.edu>
790    
791            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
792            colMeans, colSums, rowMeans and rowSums.
793    
794    2005-04-18  Douglas Bates  <bates@wisc.edu>
795    
796            * src/lgCMatrix.[ch]: code for _validate method and stub for
797            multiplication operation.
798    
799            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
800            to dgetrs.
801    
802            * src/init.c: Fix cut-and-paste error in definition of
803            dgeMatrix_matrix_solve
804    
805            * src/{many files}: Tighten code by using ALLOC_SLOT.
806    
807    2005-04-15  Douglas Bates  <bates@wisc.edu>
808    
809            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
810    
811            * DESCRIPTION: Eliminate import of stats.
812    
813    
814    2005-04-06  Douglas Bates  <bates@wisc.edu>
815    
816            * R/AllClass.R : add logical sparse matrix classes
817    
818    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * R/dgTMatrix.R: add "[" method for triplet matrices
821            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
822    
823    2005-03-31  Douglas Bates  <bates@wisc.edu>
824    
825            * DESCRIPTION (Version): release 0.95-5 to CRAN
826    
827            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
828            * R/sparseMatrix.R: %*%, crossprod()
829            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
830            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
831            * src/lmer.c (lmer_fitted): fix thinko
832    
833    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * R/AllClass.R: add two virtual sparse classes ``on top''
836    
837    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
838    
839            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
840                    correspondingly fix examples and tests/ since new()
841                    doesn't work for virtual classes.
842    
843    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * R/Matrix.R (as.matrix): method and one for unname()
846            * tests/dpoMatrix.R: tests should now be less platform dependent;
847              also run for R 2.1.0; using as.matrix()
848    
849    2005-03-15  Douglas Bates  <bates@wisc.edu>
850    
851            * R/pMatrix.R: "pMatrix" class added
852            * ....
853    
854    2005-03-14  Douglas Bates  <bates@wisc.edu>
855    
856          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
857    
858          * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization          * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
859          of general symmetric matrices and associated S4 methods.          of general symmetric matrices and associated S4 methods.
860    
861  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
862            +
863    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * R/dgeMatrix.R (setAs): and many other files: more coercion,
866              crossprod() and "%*%" methods added; tests, too.
867            * tests/matprod.R: new, for testing these
868    
869    2005-03-03  Douglas Bates  <bates@wisc.edu>
870    
871          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
872    
873  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
874    
875          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
876    
877  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
878    
879          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
880          the package.          the package.
# Line 61  Line 922 
922    
923          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
924    
925  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
926    
927          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
928          for the geMatrix class.          for the geMatrix class.
929    
930  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
931    
932          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
933    
934          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
935    
936  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
937    
938          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
939          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
940    
941  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
942    
943          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
944    
945  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
946    
947          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
948          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
949    
950  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
951    
952          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
953    
954          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
955          for tripletMatrix to matrix.          for tripletMatrix to matrix.
956    
957  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
958    
959          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
960          no longer used.          no longer used.
# Line 105  Line 966 
966          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
967          Fixes part but not all of #15.          Fixes part but not all of #15.
968    
969  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
970    
971          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
972          scalar grouping factors corrected.          scalar grouping factors corrected.
973    
974  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
975    
976          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
977    
978  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
979    
980          * 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
981          .h file can be included.          .h file can be included.
982    
983  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
984    
985          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
986          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
987    
988          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
989    
990  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
991    
992          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
993    
994  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
995    
996          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
997    
998  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
999    
1000          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1001    
1002  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1003    
1004          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1005    
1006  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1007    
1008          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1009          routines.          routines.
1010    
1011  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1012    
1013          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1014    
1015  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1016    
1017          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1018    

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