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revision 726, Thu May 12 14:59:04 2005 UTC revision 1403, Sun Aug 20 16:15:59 2006 UTC
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1  2005-05-11  Douglas Bates  <bates@bates1-home>  2006-08-20  Douglas Bates  <bates@R-project.org>
2    
3            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
4            * tests/sparseQR.R: Added
5            * man/sparseQR-class.Rd: Document methods for qr.* generics
6            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
7    
8    2006-08-19  Douglas Bates  <bates@R-project.org>
9    
10            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
11            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
12            and qr.fitted.
13            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
14            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
15    
16    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
19            the base version has no "..." argument.
20    
21            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
22    
23            * R/Matrix.R: define and
24            * NAMESPACE: export as.numeric() and as.logical() methods.
25                    Let's hope these do not badly slow down something...
26            Finally export the zapsmall() method.
27    
28    2006-08-17  Douglas Bates  <bates@R-project.org>
29    
30            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
31            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
32            * src/dtCMatrix.c :Remove code that is no longer used
33            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
34    
35    2006-08-14  Douglas Bates  <bates@R-project.org>
36    
37            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
38            Csparse_to_logical and Csparse_symmetric_to_general.
39            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
40            coercion methods between CsparseMatrix and TsparseMatrix.
41    
42    2006-08-14  Douglas Bates  <bates@R-project.org>
43    
44            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
45            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
46            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
47            possible.
48    
49    2006-08-12  Douglas Bates  <bates@R-project.org>
50    
51            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
52              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
53              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
54              generalize conversions between TsparseMatrix, CsparseMatrix,
55              denseMatrix and matrix.  Preserve triangularity property and
56              propagate Dimnames in the easy cases.
57    
58    2006-08-10  Douglas Bates  <bates@R-project.org>
59    
60            * src/lmer.c: adjust checks in glmer_init for S4SXP
61            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
62            before S4SXP but for the wrong reasons.
63    
64    2006-08-08  Douglas Bates  <bates@R-project.org>
65    
66            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
67            Later modified to return the upper triangle only.
68            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
69    
70    2006-08-07  Douglas Bates  <bates@R-project.org>
71    
72            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
73            R-level conversion to a sparse symmetric class.
74            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
75            Remove conversion to sparse symmetric classes (now done in C code).
76    
77    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
80            * man/band.Rd:  adapt the \dontshow{} unit test.
81    
82    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * DESCRIPTION (Version): 0.995-14  for CRAN
85    
86            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
87    
88            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
89            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
90    
91            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
92            * R/Tsparse.R (tril, triu, band): methods
93            * R/dgRMatrix.R (tril, ...):    ditto
94            * man/band.Rd:                  ditto
95    
96    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/Matrix.R (head, tail): directly use utils:::head.matrix
99                    to be up-to-date automatically.
100    
101    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
104    
105            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
106            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
107            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
108            such that the S4 objects are always created by the current version
109            of R and 'Matrix' class definitions.
110    
111    2006-08-01  Douglas Bates  <bates@R-project.org>
112    
113            * R/lmer.R (LMEoptimize method), tests/lmer.R,
114            inst/external/test3comp.rda: Added warnings for convergence on
115            boundary and test cases.
116    
117            * src/lmer.c (mer_postVar): Modified to return the variances that
118            are marginal to the fixed effects, not conditional on them (which
119            is what the bVar slot contents represent).
120    
121    2006-07-31  Douglas Bates  <bates@R-project.org>
122    
123            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
124            function which calls the C function mer_hat_trace2.
125    
126            * man/ranef.Rd: Include description of "postVar" argument and
127            producing a caterpillar plot.
128    
129    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * NAMESPACE:    change  "correlation" to "corMatrix"
132            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
133            * R/dpoMatrix.R: ditto
134            * R/lmer.R:      ditto
135    
136    2006-07-28  Douglas Bates  <bates@R-project.org>
137    
138            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
139            RZXinv slot's contents into a separate internal function that can
140            be used in mer_hat_trace.
141    
142    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
145            via new smart
146            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
147            utility functions.
148    
149    
150    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/Csparse.R (tril, triu, band): do return *triangular* classed
153            matrices when appropriate; band() even symmetric ones.
154            (replCmat): extend to potentially all "CsparseMatrix"
155            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
156            allow subassignment for special sparse matrices.
157    
158            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
159    
160            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
161            argument; in glmer_*(): print only if(verbose).
162    
163            speed-optimize a few places by moving REAL(.) out of loops.
164    
165            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
166    
167    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
170                    since that wrongly triggers also for M[ logi , ]
171    
172            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
173            a symmetric matrix that results in a non-symmetric one.
174            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
175    
176            * R/dMatrix.R: make round(M) work as round(M, 0)
177    
178            * R/dgTMatrix.R (image): coordinate system and axis now use
179            1-based indices, not 0-based ones.
180    
181            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
182            * tests/indexing.R: test it.
183    
184            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
185            * man/isSymmetric-methods.Rd: and document it.
186    
187            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
188            * man/SparseM-conv.Rd: docu them
189    
190            * tests/other-pkgs.R: renamed from tests/graph.R and add example
191                    for 'SparseM' conversions
192    
193    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
194    
195            * R/Matrix.R (head): added head() and tail() methods.
196    
197    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Version): 0.995-12 released to CRAN
200    
201    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * tests/simple.R: add check for correct dsT -> dgT coercion;
204                    add check for correct printing of symmetric sparse matrices.
205    
206            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
207            for sparse symmetric matrices.
208    
209            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
210            diagonal twice.
211    
212    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
213    
214            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
215            being applied to the x slot (detected by Brian Ripley).
216    
217    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
220    
221            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
222    
223    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * src/lgCMatrix.c (lgCMatrix_diag): new function
226            * R/lgCMatrix.R (diag): for new method
227    
228            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
229                 ==> construction of illegal "*gTMatrix" via new() should
230                 now be much less easy:
231            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
232    
233            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
234                    directly.
235            * man/Matrix.Rd: documents it.
236    
237    2006-07-06  Douglas Bates  <bates@R-project.org>
238    
239            * src/pedigree.c (pedigree_inbreeding): Correction in
240            initialization.  This function is not currently being used and is
241            not fully tested.
242    
243            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
244            Introduced the glmer class.  Added code for mcmcmsamp on glmer
245            objects.  Modified validity check on pedigree objects to account
246            for nonparallel patterns of missingness of parents.
247    
248            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
249            class.
250    
251    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/pMatrix.R: coercion pMatrix -> Tsparse
254    
255    2006-06-12  Douglas Bates  <bates@R-project.org>
256    
257            * DESCRIPTION (Version): 0.995-11 released to CRAN
258    
259            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
260            the output from mcmcsamp.
261    
262    2006-06-10  Douglas Bates  <bates@R-project.org>
263    
264            * R/lmer.R (simulestimate): added C code for calculating the trace
265            of the hat matrix.
266    
267    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
270            classes.
271            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
272    
273    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/dgTMatrix.R (colSums): etc. All four of
276            colSums(), rowSums(), colMeans(), rowMeans() now should work for
277            all "Matrices".
278    
279    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
280    
281            * R/lmer.R (panel.ci): Add a reference line at zero and a
282            background grid to the qqmath plot of ranef.lmer.
283    
284    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
287            grouping factors to be specified in the formula as (1|foo/bar).
288    
289    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
290    
291            * R/lmer.R (findbars and others): Change check of is.numeric to
292            !is.language to resolve the bug reported by Jacob Wegelin.
293    
294            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
295            code to evaluate inbreeding coefficients without calculating T,
296            based on code in Sargolzaei and Iwaisaki's paper.
297    
298    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
299    
300            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
301            generic and mer methods for isNested and denomDF. This denomDF was
302            an attempt to emulate that in lme but I don't think that makes
303            sense.  Use the trace of the hat matrix instead.
304    
305    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
308            the C code depending on a slot structure that's no longer valid.
309            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
310    
311    
312    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
313    
314            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
315            of lowerTriMatrix generic and methods to tril (also upper to triu)
316            and added a general band extractor.
317    
318    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
319    
320            * R/pedigree.R (pedigree): Replace sire and dam values outside the
321            allowable range with NAs. Added a corresponding check in the
322            validity check for the pedigree class.
323    
324            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
325            crossprod methods now inherits from symmetricMatrix.
326    
327    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
328    
329            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
330            generics lowerTriMatrix and upperTriMatrix along with methods for
331            the Csparse virtual class.  Also added a C function Csparse_band
332            that implements these methods by calling cholmod_band.
333    
334    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
337            erased when it was NULL.  This led to invalid subselections!
338    
339    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
342            in method for "t" so as not to lose the unit diagonal property.
343    
344    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
345    
346            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
347            and methods.  This is now an option to the ranef method for the
348            mer class.
349    
350            * src/cs_utils.c: Ensure that the nz component is -1 for a
351            compressed column-oriented matrix.  Minor formatting cleanup.
352    
353            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
354            objects.
355    
356    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
359            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
360    
361    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
362    
363            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
364            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
365    
366            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
367            for the dtCMatrix class.
368    
369    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
370    
371            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
372            and methods for it.
373    
374    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
377            arguments, such that M %*% 1:6 now works
378            * Tests/matprod.R: test the above
379    
380    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
381    
382            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
383            the ranef.lmer class.
384    
385            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
386            methods to extract the posterior variances from the bVar slot.
387    
388    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
391            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
392    
393            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
394            * tests/simple: (extended)
395    
396            * R/sparseMatrix.R (isTriangular): now using much improved
397            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
398    
399    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
400    
401            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
402            (problem report from Franklin Parlamis).  This should be done
403            generally.
404    
405    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
406    
407            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
408            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
409            update the plot methods.
410    
411    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
412    
413            * R/lmer.R (resid and ranef methods):  Added methods for the
414            "residuals" and "resid" generic but only for linear mixed model
415            fits.  Changed the ranef method to return a list of data frames so
416            that the plot methods now work.
417    
418    2006-03-16  Douglas Bates  <bates@bates2>
419    
420            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
421            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
422    
423            * DESCRIPTION (Date): New release
424    
425    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
428    
429            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
430            * man/KNex.Rd: and other help files
431            * tests/*.R: several ones needed adaption
432            * inst/doc/Comparisons.Rnw: ditto
433    
434    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
437    
438            * tests/indexing.R: tests for new [<- methods for sparse matrices.
439    
440    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
443    
444            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
445    
446    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/dMatrix.R: enable things like  M [ M < 10 ]
449            * R/dgeMatrix.R: implement it
450    
451    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/AllClass.R: define "summary.mer" and "*.lmer"
454            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
455            * R/lmer.R (show): now works with summary()
456    
457    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
460            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
461                    support the above
462    
463    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
464    
465            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
466            Use glmFit$prior.weights for weights in a glmm.
467            Allow an option usePQL = FALSE to skip the PQL steps for the
468            Laplace method (and, in time, the AGQ method).
469    
470            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
471            into a separate function internal_mer_Xfactor to be able to call
472            it from internal_bhat.
473    
474    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * tests/Class+Meth.R (tstMatrixClass): function for much better
477            testing; now again of all actual classes.
478    
479            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
480                    use macros and define make_d_matrix_* and make_i_matrix_*
481                    where _i_ is for the ldense routines:
482    
483            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
484            * src/ldense.c (lsyMatrix_as_lgeMatrix):
485    
486            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
487    
488    
489    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
492                    many different kinds of matrices.
493            * R/*.R: quite a few new methods were needed for R CMD check with
494                    new Matrix().  Very good for users playing around.
495    
496    
497    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * src/dgeMatrix.c (dMatrix_validate): new
500            * src/Mutils.c (dense_nonpacked_validate): new
501    
502            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
503    
504    
505    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
506    
507            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
508    
509    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
510    
511            * DESCRIPTION (Version): 0.99-6 released to CRAN
512    
513            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
514            segfault in cases with multiple non-nested grouping factors.
515    
516    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
519                    (Depends): also on 'utils'
520    
521            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
522            * R/diagMatrix.R (Diagonal): constructor and methods for
523            diagonal matrices
524    
525            * R/ltTMatrix.R: new "minimal methods"
526    
527    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
530            all methods (and help files).
531    
532    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
535                    for case (dimn.  op  no_dimn.)
536    
537    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
538    
539            * DESCRIPTION (Version): 0.99-2  released to CRAN
540    
541    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
542    
543            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
544            by Julian Faraway.
545    
546    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * R/Auxiliaries.R (try_as): new utility
549            * R/sparseMatrix.R: use try_as() in coercion to original class
550    
551    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
554    
555    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/Auxiliaries.R (dimNamesCheck): added
558    
559            * R/Matrix.R (as.array), (as.vector): new
560    
561    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
564                    default.
565            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
566                    "pMatrix" now contains "sparseMatrix"
567    
568    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * tests/Class+Meth.R: new tests; t(t(m)) == m
571    
572            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
573    
574            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
575            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
576    
577            * R/dspMatrix.R: typo in "t" method
578    
579    2005-09-18  Douglas Bates  <bates@wisc.edu>
580    
581            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
582            * R/Tsparse.R: instead of R/gTMatrix.R
583            * R/Csparse.R: new
584            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
585            * src/Tsparse.c: new; many trivial methods calling cholmod_()
586            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
587                            via cholmod
588    
589    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/Auxiliaries.R (non0ind): new function using new C code
592            * src/dgCMatrix.c (compressed_non_0_ij): new utility
593    
594    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
595    
596            * src/chm_common.h: header file required by all C sources that
597            call CHOLMOD functions.  It defines a cholmod_common structure
598            called 'c' whose address is passed as the last argument to
599            (virtually) every CHOLMOD function.
600    
601            * src/Pattern.c: Simple example of the use of CHOLMOD.
602    
603            * src/init.c: initialize and finalize the cholmod_common structure.
604    
605            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
606            LDL and CCOLAMD from the U. of Florida sparse matrix library.
607    
608    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * inst/test-tools.R: new file collecting the utility functions used
611                    in ./tests/*.R
612    
613            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
614            * R/Matrix.R (cbind2): methods for NULL and missing
615    
616    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * R/AllClass.R: new "index" class for "[" and "[<-":
619                    First cut at "symmetricMatrix" and "triangularMatrix"
620            * R/gTMatrix.R (.ind.prep): new function;
621                    Logical and character indexing now work too.
622            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
623            * tests/indexing.R: new, including *.Rout.save
624            * tests/dgTMatrix.R: new
625    
626    2005-08-29  Douglas Bates  <bates@wisc.edu>
627    
628            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
629            indicator pos not being updated.  Also enforced upper triangular
630            for symmetric case.  Need to coerce edges component of elements of
631            edge list - grr! (Why don't they define their classes cleanly?)
632    
633    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/Matrix.R:  added first "[<-" methods; not yet functional
636            * R/denseMatrix.R: ditto
637            * man/Subassign-methods.Rd: new help file for these
638    
639    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * DESCRIPTION (Version): 0.98-6
642    
643            * R/denseMatrix.R: new file for "[" fallback methods for all dense
644            matrices.
645    
646    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
649                    as( <logical>, "matrix")
650    
651            * R/pMatrix.R: coercion to "lgTMatrix"
652    
653            * R/gTMatrix.R: new virtual class to define "[" methods for.
654            * man/gTMatrix-class.Rd:
655            * General slight re-organization of where "[" methods are defined.
656              more to come.
657    
658    2005-08-18  Douglas Bates  <bates@wisc.edu>
659    
660            * DESCRIPTION (Version): 0.98-5  released to CRAN
661    
662            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
663            * .....
664    
665    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
666    
667            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
668            or glmer objects.
669    
670    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
673    
674    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
675    
676            * R/HBMM.R: finish re-writing R-only code.
677    
678    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
679    
680            * man/externalFormats.Rd: move documentation for writeHB and
681            writeMM here.
682    
683            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
684            (suggested by Paul Roecker).
685    
686            * tests/validObj.R (assertError): Comment out test that is failing
687            after recent changes in r-devel.
688    
689    
690    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/AllClass.R: intermediate virtual class "denseMatrix"
693            * man/denseMatrix-class.Rd
694            * NAMESPACE: export it, and also export
695            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
696    
697    2005-08-10  Douglas Bates  <bates@wisc.edu>
698    
699            * DESCRIPTION (Version): 0.98-3 to CRAN
700    
701            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
702            matrix_solve code (which was really, really wrong).
703    
704    2005-08-07  Douglas Bates  <bates@wisc.edu>
705    
706            * DESCRIPTION (Version): 0.98-2
707    
708            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
709    
710            * R/lmer.R (abbrvNms): new
711            * R/lmer.R (mcmcsamp): allow transformed parameters
712            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
713            for the Harwell-Boeing and the MatrixMarket formats.
714    
715    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * man/dtrMatrix-class.Rd: add examples
718            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
719    
720            * TODO: note the dtpMatrix (docu) bug
721    
722            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
723            in order to ensure that new as.matrix() is used by old functions,
724            e.g., svd(), qr(), eigen(), dist(),..;
725                  apply(), also matplot() or pairs().
726    
727    
728    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
729    
730            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
731              add comments about 'control' / lmerControl() arguments
732    
733    2005-07-27  Douglas Bates  <bates@wisc.edu>
734    
735            * man/sleepstudy.Rd: Added the sleep data set.
736            * DESCRIPTION (Version): 0.98-1  released to CRAN
737    
738    2005-07-12  Douglas Bates  <bates@wisc.edu>
739            * man/sleepstudy.Rd: Added the sleep data set.
740    
741            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
742            .Call calls that were producing spurious output.
743    
744    2005-07-05  Douglas Bates  <bates@wisc.edu>
745    
746            * R/lmer.R (lmer): stored updated variance component estimates in
747            mer object for the generalized model.  (Bug reported by Renaud
748            Lancelot).
749    
750    2005-07-03  Douglas Bates  <bates@wisc.edu>
751    
752            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
753            unidimensional case.
754    
755    2005-06-08  Douglas Bates  <bates@wisc.edu>
756    
757            * DESCRIPTION (Version): 0.96-1
758    
759            * moved  lmer-class' R and C code moved from lme4 to here
760    
761    2005-06-04  Douglas Bates  <bates@wisc.edu>
762    
763            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
764            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
765    
766    2005-06-02  Douglas Bates  <bates@wisc.edu>
767    
768            * src/Makefile.win: Forgot to update this when Makefile changed.
769    
770    2005-05-11  Douglas Bates  <bates@wisc.edu>
771    
772          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
773          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
774    
775  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
776    
777          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
778          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 781 
781          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
782          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
783    
784  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
785    
786          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
787          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
788    
789  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
790    
791          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
792          multiplication operation.          multiplication operation.
# Line 30  Line 799 
799    
800          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
801    
802  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
803    
804          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
805    
806          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
807    
808    
809  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
810    
811          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
812    
# Line 46  Line 815 
815          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
816          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
817    
818  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
819    
820          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
821    
# Line 72  Line 841 
841          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
842            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
843    
844  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
845    
846          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
847          * ....          * ....
848    
849  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
850    
851          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
852    
# Line 92  Line 861 
861            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
862          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
863    
864  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
865    
866          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
867    
868  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
869    
870          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
871    
872  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
873    
874          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
875          the package.          the package.
# Line 148  Line 917 
917    
918          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
919    
920  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
921    
922          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
923          for the geMatrix class.          for the geMatrix class.
924    
925  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
926    
927          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
928    
929          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
930    
931  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
932    
933          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
934          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
935    
936  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
937    
938          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
939    
940  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
941    
942          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
943          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
944    
945  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
946    
947          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
948    
949          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
950          for tripletMatrix to matrix.          for tripletMatrix to matrix.
951    
952  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
953    
954          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
955          no longer used.          no longer used.
# Line 192  Line 961 
961          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
962          Fixes part but not all of #15.          Fixes part but not all of #15.
963    
964  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
965    
966          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
967          scalar grouping factors corrected.          scalar grouping factors corrected.
968    
969  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
970    
971          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
972    
973  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
974    
975          * 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
976          .h file can be included.          .h file can be included.
977    
978  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
979    
980          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
981          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
982    
983          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
984    
985  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
986    
987          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
988    
989  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
990    
991          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
992    
993  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
994    
995          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
996    
997  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
998    
999          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1000    
1001  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1002    
1003          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1004          routines.          routines.
1005    
1006  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1007    
1008          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1009    
1010  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1011    
1012          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1013    

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