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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1365, Thu Aug 10 18:52:55 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-08-10  Douglas Bates  <bates@R-project.org>
2    
3            * src/lmer.c: adjust checks in glmer_init for S4SXP
4            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
5            before S4SXP but for the wrong reasons.
6    
7    2006-08-08  Douglas Bates  <bates@R-project.org>
8    
9            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
10            Later modified to return the upper triangle only.
11            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
12    
13    2006-08-07  Douglas Bates  <bates@R-project.org>
14    
15            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
16            R-level conversion to a sparse symmetric class.
17            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
18            Remove conversion to sparse symmetric classes (now done in C code).
19    
20    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
23            * man/band.Rd:  adapt the \dontshow{} unit test.
24    
25    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * DESCRIPTION (Version): 0.995-14  for CRAN
28    
29            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
30    
31            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
32            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
33    
34            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
35            * R/Tsparse.R (tril, triu, band): methods
36            * R/dgRMatrix.R (tril, ...):    ditto
37            * man/band.Rd:                  ditto
38    
39    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Matrix.R (head, tail): directly use utils:::head.matrix
42                    to be up-to-date automatically.
43    
44    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
47    
48            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
49            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
50            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
51            such that the S4 objects are always created by the current version
52            of R and 'Matrix' class definitions.
53    
54    2006-08-01  Douglas Bates  <bates@R-project.org>
55    
56            * R/lmer.R (LMEoptimize method), tests/lmer.R,
57            inst/external/test3comp.rda: Added warnings for convergence on
58            boundary and test cases.
59    
60            * src/lmer.c (mer_postVar): Modified to return the variances that
61            are marginal to the fixed effects, not conditional on them (which
62            is what the bVar slot contents represent).
63    
64    2006-07-31  Douglas Bates  <bates@R-project.org>
65    
66            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
67            function which calls the C function mer_hat_trace2.
68    
69            * man/ranef.Rd: Include description of "postVar" argument and
70            producing a caterpillar plot.
71    
72    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * NAMESPACE:    change  "correlation" to "corMatrix"
75            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
76            * R/dpoMatrix.R: ditto
77            * R/lmer.R:      ditto
78    
79    2006-07-28  Douglas Bates  <bates@R-project.org>
80    
81            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
82            RZXinv slot's contents into a separate internal function that can
83            be used in mer_hat_trace.
84    
85    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
88            via new smart
89            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
90            utility functions.
91    
92    
93    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/Csparse.R (tril, triu, band): do return *triangular* classed
96            matrices when appropriate; band() even symmetric ones.
97            (replCmat): extend to potentially all "CsparseMatrix"
98            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
99            allow subassignment for special sparse matrices.
100    
101            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
102    
103            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
104            argument; in glmer_*(): print only if(verbose).
105    
106            speed-optimize a few places by moving REAL(.) out of loops.
107    
108            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
109    
110    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
113                    since that wrongly triggers also for M[ logi , ]
114    
115            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
116            a symmetric matrix that results in a non-symmetric one.
117            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
118    
119            * R/dMatrix.R: make round(M) work as round(M, 0)
120    
121            * R/dgTMatrix.R (image): coordinate system and axis now use
122            1-based indices, not 0-based ones.
123    
124            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
125            * tests/indexing.R: test it.
126    
127            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
128            * man/isSymmetric-methods.Rd: and document it.
129    
130            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
131            * man/SparseM-conv.Rd: docu them
132    
133            * tests/other-pkgs.R: renamed from tests/graph.R and add example
134                    for 'SparseM' conversions
135    
136    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
137    
138            * R/Matrix.R (head): added head() and tail() methods.
139    
140    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * DESCRIPTION (Version): 0.995-12 released to CRAN
143    
144    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * tests/simple.R: add check for correct dsT -> dgT coercion;
147                    add check for correct printing of symmetric sparse matrices.
148    
149            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
150            for sparse symmetric matrices.
151    
152            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
153            diagonal twice.
154    
155    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
156    
157            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
158            being applied to the x slot (detected by Brian Ripley).
159    
160    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
163    
164            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
165    
166    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/lgCMatrix.c (lgCMatrix_diag): new function
169            * R/lgCMatrix.R (diag): for new method
170    
171            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
172                 ==> construction of illegal "*gTMatrix" via new() should
173                 now be much less easy:
174            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
175    
176            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
177                    directly.
178            * man/Matrix.Rd: documents it.
179    
180    2006-07-06  Douglas Bates  <bates@R-project.org>
181    
182            * src/pedigree.c (pedigree_inbreeding): Correction in
183            initialization.  This function is not currently being used and is
184            not fully tested.
185    
186            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
187            Introduced the glmer class.  Added code for mcmcmsamp on glmer
188            objects.  Modified validity check on pedigree objects to account
189            for nonparallel patterns of missingness of parents.
190    
191            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
192            class.
193    
194    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/pMatrix.R: coercion pMatrix -> Tsparse
197    
198    2006-06-12  Douglas Bates  <bates@R-project.org>
199    
200            * DESCRIPTION (Version): 0.995-11 released to CRAN
201    
202            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
203            the output from mcmcsamp.
204    
205    2006-06-10  Douglas Bates  <bates@R-project.org>
206    
207            * R/lmer.R (simulestimate): added C code for calculating the trace
208            of the hat matrix.
209    
210    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
213            classes.
214            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
215    
216    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/dgTMatrix.R (colSums): etc. All four of
219            colSums(), rowSums(), colMeans(), rowMeans() now should work for
220            all "Matrices".
221    
222    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
223    
224            * R/lmer.R (panel.ci): Add a reference line at zero and a
225            background grid to the qqmath plot of ranef.lmer.
226    
227    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
228    
229            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
230            grouping factors to be specified in the formula as (1|foo/bar).
231    
232    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
233    
234            * R/lmer.R (findbars and others): Change check of is.numeric to
235            !is.language to resolve the bug reported by Jacob Wegelin.
236    
237            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
238            code to evaluate inbreeding coefficients without calculating T,
239            based on code in Sargolzaei and Iwaisaki's paper.
240    
241    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
242    
243            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
244            generic and mer methods for isNested and denomDF. This denomDF was
245            an attempt to emulate that in lme but I don't think that makes
246            sense.  Use the trace of the hat matrix instead.
247    
248    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
251            the C code depending on a slot structure that's no longer valid.
252            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
253    
254    
255    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
256    
257            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
258            of lowerTriMatrix generic and methods to tril (also upper to triu)
259            and added a general band extractor.
260    
261    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
262    
263            * R/pedigree.R (pedigree): Replace sire and dam values outside the
264            allowable range with NAs. Added a corresponding check in the
265            validity check for the pedigree class.
266    
267            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
268            crossprod methods now inherits from symmetricMatrix.
269    
270    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
273            generics lowerTriMatrix and upperTriMatrix along with methods for
274            the Csparse virtual class.  Also added a C function Csparse_band
275            that implements these methods by calling cholmod_band.
276    
277    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
280            erased when it was NULL.  This led to invalid subselections!
281    
282    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
283    
284            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
285            in method for "t" so as not to lose the unit diagonal property.
286    
287    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
288    
289            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
290            and methods.  This is now an option to the ranef method for the
291            mer class.
292    
293            * src/cs_utils.c: Ensure that the nz component is -1 for a
294            compressed column-oriented matrix.  Minor formatting cleanup.
295    
296            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
297            objects.
298    
299    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
302            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
303    
304    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
305    
306            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
307            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
308    
309            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
310            for the dtCMatrix class.
311    
312    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
313    
314            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
315            and methods for it.
316    
317    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
320            arguments, such that M %*% 1:6 now works
321            * Tests/matprod.R: test the above
322    
323    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
326            the ranef.lmer class.
327    
328            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
329            methods to extract the posterior variances from the bVar slot.
330    
331    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
334            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
335    
336            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
337            * tests/simple: (extended)
338    
339            * R/sparseMatrix.R (isTriangular): now using much improved
340            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
341    
342    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
343    
344            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
345            (problem report from Franklin Parlamis).  This should be done
346            generally.
347    
348    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
349    
350            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
351            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
352            update the plot methods.
353    
354    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
355    
356            * R/lmer.R (resid and ranef methods):  Added methods for the
357            "residuals" and "resid" generic but only for linear mixed model
358            fits.  Changed the ranef method to return a list of data frames so
359            that the plot methods now work.
360    
361    2006-03-16  Douglas Bates  <bates@bates2>
362    
363            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
364            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
365    
366            * DESCRIPTION (Date): New release
367    
368    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
371    
372            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
373            * man/KNex.Rd: and other help files
374            * tests/*.R: several ones needed adaption
375            * inst/doc/Comparisons.Rnw: ditto
376    
377    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
380    
381            * tests/indexing.R: tests for new [<- methods for sparse matrices.
382    
383    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
386    
387            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
388    
389    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/dMatrix.R: enable things like  M [ M < 10 ]
392            * R/dgeMatrix.R: implement it
393    
394    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/AllClass.R: define "summary.mer" and "*.lmer"
397            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
398            * R/lmer.R (show): now works with summary()
399    
400    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
403            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
404                    support the above
405    
406    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
407    
408            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
409            Use glmFit$prior.weights for weights in a glmm.
410            Allow an option usePQL = FALSE to skip the PQL steps for the
411            Laplace method (and, in time, the AGQ method).
412    
413            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
414            into a separate function internal_mer_Xfactor to be able to call
415            it from internal_bhat.
416    
417    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * tests/Class+Meth.R (tstMatrixClass): function for much better
420            testing; now again of all actual classes.
421    
422            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
423                    use macros and define make_d_matrix_* and make_i_matrix_*
424                    where _i_ is for the ldense routines:
425    
426            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
427            * src/ldense.c (lsyMatrix_as_lgeMatrix):
428    
429            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
430    
431    
432    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
435                    many different kinds of matrices.
436            * R/*.R: quite a few new methods were needed for R CMD check with
437                    new Matrix().  Very good for users playing around.
438    
439    
440    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * src/dgeMatrix.c (dMatrix_validate): new
443            * src/Mutils.c (dense_nonpacked_validate): new
444    
445            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
446    
447    
448    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
449    
450            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
451    
452    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
453    
454            * DESCRIPTION (Version): 0.99-6 released to CRAN
455    
456            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
457            segfault in cases with multiple non-nested grouping factors.
458    
459    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
462                    (Depends): also on 'utils'
463    
464            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
465            * R/diagMatrix.R (Diagonal): constructor and methods for
466            diagonal matrices
467    
468            * R/ltTMatrix.R: new "minimal methods"
469    
470    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
473            all methods (and help files).
474    
475    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
478                    for case (dimn.  op  no_dimn.)
479    
480    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
481    
482            * DESCRIPTION (Version): 0.99-2  released to CRAN
483    
484    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
485    
486            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
487            by Julian Faraway.
488    
489    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * R/Auxiliaries.R (try_as): new utility
492            * R/sparseMatrix.R: use try_as() in coercion to original class
493    
494    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
497    
498    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/Auxiliaries.R (dimNamesCheck): added
501    
502            * R/Matrix.R (as.array), (as.vector): new
503    
504    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
507                    default.
508            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
509                    "pMatrix" now contains "sparseMatrix"
510    
511    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * tests/Class+Meth.R: new tests; t(t(m)) == m
514    
515            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
516    
517            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
518            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
519    
520            * R/dspMatrix.R: typo in "t" method
521    
522    2005-09-18  Douglas Bates  <bates@wisc.edu>
523    
524            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
525            * R/Tsparse.R: instead of R/gTMatrix.R
526            * R/Csparse.R: new
527            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
528            * src/Tsparse.c: new; many trivial methods calling cholmod_()
529            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
530                            via cholmod
531    
532    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/Auxiliaries.R (non0ind): new function using new C code
535            * src/dgCMatrix.c (compressed_non_0_ij): new utility
536    
537    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
538    
539            * src/chm_common.h: header file required by all C sources that
540            call CHOLMOD functions.  It defines a cholmod_common structure
541            called 'c' whose address is passed as the last argument to
542            (virtually) every CHOLMOD function.
543    
544            * src/Pattern.c: Simple example of the use of CHOLMOD.
545    
546            * src/init.c: initialize and finalize the cholmod_common structure.
547    
548            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
549            LDL and CCOLAMD from the U. of Florida sparse matrix library.
550    
551    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * inst/test-tools.R: new file collecting the utility functions used
554                    in ./tests/*.R
555    
556            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
557            * R/Matrix.R (cbind2): methods for NULL and missing
558    
559    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/AllClass.R: new "index" class for "[" and "[<-":
562                    First cut at "symmetricMatrix" and "triangularMatrix"
563            * R/gTMatrix.R (.ind.prep): new function;
564                    Logical and character indexing now work too.
565            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
566            * tests/indexing.R: new, including *.Rout.save
567            * tests/dgTMatrix.R: new
568    
569    2005-08-29  Douglas Bates  <bates@wisc.edu>
570    
571            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
572            indicator pos not being updated.  Also enforced upper triangular
573            for symmetric case.  Need to coerce edges component of elements of
574            edge list - grr! (Why don't they define their classes cleanly?)
575    
576    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/Matrix.R:  added first "[<-" methods; not yet functional
579            * R/denseMatrix.R: ditto
580            * man/Subassign-methods.Rd: new help file for these
581    
582    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * DESCRIPTION (Version): 0.98-6
585    
586            * R/denseMatrix.R: new file for "[" fallback methods for all dense
587            matrices.
588    
589    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
592                    as( <logical>, "matrix")
593    
594            * R/pMatrix.R: coercion to "lgTMatrix"
595    
596            * R/gTMatrix.R: new virtual class to define "[" methods for.
597            * man/gTMatrix-class.Rd:
598            * General slight re-organization of where "[" methods are defined.
599              more to come.
600    
601    2005-08-18  Douglas Bates  <bates@wisc.edu>
602    
603            * DESCRIPTION (Version): 0.98-5  released to CRAN
604    
605            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
606            * .....
607    
608    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
609    
610            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
611            or glmer objects.
612    
613    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
616    
617    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
618    
619            * R/HBMM.R: finish re-writing R-only code.
620    
621    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
622    
623            * man/externalFormats.Rd: move documentation for writeHB and
624            writeMM here.
625    
626            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
627            (suggested by Paul Roecker).
628    
629            * tests/validObj.R (assertError): Comment out test that is failing
630            after recent changes in r-devel.
631    
632    
633    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/AllClass.R: intermediate virtual class "denseMatrix"
636            * man/denseMatrix-class.Rd
637            * NAMESPACE: export it, and also export
638            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
639    
640    2005-08-10  Douglas Bates  <bates@wisc.edu>
641    
642            * DESCRIPTION (Version): 0.98-3 to CRAN
643    
644            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
645            matrix_solve code (which was really, really wrong).
646    
647    2005-08-07  Douglas Bates  <bates@wisc.edu>
648    
649            * DESCRIPTION (Version): 0.98-2
650    
651            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
652    
653            * R/lmer.R (abbrvNms): new
654            * R/lmer.R (mcmcsamp): allow transformed parameters
655            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
656            for the Harwell-Boeing and the MatrixMarket formats.
657    
658    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * man/dtrMatrix-class.Rd: add examples
661            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
662    
663            * TODO: note the dtpMatrix (docu) bug
664    
665            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
666            in order to ensure that new as.matrix() is used by old functions,
667            e.g., svd(), qr(), eigen(), dist(),..;
668                  apply(), also matplot() or pairs().
669    
670    
671    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
674              add comments about 'control' / lmerControl() arguments
675    
676    2005-07-27  Douglas Bates  <bates@wisc.edu>
677    
678            * man/sleepstudy.Rd: Added the sleep data set.
679            * DESCRIPTION (Version): 0.98-1  released to CRAN
680    
681    2005-07-12  Douglas Bates  <bates@wisc.edu>
682            * man/sleepstudy.Rd: Added the sleep data set.
683    
684            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
685            .Call calls that were producing spurious output.
686    
687    2005-07-05  Douglas Bates  <bates@wisc.edu>
688    
689            * R/lmer.R (lmer): stored updated variance component estimates in
690            mer object for the generalized model.  (Bug reported by Renaud
691            Lancelot).
692    
693    2005-07-03  Douglas Bates  <bates@wisc.edu>
694    
695            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
696            unidimensional case.
697    
698    2005-06-08  Douglas Bates  <bates@wisc.edu>
699    
700            * DESCRIPTION (Version): 0.96-1
701    
702            * moved  lmer-class' R and C code moved from lme4 to here
703    
704    2005-06-04  Douglas Bates  <bates@wisc.edu>
705    
706            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
707            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
708    
709    2005-06-02  Douglas Bates  <bates@wisc.edu>
710    
711            * src/Makefile.win: Forgot to update this when Makefile changed.
712    
713    2005-05-11  Douglas Bates  <bates@wisc.edu>
714    
715            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
716            bug reported by Kurt Hornik and Michael Hahsler.
717    
718    2005-05-10  Douglas Bates  <bates@wisc.edu>
719    
720            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
721            logical sparse matrices.  These will also be used in the symbolic
722            analysis for lmer objects.
723    
724            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
725            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
726    
727    2005-05-06  Douglas Bates  <bates@wisc.edu>
728    
729            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
730            colMeans, colSums, rowMeans and rowSums.
731    
732    2005-04-18  Douglas Bates  <bates@wisc.edu>
733    
734            * src/lgCMatrix.[ch]: code for _validate method and stub for
735            multiplication operation.
736    
737            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
738            to dgetrs.
739    
740            * src/init.c: Fix cut-and-paste error in definition of
741            dgeMatrix_matrix_solve
742    
743            * src/{many files}: Tighten code by using ALLOC_SLOT.
744    
745    2005-04-15  Douglas Bates  <bates@wisc.edu>
746    
747            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
748    
749            * DESCRIPTION: Eliminate import of stats.
750    
751    
752    2005-04-06  Douglas Bates  <bates@wisc.edu>
753    
754            * R/AllClass.R : add logical sparse matrix classes
755    
756    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/dgTMatrix.R: add "[" method for triplet matrices
759            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
760    
761    2005-03-31  Douglas Bates  <bates@wisc.edu>
762    
763            * DESCRIPTION (Version): release 0.95-5 to CRAN
764    
765            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
766            * R/sparseMatrix.R: %*%, crossprod()
767            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
768            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
769            * src/lmer.c (lmer_fitted): fix thinko
770    
771    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/AllClass.R: add two virtual sparse classes ``on top''
774    
775    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
778                    correspondingly fix examples and tests/ since new()
779                    doesn't work for virtual classes.
780    
781    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
782    
783            * R/Matrix.R (as.matrix): method and one for unname()
784            * tests/dpoMatrix.R: tests should now be less platform dependent;
785              also run for R 2.1.0; using as.matrix()
786    
787    2005-03-15  Douglas Bates  <bates@wisc.edu>
788    
789            * R/pMatrix.R: "pMatrix" class added
790            * ....
791    
792    2005-03-14  Douglas Bates  <bates@wisc.edu>
793    
794            * R/dtpMatrix.R: Add unpack method and an example.
795    
796            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
797            of general symmetric matrices and associated S4 methods.
798    
799    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
800            +
801    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * R/dgeMatrix.R (setAs): and many other files: more coercion,
804              crossprod() and "%*%" methods added; tests, too.
805            * tests/matprod.R: new, for testing these
806    
807    2005-03-03  Douglas Bates  <bates@wisc.edu>
808    
809            * src/lmer.c (lmer_fitted): Added.
810    
811    2005-03-02  Douglas Bates  <bates@wisc.edu>
812    
813            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
814    
815    2005-02-28  Douglas Bates  <bates@wisc.edu>
816    
817            * src/*.c,po/,inst/po: Internationalization and localization of
818            the package.
819    
820            * src/ldl.[ch]: Removed these as their contents are referenced in the
821            R_ldl.c file.
822    
823            * src/flame.[ch]: Removed these source files.
824    
825            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
826    
827            * src/LU.[ch],src/init.c: absorb in factorizations
828    
829            * src/Mutils.h: prepare for internationalization
830    
831            * src/cblas.h: move the enum definitions to Mutils.h and remove
832            this file
833    
834    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
837    
838            * R/dtrMatrix.R: fix t() method
839    
840            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
841            * NAMESPACE: export them (and import generics from "methods")
842            * tests/group-methods.R : and test them.
843    
844            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
845            border case
846    
847    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
848    
849            * DESCRIPTION (Version): 0.95-2  released to CRAN
850    
851            * src/dgBCMatrix.c:
852            * src/lmer.c: many changes
853            * ...
854    
855    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * R/Matrix.R: add more sophisticated show() method.
858    
859    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
860    
861            * */* : almost complete reorganization of classes.
862    
863    2005-01-26  Douglas Bates  <bates@wisc.edu>
864    
865            * R/AllGeneric.R: Added matrix exponential generic expm and a method
866            for the geMatrix class.
867    
868    2005-01-24  Douglas Bates  <bates@wisc.edu>
869    
870            * src/Makefile (clean): Remove *.a and *.so
871    
872            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
873    
874    2005-01-23  Douglas Bates  <bates@wisc.edu>
875    
876            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
877            had an effect in cases with more than 2 grouping factors.
878    
879    2005-01-03  Douglas Bates  <bates@wisc.edu>
880    
881            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
882    
883    2004-12-23  Douglas Bates  <bates@wisc.edu>
884    
885            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
886            and R_useDynamicSymbols (suggested by B.D.Ripley).
887    
888    2004-12-14  Douglas Bates  <bates@wisc.edu>
889    
890            * R/sscMatrix.R: Add determinant methods
891    
892            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
893            for tripletMatrix to matrix.
894    
895    2004-12-13  Douglas Bates  <bates@wisc.edu>
896    
897            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
898            no longer used.
899    
900            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
901            with dynamic allocation of scratch arrays.
902    
903            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
904            for multivariate random effects with multiple grouping factors.
905            Fixes part but not all of #15.
906    
907    2004-12-03  Douglas Bates  <bates@wisc.edu>
908    
909            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
910            scalar grouping factors corrected.
911    
912    2004-11-29  Douglas Bates  <bates@wisc.edu>
913    
914            * src/bCrosstab.c: remove diag_update which is no longer used
915    
916    2004-11-16  Douglas Bates  <bates@wisc.edu>
917    
918          * 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
919          .h file can be included.          .h file can be included.
920    
921  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
922    
923          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
924          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
925    
926          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
927    
928  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
929    
930          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
931    
932  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
933    
934          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
935    
936  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
937    
938          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
939    
940  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
941    
942          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
943    
944  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
945    
946          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
947          routines.          routines.
948    
949  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
950    
951          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
952    
953  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
954    
955          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
956    

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