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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1411, Tue Aug 22 01:01:23 2006 UTC
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1    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            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
6            inverses.
7            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
8            -Wall warnings.
9            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
10            Use dup_mMatrix_as_dgeMatrix.
11    
12    2006-08-20  Douglas Bates  <bates@R-project.org>
13    
14            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
15            * tests/sparseQR.R: Added
16            * man/sparseQR-class.Rd: Document methods for qr.* generics
17            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
18    
19    2006-08-19  Douglas Bates  <bates@R-project.org>
20    
21            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
22            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
23            and qr.fitted.
24            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
25            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
26    
27    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
30            the base version has no "..." argument.
31    
32            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
33    
34            * R/Matrix.R: define and
35            * NAMESPACE: export as.numeric() and as.logical() methods.
36                    Let's hope these do not badly slow down something...
37            Finally export the zapsmall() method.
38    
39    2006-08-17  Douglas Bates  <bates@R-project.org>
40    
41            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
42            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
43            * src/dtCMatrix.c :Remove code that is no longer used
44            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
45    
46    2006-08-14  Douglas Bates  <bates@R-project.org>
47    
48            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
49            Csparse_to_logical and Csparse_symmetric_to_general.
50            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
51            coercion methods between CsparseMatrix and TsparseMatrix.
52    
53    2006-08-14  Douglas Bates  <bates@R-project.org>
54    
55            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
56            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
57            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
58            possible.
59    
60    2006-08-12  Douglas Bates  <bates@R-project.org>
61    
62            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
63              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
64              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
65              generalize conversions between TsparseMatrix, CsparseMatrix,
66              denseMatrix and matrix.  Preserve triangularity property and
67              propagate Dimnames in the easy cases.
68    
69    2006-08-10  Douglas Bates  <bates@R-project.org>
70    
71            * src/lmer.c: adjust checks in glmer_init for S4SXP
72            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
73            before S4SXP but for the wrong reasons.
74    
75    2006-08-08  Douglas Bates  <bates@R-project.org>
76    
77            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
78            Later modified to return the upper triangle only.
79            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
80    
81    2006-08-07  Douglas Bates  <bates@R-project.org>
82    
83            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
84            R-level conversion to a sparse symmetric class.
85            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
86            Remove conversion to sparse symmetric classes (now done in C code).
87    
88    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
91            * man/band.Rd:  adapt the \dontshow{} unit test.
92    
93    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * DESCRIPTION (Version): 0.995-14  for CRAN
96    
97            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
98    
99            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
100            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
101    
102            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
103            * R/Tsparse.R (tril, triu, band): methods
104            * R/dgRMatrix.R (tril, ...):    ditto
105            * man/band.Rd:                  ditto
106    
107    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R (head, tail): directly use utils:::head.matrix
110                    to be up-to-date automatically.
111    
112    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
115    
116            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
117            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
118            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
119            such that the S4 objects are always created by the current version
120            of R and 'Matrix' class definitions.
121    
122    2006-08-01  Douglas Bates  <bates@R-project.org>
123    
124            * R/lmer.R (LMEoptimize method), tests/lmer.R,
125            inst/external/test3comp.rda: Added warnings for convergence on
126            boundary and test cases.
127    
128            * src/lmer.c (mer_postVar): Modified to return the variances that
129            are marginal to the fixed effects, not conditional on them (which
130            is what the bVar slot contents represent).
131    
132    2006-07-31  Douglas Bates  <bates@R-project.org>
133    
134            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
135            function which calls the C function mer_hat_trace2.
136    
137            * man/ranef.Rd: Include description of "postVar" argument and
138            producing a caterpillar plot.
139    
140    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * NAMESPACE:    change  "correlation" to "corMatrix"
143            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
144            * R/dpoMatrix.R: ditto
145            * R/lmer.R:      ditto
146    
147    2006-07-28  Douglas Bates  <bates@R-project.org>
148    
149            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
150            RZXinv slot's contents into a separate internal function that can
151            be used in mer_hat_trace.
152    
153    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
156            via new smart
157            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
158            utility functions.
159    
160    
161    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/Csparse.R (tril, triu, band): do return *triangular* classed
164            matrices when appropriate; band() even symmetric ones.
165            (replCmat): extend to potentially all "CsparseMatrix"
166            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
167            allow subassignment for special sparse matrices.
168    
169            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
170    
171            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
172            argument; in glmer_*(): print only if(verbose).
173    
174            speed-optimize a few places by moving REAL(.) out of loops.
175    
176            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
177    
178    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
181                    since that wrongly triggers also for M[ logi , ]
182    
183            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
184            a symmetric matrix that results in a non-symmetric one.
185            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
186    
187            * R/dMatrix.R: make round(M) work as round(M, 0)
188    
189            * R/dgTMatrix.R (image): coordinate system and axis now use
190            1-based indices, not 0-based ones.
191    
192            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
193            * tests/indexing.R: test it.
194    
195            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
196            * man/isSymmetric-methods.Rd: and document it.
197    
198            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
199            * man/SparseM-conv.Rd: docu them
200    
201            * tests/other-pkgs.R: renamed from tests/graph.R and add example
202                    for 'SparseM' conversions
203    
204    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
205    
206            * R/Matrix.R (head): added head() and tail() methods.
207    
208    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * DESCRIPTION (Version): 0.995-12 released to CRAN
211    
212    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * tests/simple.R: add check for correct dsT -> dgT coercion;
215                    add check for correct printing of symmetric sparse matrices.
216    
217            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
218            for sparse symmetric matrices.
219    
220            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
221            diagonal twice.
222    
223    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
224    
225            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
226            being applied to the x slot (detected by Brian Ripley).
227    
228    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
231    
232            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
233    
234    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/lgCMatrix.c (lgCMatrix_diag): new function
237            * R/lgCMatrix.R (diag): for new method
238    
239            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
240                 ==> construction of illegal "*gTMatrix" via new() should
241                 now be much less easy:
242            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
243    
244            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
245                    directly.
246            * man/Matrix.Rd: documents it.
247    
248    2006-07-06  Douglas Bates  <bates@R-project.org>
249    
250            * src/pedigree.c (pedigree_inbreeding): Correction in
251            initialization.  This function is not currently being used and is
252            not fully tested.
253    
254            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
255            Introduced the glmer class.  Added code for mcmcmsamp on glmer
256            objects.  Modified validity check on pedigree objects to account
257            for nonparallel patterns of missingness of parents.
258    
259            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
260            class.
261    
262    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/pMatrix.R: coercion pMatrix -> Tsparse
265    
266    2006-06-12  Douglas Bates  <bates@R-project.org>
267    
268            * DESCRIPTION (Version): 0.995-11 released to CRAN
269    
270            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
271            the output from mcmcsamp.
272    
273    2006-06-10  Douglas Bates  <bates@R-project.org>
274    
275            * R/lmer.R (simulestimate): added C code for calculating the trace
276            of the hat matrix.
277    
278    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
281            classes.
282            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
283    
284    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/dgTMatrix.R (colSums): etc. All four of
287            colSums(), rowSums(), colMeans(), rowMeans() now should work for
288            all "Matrices".
289    
290    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
291    
292            * R/lmer.R (panel.ci): Add a reference line at zero and a
293            background grid to the qqmath plot of ranef.lmer.
294    
295    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
298            grouping factors to be specified in the formula as (1|foo/bar).
299    
300    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
301    
302            * R/lmer.R (findbars and others): Change check of is.numeric to
303            !is.language to resolve the bug reported by Jacob Wegelin.
304    
305            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
306            code to evaluate inbreeding coefficients without calculating T,
307            based on code in Sargolzaei and Iwaisaki's paper.
308    
309    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
310    
311            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
312            generic and mer methods for isNested and denomDF. This denomDF was
313            an attempt to emulate that in lme but I don't think that makes
314            sense.  Use the trace of the hat matrix instead.
315    
316    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
319            the C code depending on a slot structure that's no longer valid.
320            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
321    
322    
323    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
324    
325            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
326            of lowerTriMatrix generic and methods to tril (also upper to triu)
327            and added a general band extractor.
328    
329    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * R/pedigree.R (pedigree): Replace sire and dam values outside the
332            allowable range with NAs. Added a corresponding check in the
333            validity check for the pedigree class.
334    
335            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
336            crossprod methods now inherits from symmetricMatrix.
337    
338    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
339    
340            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
341            generics lowerTriMatrix and upperTriMatrix along with methods for
342            the Csparse virtual class.  Also added a C function Csparse_band
343            that implements these methods by calling cholmod_band.
344    
345    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
348            erased when it was NULL.  This led to invalid subselections!
349    
350    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
351    
352            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
353            in method for "t" so as not to lose the unit diagonal property.
354    
355    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
356    
357            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
358            and methods.  This is now an option to the ranef method for the
359            mer class.
360    
361            * src/cs_utils.c: Ensure that the nz component is -1 for a
362            compressed column-oriented matrix.  Minor formatting cleanup.
363    
364            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
365            objects.
366    
367    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
370            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
371    
372    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
375            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
376    
377            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
378            for the dtCMatrix class.
379    
380    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
381    
382            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
383            and methods for it.
384    
385    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
388            arguments, such that M %*% 1:6 now works
389            * Tests/matprod.R: test the above
390    
391    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
392    
393            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
394            the ranef.lmer class.
395    
396            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
397            methods to extract the posterior variances from the bVar slot.
398    
399    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
402            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
403    
404            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
405            * tests/simple: (extended)
406    
407            * R/sparseMatrix.R (isTriangular): now using much improved
408            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
409    
410    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
411    
412            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
413            (problem report from Franklin Parlamis).  This should be done
414            generally.
415    
416    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
419            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
420            update the plot methods.
421    
422    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
423    
424            * R/lmer.R (resid and ranef methods):  Added methods for the
425            "residuals" and "resid" generic but only for linear mixed model
426            fits.  Changed the ranef method to return a list of data frames so
427            that the plot methods now work.
428    
429    2006-03-16  Douglas Bates  <bates@bates2>
430    
431            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
432            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
433    
434            * DESCRIPTION (Date): New release
435    
436    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
439    
440            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
441            * man/KNex.Rd: and other help files
442            * tests/*.R: several ones needed adaption
443            * inst/doc/Comparisons.Rnw: ditto
444    
445    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
448    
449            * tests/indexing.R: tests for new [<- methods for sparse matrices.
450    
451    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
454    
455            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
456    
457    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/dMatrix.R: enable things like  M [ M < 10 ]
460            * R/dgeMatrix.R: implement it
461    
462    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/AllClass.R: define "summary.mer" and "*.lmer"
465            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
466            * R/lmer.R (show): now works with summary()
467    
468    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
471            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
472                    support the above
473    
474  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
475    
476          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
# Line 171  Line 644 
644  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
647          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
648          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
649    
650  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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