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revision 1200, Mon Jan 23 16:01:20 2006 UTC revision 1405, Mon Aug 21 14:43:00 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    
6    2006-08-20  Douglas Bates  <bates@R-project.org>
7    
8            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
9            * tests/sparseQR.R: Added
10            * man/sparseQR-class.Rd: Document methods for qr.* generics
11            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
12    
13    2006-08-19  Douglas Bates  <bates@R-project.org>
14    
15            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
16            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
17            and qr.fitted.
18            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
19            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
20    
21    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
24            the base version has no "..." argument.
25    
26            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
27    
28            * R/Matrix.R: define and
29            * NAMESPACE: export as.numeric() and as.logical() methods.
30                    Let's hope these do not badly slow down something...
31            Finally export the zapsmall() method.
32    
33    2006-08-17  Douglas Bates  <bates@R-project.org>
34    
35            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
36            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
37            * src/dtCMatrix.c :Remove code that is no longer used
38            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
39    
40    2006-08-14  Douglas Bates  <bates@R-project.org>
41    
42            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
43            Csparse_to_logical and Csparse_symmetric_to_general.
44            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
45            coercion methods between CsparseMatrix and TsparseMatrix.
46    
47    2006-08-14  Douglas Bates  <bates@R-project.org>
48    
49            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
50            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
51            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
52            possible.
53    
54    2006-08-12  Douglas Bates  <bates@R-project.org>
55    
56            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
57              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
58              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
59              generalize conversions between TsparseMatrix, CsparseMatrix,
60              denseMatrix and matrix.  Preserve triangularity property and
61              propagate Dimnames in the easy cases.
62    
63    2006-08-10  Douglas Bates  <bates@R-project.org>
64    
65            * src/lmer.c: adjust checks in glmer_init for S4SXP
66            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
67            before S4SXP but for the wrong reasons.
68    
69    2006-08-08  Douglas Bates  <bates@R-project.org>
70    
71            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
72            Later modified to return the upper triangle only.
73            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
74    
75    2006-08-07  Douglas Bates  <bates@R-project.org>
76    
77            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
78            R-level conversion to a sparse symmetric class.
79            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
80            Remove conversion to sparse symmetric classes (now done in C code).
81    
82    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
85            * man/band.Rd:  adapt the \dontshow{} unit test.
86    
87    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * DESCRIPTION (Version): 0.995-14  for CRAN
90    
91            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
92    
93            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
94            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
95    
96            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
97            * R/Tsparse.R (tril, triu, band): methods
98            * R/dgRMatrix.R (tril, ...):    ditto
99            * man/band.Rd:                  ditto
100    
101    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Matrix.R (head, tail): directly use utils:::head.matrix
104                    to be up-to-date automatically.
105    
106    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
109    
110            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
111            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
112            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
113            such that the S4 objects are always created by the current version
114            of R and 'Matrix' class definitions.
115    
116    2006-08-01  Douglas Bates  <bates@R-project.org>
117    
118            * R/lmer.R (LMEoptimize method), tests/lmer.R,
119            inst/external/test3comp.rda: Added warnings for convergence on
120            boundary and test cases.
121    
122            * src/lmer.c (mer_postVar): Modified to return the variances that
123            are marginal to the fixed effects, not conditional on them (which
124            is what the bVar slot contents represent).
125    
126    2006-07-31  Douglas Bates  <bates@R-project.org>
127    
128            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
129            function which calls the C function mer_hat_trace2.
130    
131            * man/ranef.Rd: Include description of "postVar" argument and
132            producing a caterpillar plot.
133    
134    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * NAMESPACE:    change  "correlation" to "corMatrix"
137            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
138            * R/dpoMatrix.R: ditto
139            * R/lmer.R:      ditto
140    
141    2006-07-28  Douglas Bates  <bates@R-project.org>
142    
143            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
144            RZXinv slot's contents into a separate internal function that can
145            be used in mer_hat_trace.
146    
147    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
150            via new smart
151            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
152            utility functions.
153    
154    
155    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/Csparse.R (tril, triu, band): do return *triangular* classed
158            matrices when appropriate; band() even symmetric ones.
159            (replCmat): extend to potentially all "CsparseMatrix"
160            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
161            allow subassignment for special sparse matrices.
162    
163            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
164    
165            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
166            argument; in glmer_*(): print only if(verbose).
167    
168            speed-optimize a few places by moving REAL(.) out of loops.
169    
170            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
171    
172    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
175                    since that wrongly triggers also for M[ logi , ]
176    
177            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
178            a symmetric matrix that results in a non-symmetric one.
179            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
180    
181            * R/dMatrix.R: make round(M) work as round(M, 0)
182    
183            * R/dgTMatrix.R (image): coordinate system and axis now use
184            1-based indices, not 0-based ones.
185    
186            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
187            * tests/indexing.R: test it.
188    
189            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
190            * man/isSymmetric-methods.Rd: and document it.
191    
192            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
193            * man/SparseM-conv.Rd: docu them
194    
195            * tests/other-pkgs.R: renamed from tests/graph.R and add example
196                    for 'SparseM' conversions
197    
198    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
199    
200            * R/Matrix.R (head): added head() and tail() methods.
201    
202    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * DESCRIPTION (Version): 0.995-12 released to CRAN
205    
206    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * tests/simple.R: add check for correct dsT -> dgT coercion;
209                    add check for correct printing of symmetric sparse matrices.
210    
211            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
212            for sparse symmetric matrices.
213    
214            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
215            diagonal twice.
216    
217    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
218    
219            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
220            being applied to the x slot (detected by Brian Ripley).
221    
222    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
225    
226            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
227    
228    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * src/lgCMatrix.c (lgCMatrix_diag): new function
231            * R/lgCMatrix.R (diag): for new method
232    
233            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
234                 ==> construction of illegal "*gTMatrix" via new() should
235                 now be much less easy:
236            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
237    
238            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
239                    directly.
240            * man/Matrix.Rd: documents it.
241    
242    2006-07-06  Douglas Bates  <bates@R-project.org>
243    
244            * src/pedigree.c (pedigree_inbreeding): Correction in
245            initialization.  This function is not currently being used and is
246            not fully tested.
247    
248            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
249            Introduced the glmer class.  Added code for mcmcmsamp on glmer
250            objects.  Modified validity check on pedigree objects to account
251            for nonparallel patterns of missingness of parents.
252    
253            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
254            class.
255    
256    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/pMatrix.R: coercion pMatrix -> Tsparse
259    
260    2006-06-12  Douglas Bates  <bates@R-project.org>
261    
262            * DESCRIPTION (Version): 0.995-11 released to CRAN
263    
264            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
265            the output from mcmcsamp.
266    
267    2006-06-10  Douglas Bates  <bates@R-project.org>
268    
269            * R/lmer.R (simulestimate): added C code for calculating the trace
270            of the hat matrix.
271    
272    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
275            classes.
276            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
277    
278    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/dgTMatrix.R (colSums): etc. All four of
281            colSums(), rowSums(), colMeans(), rowMeans() now should work for
282            all "Matrices".
283    
284    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * R/lmer.R (panel.ci): Add a reference line at zero and a
287            background grid to the qqmath plot of ranef.lmer.
288    
289    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
290    
291            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
292            grouping factors to be specified in the formula as (1|foo/bar).
293    
294    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
295    
296            * R/lmer.R (findbars and others): Change check of is.numeric to
297            !is.language to resolve the bug reported by Jacob Wegelin.
298    
299            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
300            code to evaluate inbreeding coefficients without calculating T,
301            based on code in Sargolzaei and Iwaisaki's paper.
302    
303    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
304    
305            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
306            generic and mer methods for isNested and denomDF. This denomDF was
307            an attempt to emulate that in lme but I don't think that makes
308            sense.  Use the trace of the hat matrix instead.
309    
310    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
313            the C code depending on a slot structure that's no longer valid.
314            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
315    
316    
317    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
318    
319            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
320            of lowerTriMatrix generic and methods to tril (also upper to triu)
321            and added a general band extractor.
322    
323    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * R/pedigree.R (pedigree): Replace sire and dam values outside the
326            allowable range with NAs. Added a corresponding check in the
327            validity check for the pedigree class.
328    
329            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
330            crossprod methods now inherits from symmetricMatrix.
331    
332    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
333    
334            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
335            generics lowerTriMatrix and upperTriMatrix along with methods for
336            the Csparse virtual class.  Also added a C function Csparse_band
337            that implements these methods by calling cholmod_band.
338    
339    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
342            erased when it was NULL.  This led to invalid subselections!
343    
344    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
345    
346            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
347            in method for "t" so as not to lose the unit diagonal property.
348    
349    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
350    
351            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
352            and methods.  This is now an option to the ranef method for the
353            mer class.
354    
355            * src/cs_utils.c: Ensure that the nz component is -1 for a
356            compressed column-oriented matrix.  Minor formatting cleanup.
357    
358            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
359            objects.
360    
361    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
364            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
365    
366    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
367    
368            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
369            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
370    
371            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
372            for the dtCMatrix class.
373    
374    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
375    
376            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
377            and methods for it.
378    
379    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
382            arguments, such that M %*% 1:6 now works
383            * Tests/matprod.R: test the above
384    
385    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
386    
387            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
388            the ranef.lmer class.
389    
390            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
391            methods to extract the posterior variances from the bVar slot.
392    
393    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
396            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
397    
398            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
399            * tests/simple: (extended)
400    
401            * R/sparseMatrix.R (isTriangular): now using much improved
402            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
403    
404    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
405    
406            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
407            (problem report from Franklin Parlamis).  This should be done
408            generally.
409    
410    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
411    
412            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
413            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
414            update the plot methods.
415    
416    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * R/lmer.R (resid and ranef methods):  Added methods for the
419            "residuals" and "resid" generic but only for linear mixed model
420            fits.  Changed the ranef method to return a list of data frames so
421            that the plot methods now work.
422    
423    2006-03-16  Douglas Bates  <bates@bates2>
424    
425            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
426            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
427    
428            * DESCRIPTION (Date): New release
429    
430    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
433    
434            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
435            * man/KNex.Rd: and other help files
436            * tests/*.R: several ones needed adaption
437            * inst/doc/Comparisons.Rnw: ditto
438    
439    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
442    
443            * tests/indexing.R: tests for new [<- methods for sparse matrices.
444    
445    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
448    
449            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
450    
451    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/dMatrix.R: enable things like  M [ M < 10 ]
454            * R/dgeMatrix.R: implement it
455    
456    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/AllClass.R: define "summary.mer" and "*.lmer"
459            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
460            * R/lmer.R (show): now works with summary()
461    
462    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
465            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
466                    support the above
467    
468    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
469    
470            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
471            Use glmFit$prior.weights for weights in a glmm.
472            Allow an option usePQL = FALSE to skip the PQL steps for the
473            Laplace method (and, in time, the AGQ method).
474    
475            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
476            into a separate function internal_mer_Xfactor to be able to call
477            it from internal_bhat.
478    
479  2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481          * tests/Class+Meth.R (tstMatrixClass): function for much better          * tests/Class+Meth.R (tstMatrixClass): function for much better
# Line 160  Line 638 
638  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
641          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
642          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
643    
644  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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