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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1538, Fri Sep 8 13:18:50 2006 UTC
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1    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
4            for exported functions
5            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
6            Remove partitioning algorithms for sparse matrix reordering.  The
7            copyright on the Metis code was problematic and the methods were
8            rarely used.
9            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
10            operations are now done entirely in CHOLMOD code.
11    
12    2006-09-06  Douglas Bates  <bates@R-project.org>
13    
14            * src/Mutils.h: Remove functions that are no longer used.
15    
16    2006-09-04  Douglas Bates  <bates@R-project.org>
17    
18            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
19            * src/DEPS.mkf: update
20    
21    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * created branches/Matrix-for-R-2.3.x;  on trunk: do
24            * DESCRIPTION (Version): 0.9975-0
25            (Depends): R (>= 2.4.0)
26    
27    2006-09-01  Douglas Bates  <bates@R-project.org>
28    
29            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
30    
31    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
34            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
35    
36            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
37    
38    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
41            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
42            * R/dsparseMatrix.R: dito
43            * R/Csparse.R: dito
44    
45    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/dMatrix.R (Compare): improve availability of "<", etc
48            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
49    
50    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
53            of a 0-index which was used as 1-index (..hmm)
54    
55            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
56    
57            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
58            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
59            (.is.diagonal): dito
60    
61            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
62    
63            * R/Matrix.R (Matrix): also work for NA data
64    
65    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
68            in all cases.
69    
70    2006-08-27  Douglas Bates  <bates@R-project.org>
71    
72            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
73            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
74    
75    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
78            subclasses of "ddenseMatrix"
79            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
80            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
81            instead of half dozen specialized ones.
82    
83    2006-08-25  Douglas Bates  <bates@R-project.org>
84    
85            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
86            <tillard@cirad.fr> - ordering standard errors to match effects.
87    
88    2006-08-24  Douglas Bates  <bates@R-project.org>
89    
90            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
91            on R_ldl.
92            * R/lCholCMatrix.R,
93            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
94            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
95            * many files in ./R and ./src: Use more general version of
96            dup_mMatrix_as_dgeMatrix to simplify method definitions.
97            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
98            dtpMatrix, dspMatrix and dppMatrix conversions.
99    
100    
101    2006-08-23  Douglas Bates  <bates@R-project.org>
102    
103            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
104            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
105            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
106            dgeMatrix_crossprod (may need to do this in other places).
107            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
108            generic and method for dsCMatrix.  Use CHOLMOD for chol().
109    
110    2006-08-22  Douglas Bates  <bates@R-project.org>
111    
112            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
113            types of classed Matrices, matrices or numeric or logical vectors.
114            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
115            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
116            to Mutils.h (as an inline) and change name to Matrix_check_class;
117            fixes in as_cholmod_factor and chm_factor_to_SEXP.
118            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
119            dsCMatrix_matrix_solve.  Comment out vestigial functions.
120            * src/Csparse.c: use diag_P and uplo_P macros.
121    
122    2006-08-21  Douglas Bates  <bates@R-project.org>
123    
124            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
125            valgrind.
126            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
127            inverses.
128            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
129            -Wall warnings.
130            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
131            Use dup_mMatrix_as_dgeMatrix.
132    
133    2006-08-20  Douglas Bates  <bates@R-project.org>
134    
135            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
136            * tests/sparseQR.R: Added
137            * man/sparseQR-class.Rd: Document methods for qr.* generics
138            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
139    
140    2006-08-19  Douglas Bates  <bates@R-project.org>
141    
142            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
143            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
144            and qr.fitted.
145            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
146            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
147    
148    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
151            the base version has no "..." argument.
152    
153            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
154    
155            * R/Matrix.R: define and
156            * NAMESPACE: export as.numeric() and as.logical() methods.
157                    Let's hope these do not badly slow down something...
158            Finally export the zapsmall() method.
159    
160    2006-08-17  Douglas Bates  <bates@R-project.org>
161    
162            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
163            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
164            * src/dtCMatrix.c :Remove code that is no longer used
165            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
166    
167    2006-08-14  Douglas Bates  <bates@R-project.org>
168    
169            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
170            Csparse_to_logical and Csparse_symmetric_to_general.
171            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
172            coercion methods between CsparseMatrix and TsparseMatrix.
173    
174    2006-08-14  Douglas Bates  <bates@R-project.org>
175    
176            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
177            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
178            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
179            possible.
180    
181    2006-08-12  Douglas Bates  <bates@R-project.org>
182    
183            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
184              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
185              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
186              generalize conversions between TsparseMatrix, CsparseMatrix,
187              denseMatrix and matrix.  Preserve triangularity property and
188              propagate Dimnames in the easy cases.
189    
190    2006-08-10  Douglas Bates  <bates@R-project.org>
191    
192            * src/lmer.c: adjust checks in glmer_init for S4SXP
193            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
194            before S4SXP but for the wrong reasons.
195    
196    2006-08-08  Douglas Bates  <bates@R-project.org>
197    
198            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
199            Later modified to return the upper triangle only.
200            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
201    
202    2006-08-07  Douglas Bates  <bates@R-project.org>
203    
204            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
205            R-level conversion to a sparse symmetric class.
206            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
207            Remove conversion to sparse symmetric classes (now done in C code).
208    
209    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
212            * man/band.Rd:  adapt the \dontshow{} unit test.
213    
214    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * DESCRIPTION (Version): 0.995-14  for CRAN
217    
218            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
219    
220            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
221            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
222    
223            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
224            * R/Tsparse.R (tril, triu, band): methods
225            * R/dgRMatrix.R (tril, ...):    ditto
226            * man/band.Rd:                  ditto
227    
228    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Matrix.R (head, tail): directly use utils:::head.matrix
231                    to be up-to-date automatically.
232    
233    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
236    
237            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
238            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
239            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
240            such that the S4 objects are always created by the current version
241            of R and 'Matrix' class definitions.
242    
243    2006-08-01  Douglas Bates  <bates@R-project.org>
244    
245            * R/lmer.R (LMEoptimize method), tests/lmer.R,
246            inst/external/test3comp.rda: Added warnings for convergence on
247            boundary and test cases.
248    
249            * src/lmer.c (mer_postVar): Modified to return the variances that
250            are marginal to the fixed effects, not conditional on them (which
251            is what the bVar slot contents represent).
252    
253    2006-07-31  Douglas Bates  <bates@R-project.org>
254    
255            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
256            function which calls the C function mer_hat_trace2.
257    
258            * man/ranef.Rd: Include description of "postVar" argument and
259            producing a caterpillar plot.
260    
261    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * NAMESPACE:    change  "correlation" to "corMatrix"
264            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
265            * R/dpoMatrix.R: ditto
266            * R/lmer.R:      ditto
267    
268    2006-07-28  Douglas Bates  <bates@R-project.org>
269    
270            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
271            RZXinv slot's contents into a separate internal function that can
272            be used in mer_hat_trace.
273    
274    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
277            via new smart
278            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
279            utility functions.
280    
281    
282    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/Csparse.R (tril, triu, band): do return *triangular* classed
285            matrices when appropriate; band() even symmetric ones.
286            (replCmat): extend to potentially all "CsparseMatrix"
287            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
288            allow subassignment for special sparse matrices.
289    
290            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
291    
292            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
293            argument; in glmer_*(): print only if(verbose).
294    
295            speed-optimize a few places by moving REAL(.) out of loops.
296    
297            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
298    
299    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
302                    since that wrongly triggers also for M[ logi , ]
303    
304            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
305            a symmetric matrix that results in a non-symmetric one.
306            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
307    
308            * R/dMatrix.R: make round(M) work as round(M, 0)
309    
310            * R/dgTMatrix.R (image): coordinate system and axis now use
311            1-based indices, not 0-based ones.
312    
313            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
314            * tests/indexing.R: test it.
315    
316            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
317            * man/isSymmetric-methods.Rd: and document it.
318    
319            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
320            * man/SparseM-conv.Rd: docu them
321    
322            * tests/other-pkgs.R: renamed from tests/graph.R and add example
323                    for 'SparseM' conversions
324    
325    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
326    
327            * R/Matrix.R (head): added head() and tail() methods.
328    
329    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * DESCRIPTION (Version): 0.995-12 released to CRAN
332    
333    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * tests/simple.R: add check for correct dsT -> dgT coercion;
336                    add check for correct printing of symmetric sparse matrices.
337    
338            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
339            for sparse symmetric matrices.
340    
341            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
342            diagonal twice.
343    
344    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
345    
346            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
347            being applied to the x slot (detected by Brian Ripley).
348    
349    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
352    
353            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
354    
355    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * src/lgCMatrix.c (lgCMatrix_diag): new function
358            * R/lgCMatrix.R (diag): for new method
359    
360            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
361                 ==> construction of illegal "*gTMatrix" via new() should
362                 now be much less easy:
363            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
364    
365            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
366                    directly.
367            * man/Matrix.Rd: documents it.
368    
369    2006-07-06  Douglas Bates  <bates@R-project.org>
370    
371            * src/pedigree.c (pedigree_inbreeding): Correction in
372            initialization.  This function is not currently being used and is
373            not fully tested.
374    
375            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
376            Introduced the glmer class.  Added code for mcmcmsamp on glmer
377            objects.  Modified validity check on pedigree objects to account
378            for nonparallel patterns of missingness of parents.
379    
380            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
381            class.
382    
383    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/pMatrix.R: coercion pMatrix -> Tsparse
386    
387    2006-06-12  Douglas Bates  <bates@R-project.org>
388    
389            * DESCRIPTION (Version): 0.995-11 released to CRAN
390    
391            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
392            the output from mcmcsamp.
393    
394    2006-06-10  Douglas Bates  <bates@R-project.org>
395    
396            * R/lmer.R (simulestimate): added C code for calculating the trace
397            of the hat matrix.
398    
399    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
402            classes.
403            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
404    
405    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/dgTMatrix.R (colSums): etc. All four of
408            colSums(), rowSums(), colMeans(), rowMeans() now should work for
409            all "Matrices".
410    
411    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
412    
413            * R/lmer.R (panel.ci): Add a reference line at zero and a
414            background grid to the qqmath plot of ranef.lmer.
415    
416    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
419            grouping factors to be specified in the formula as (1|foo/bar).
420    
421    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
422    
423            * R/lmer.R (findbars and others): Change check of is.numeric to
424            !is.language to resolve the bug reported by Jacob Wegelin.
425    
426            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
427            code to evaluate inbreeding coefficients without calculating T,
428            based on code in Sargolzaei and Iwaisaki's paper.
429    
430    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
431    
432            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
433            generic and mer methods for isNested and denomDF. This denomDF was
434            an attempt to emulate that in lme but I don't think that makes
435            sense.  Use the trace of the hat matrix instead.
436    
437  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
440          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
441          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
442    
443    
444  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 561 
561          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
562          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
563          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
564          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
565    
566  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
# Line 329  Line 765 
765  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
768          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
769          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
770    
771  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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