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revision 1300, Mon Jun 12 10:52:01 2006 UTC revision 1548, Mon Sep 11 22:13:07 2006 UTC
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1    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
4                    Matrices, since "lMatrix", also "lsparseM" can have NA
5            * R/ndenseMatrix.R, etc: new source files
6            * man/nsparseMatrix-classes.Rd, etc: new help files
7            * tests/: adaptions
8            * src/chm_common.c (chm_dense_to_SEXP): and others:
9                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
10            * src/Csparse.c, etc: dito
11    
12    2006-09-11  Douglas Bates  <bates@R-project.org>
13    
14            * src/Mutils.[ch],init.c inst/include/*.h: Move the
15            alloc_d**Matrix functions to the lme4 package.
16    
17    2006-09-09  Douglas Bates  <bates@R-project.org>
18    
19            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
20            fixed
21    
22    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/lMatrix.R: new
25    
26            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
27    
28            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
29            * man/tcrossprod.Rd: dito
30    
31    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
34            for exported functions
35            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
36            Remove partitioning algorithms for sparse matrix reordering.  The
37            copyright on the Metis code was problematic and the methods were
38            rarely used.
39            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
40            operations are now done entirely in CHOLMOD code.
41    
42    2006-09-06  Douglas Bates  <bates@R-project.org>
43    
44            * src/Mutils.h: Remove functions that are no longer used.
45    
46    2006-09-04  Douglas Bates  <bates@R-project.org>
47    
48            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
49            * src/DEPS.mkf: update
50    
51    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * created branches/Matrix-for-R-2.3.x;  on trunk: do
54            * DESCRIPTION (Version): 0.9975-0
55            (Depends): R (>= 2.4.0)
56    
57    2006-09-01  Douglas Bates  <bates@R-project.org>
58    
59            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
60    
61    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
64            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
65    
66            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
67    
68    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
71            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
72            * R/dsparseMatrix.R: dito
73            * R/Csparse.R: dito
74    
75    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/dMatrix.R (Compare): improve availability of "<", etc
78            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
79    
80    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
83            of a 0-index which was used as 1-index (..hmm)
84    
85            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
86    
87            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
88            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
89            (.is.diagonal): dito
90    
91            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
92    
93            * R/Matrix.R (Matrix): also work for NA data
94    
95    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
98            in all cases.
99    
100    2006-08-27  Douglas Bates  <bates@R-project.org>
101    
102            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
103            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
104    
105    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
108            subclasses of "ddenseMatrix"
109            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
110            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
111            instead of half dozen specialized ones.
112    
113    2006-08-25  Douglas Bates  <bates@R-project.org>
114    
115            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
116            <tillard@cirad.fr> - ordering standard errors to match effects.
117    
118    2006-08-24  Douglas Bates  <bates@R-project.org>
119    
120            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
121            on R_ldl.
122            * R/lCholCMatrix.R,
123            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
124            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
125            * many files in ./R and ./src: Use more general version of
126            dup_mMatrix_as_dgeMatrix to simplify method definitions.
127            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
128            dtpMatrix, dspMatrix and dppMatrix conversions.
129    
130    
131    2006-08-23  Douglas Bates  <bates@R-project.org>
132    
133            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
134            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
135            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
136            dgeMatrix_crossprod (may need to do this in other places).
137            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
138            generic and method for dsCMatrix.  Use CHOLMOD for chol().
139    
140    2006-08-22  Douglas Bates  <bates@R-project.org>
141    
142            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
143            types of classed Matrices, matrices or numeric or logical vectors.
144            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
145            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
146            to Mutils.h (as an inline) and change name to Matrix_check_class;
147            fixes in as_cholmod_factor and chm_factor_to_SEXP.
148            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
149            dsCMatrix_matrix_solve.  Comment out vestigial functions.
150            * src/Csparse.c: use diag_P and uplo_P macros.
151    
152    2006-08-21  Douglas Bates  <bates@R-project.org>
153    
154            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
155            valgrind.
156            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
157            inverses.
158            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
159            -Wall warnings.
160            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
161            Use dup_mMatrix_as_dgeMatrix.
162    
163    2006-08-20  Douglas Bates  <bates@R-project.org>
164    
165            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
166            * tests/sparseQR.R: Added
167            * man/sparseQR-class.Rd: Document methods for qr.* generics
168            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
169    
170    2006-08-19  Douglas Bates  <bates@R-project.org>
171    
172            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
173            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
174            and qr.fitted.
175            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
176            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
177    
178    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
181            the base version has no "..." argument.
182    
183            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
184    
185            * R/Matrix.R: define and
186            * NAMESPACE: export as.numeric() and as.logical() methods.
187                    Let's hope these do not badly slow down something...
188            Finally export the zapsmall() method.
189    
190    2006-08-17  Douglas Bates  <bates@R-project.org>
191    
192            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
193            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
194            * src/dtCMatrix.c :Remove code that is no longer used
195            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
196    
197    2006-08-14  Douglas Bates  <bates@R-project.org>
198    
199            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
200            Csparse_to_logical and Csparse_symmetric_to_general.
201            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
202            coercion methods between CsparseMatrix and TsparseMatrix.
203    
204    2006-08-14  Douglas Bates  <bates@R-project.org>
205    
206            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
207            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
208            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
209            possible.
210    
211    2006-08-12  Douglas Bates  <bates@R-project.org>
212    
213            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
214              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
215              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
216              generalize conversions between TsparseMatrix, CsparseMatrix,
217              denseMatrix and matrix.  Preserve triangularity property and
218              propagate Dimnames in the easy cases.
219    
220    2006-08-10  Douglas Bates  <bates@R-project.org>
221    
222            * src/lmer.c: adjust checks in glmer_init for S4SXP
223            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
224            before S4SXP but for the wrong reasons.
225    
226    2006-08-08  Douglas Bates  <bates@R-project.org>
227    
228            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
229            Later modified to return the upper triangle only.
230            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
231    
232    2006-08-07  Douglas Bates  <bates@R-project.org>
233    
234            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
235            R-level conversion to a sparse symmetric class.
236            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
237            Remove conversion to sparse symmetric classes (now done in C code).
238    
239    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
242            * man/band.Rd:  adapt the \dontshow{} unit test.
243    
244    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * DESCRIPTION (Version): 0.995-14  for CRAN
247    
248            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
249    
250            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
251            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
252    
253            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
254            * R/Tsparse.R (tril, triu, band): methods
255            * R/dgRMatrix.R (tril, ...):    ditto
256            * man/band.Rd:                  ditto
257    
258    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Matrix.R (head, tail): directly use utils:::head.matrix
261                    to be up-to-date automatically.
262    
263    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
266    
267            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
268            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
269            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
270            such that the S4 objects are always created by the current version
271            of R and 'Matrix' class definitions.
272    
273    2006-08-01  Douglas Bates  <bates@R-project.org>
274    
275            * R/lmer.R (LMEoptimize method), tests/lmer.R,
276            inst/external/test3comp.rda: Added warnings for convergence on
277            boundary and test cases.
278    
279            * src/lmer.c (mer_postVar): Modified to return the variances that
280            are marginal to the fixed effects, not conditional on them (which
281            is what the bVar slot contents represent).
282    
283    2006-07-31  Douglas Bates  <bates@R-project.org>
284    
285            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
286            function which calls the C function mer_hat_trace2.
287    
288            * man/ranef.Rd: Include description of "postVar" argument and
289            producing a caterpillar plot.
290    
291    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * NAMESPACE:    change  "correlation" to "corMatrix"
294            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
295            * R/dpoMatrix.R: ditto
296            * R/lmer.R:      ditto
297    
298    2006-07-28  Douglas Bates  <bates@R-project.org>
299    
300            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
301            RZXinv slot's contents into a separate internal function that can
302            be used in mer_hat_trace.
303    
304    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
307            via new smart
308            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
309            utility functions.
310    
311    
312    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Csparse.R (tril, triu, band): do return *triangular* classed
315            matrices when appropriate; band() even symmetric ones.
316            (replCmat): extend to potentially all "CsparseMatrix"
317            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
318            allow subassignment for special sparse matrices.
319    
320            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
321    
322            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
323            argument; in glmer_*(): print only if(verbose).
324    
325            speed-optimize a few places by moving REAL(.) out of loops.
326    
327            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
328    
329    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
332                    since that wrongly triggers also for M[ logi , ]
333    
334            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
335            a symmetric matrix that results in a non-symmetric one.
336            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
337    
338            * R/dMatrix.R: make round(M) work as round(M, 0)
339    
340            * R/dgTMatrix.R (image): coordinate system and axis now use
341            1-based indices, not 0-based ones.
342    
343            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
344            * tests/indexing.R: test it.
345    
346            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
347            * man/isSymmetric-methods.Rd: and document it.
348    
349            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
350            * man/SparseM-conv.Rd: docu them
351    
352            * tests/other-pkgs.R: renamed from tests/graph.R and add example
353                    for 'SparseM' conversions
354    
355    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
356    
357            * R/Matrix.R (head): added head() and tail() methods.
358    
359    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * DESCRIPTION (Version): 0.995-12 released to CRAN
362    
363    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * tests/simple.R: add check for correct dsT -> dgT coercion;
366                    add check for correct printing of symmetric sparse matrices.
367    
368            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
369            for sparse symmetric matrices.
370    
371            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
372            diagonal twice.
373    
374    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
375    
376            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
377            being applied to the x slot (detected by Brian Ripley).
378    
379    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
382    
383            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
384    
385    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * src/lgCMatrix.c (lgCMatrix_diag): new function
388            * R/lgCMatrix.R (diag): for new method
389    
390            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
391                 ==> construction of illegal "*gTMatrix" via new() should
392                 now be much less easy:
393            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
394    
395            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
396                    directly.
397            * man/Matrix.Rd: documents it.
398    
399    2006-07-06  Douglas Bates  <bates@R-project.org>
400    
401            * src/pedigree.c (pedigree_inbreeding): Correction in
402            initialization.  This function is not currently being used and is
403            not fully tested.
404    
405            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
406            Introduced the glmer class.  Added code for mcmcmsamp on glmer
407            objects.  Modified validity check on pedigree objects to account
408            for nonparallel patterns of missingness of parents.
409    
410            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
411            class.
412    
413    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/pMatrix.R: coercion pMatrix -> Tsparse
416    
417  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
418    
419            * DESCRIPTION (Version): 0.995-11 released to CRAN
420    
421          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
422          the output from mcmcsamp.          the output from mcmcsamp.
423    
# Line 12  Line 430 
430    
431          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
432          classes.          classes.
433            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
434    
435  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
# Line 49  Line 468 
468    
469          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
470          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.
471          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
472    
473    
474  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 172  Line 591 
591          * 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)
592          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
593          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
594          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
595    
596  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
# Line 376  Line 795 
795  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
798          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
799          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
800    
801  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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