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revision 1316, Tue Jul 11 22:00:41 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>  2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
375    
376          * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER          * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
377          being applied to the x slot (detected by Brian Ripley).  Possible          being applied to the x slot (detected by Brian Ripley).
         problem with copying the diagonal elements twice?  
378    
379  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
# Line 44  Line 416 
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 94  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 217  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 421  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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