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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1544, Sat Sep 9 14:04:24 2006 UTC
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1    2006-09-09  Douglas Bates  <bates@R-project.org>
2    
3            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
4            fixed
5    
6    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
9    
10            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
11            * man/tcrossprod.Rd: dito
12    
13    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
16            for exported functions
17            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
18            Remove partitioning algorithms for sparse matrix reordering.  The
19            copyright on the Metis code was problematic and the methods were
20            rarely used.
21            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
22            operations are now done entirely in CHOLMOD code.
23    
24    2006-09-06  Douglas Bates  <bates@R-project.org>
25    
26            * src/Mutils.h: Remove functions that are no longer used.
27    
28    2006-09-04  Douglas Bates  <bates@R-project.org>
29    
30            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
31            * src/DEPS.mkf: update
32    
33    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * created branches/Matrix-for-R-2.3.x;  on trunk: do
36            * DESCRIPTION (Version): 0.9975-0
37            (Depends): R (>= 2.4.0)
38    
39    2006-09-01  Douglas Bates  <bates@R-project.org>
40    
41            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
42    
43    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
46            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
47    
48            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
49    
50    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
53            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
54            * R/dsparseMatrix.R: dito
55            * R/Csparse.R: dito
56    
57    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/dMatrix.R (Compare): improve availability of "<", etc
60            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
61    
62    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
65            of a 0-index which was used as 1-index (..hmm)
66    
67            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
68    
69            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
70            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
71            (.is.diagonal): dito
72    
73            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
74    
75            * R/Matrix.R (Matrix): also work for NA data
76    
77    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
80            in all cases.
81    
82    2006-08-27  Douglas Bates  <bates@R-project.org>
83    
84            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
85            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
86    
87    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
90            subclasses of "ddenseMatrix"
91            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
92            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
93            instead of half dozen specialized ones.
94    
95    2006-08-25  Douglas Bates  <bates@R-project.org>
96    
97            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
98            <tillard@cirad.fr> - ordering standard errors to match effects.
99    
100    2006-08-24  Douglas Bates  <bates@R-project.org>
101    
102            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
103            on R_ldl.
104            * R/lCholCMatrix.R,
105            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
106            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
107            * many files in ./R and ./src: Use more general version of
108            dup_mMatrix_as_dgeMatrix to simplify method definitions.
109            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
110            dtpMatrix, dspMatrix and dppMatrix conversions.
111    
112    
113    2006-08-23  Douglas Bates  <bates@R-project.org>
114    
115            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
116            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
117            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
118            dgeMatrix_crossprod (may need to do this in other places).
119            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
120            generic and method for dsCMatrix.  Use CHOLMOD for chol().
121    
122    2006-08-22  Douglas Bates  <bates@R-project.org>
123    
124            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
125            types of classed Matrices, matrices or numeric or logical vectors.
126            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
127            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
128            to Mutils.h (as an inline) and change name to Matrix_check_class;
129            fixes in as_cholmod_factor and chm_factor_to_SEXP.
130            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
131            dsCMatrix_matrix_solve.  Comment out vestigial functions.
132            * src/Csparse.c: use diag_P and uplo_P macros.
133    
134    2006-08-21  Douglas Bates  <bates@R-project.org>
135    
136            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
137            valgrind.
138            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
139            inverses.
140            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
141            -Wall warnings.
142            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
143            Use dup_mMatrix_as_dgeMatrix.
144    
145    2006-08-20  Douglas Bates  <bates@R-project.org>
146    
147            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
148            * tests/sparseQR.R: Added
149            * man/sparseQR-class.Rd: Document methods for qr.* generics
150            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
151    
152    2006-08-19  Douglas Bates  <bates@R-project.org>
153    
154            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
155            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
156            and qr.fitted.
157            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
158            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
159    
160    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
163            the base version has no "..." argument.
164    
165            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
166    
167            * R/Matrix.R: define and
168            * NAMESPACE: export as.numeric() and as.logical() methods.
169                    Let's hope these do not badly slow down something...
170            Finally export the zapsmall() method.
171    
172    2006-08-17  Douglas Bates  <bates@R-project.org>
173    
174            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
175            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
176            * src/dtCMatrix.c :Remove code that is no longer used
177            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
178    
179    2006-08-14  Douglas Bates  <bates@R-project.org>
180    
181            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
182            Csparse_to_logical and Csparse_symmetric_to_general.
183            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
184            coercion methods between CsparseMatrix and TsparseMatrix.
185    
186    2006-08-14  Douglas Bates  <bates@R-project.org>
187    
188            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
189            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
190            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
191            possible.
192    
193    2006-08-12  Douglas Bates  <bates@R-project.org>
194    
195            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
196              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
197              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
198              generalize conversions between TsparseMatrix, CsparseMatrix,
199              denseMatrix and matrix.  Preserve triangularity property and
200              propagate Dimnames in the easy cases.
201    
202    2006-08-10  Douglas Bates  <bates@R-project.org>
203    
204            * src/lmer.c: adjust checks in glmer_init for S4SXP
205            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
206            before S4SXP but for the wrong reasons.
207    
208    2006-08-08  Douglas Bates  <bates@R-project.org>
209    
210            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
211            Later modified to return the upper triangle only.
212            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
213    
214    2006-08-07  Douglas Bates  <bates@R-project.org>
215    
216            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
217            R-level conversion to a sparse symmetric class.
218            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
219            Remove conversion to sparse symmetric classes (now done in C code).
220    
221    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
224            * man/band.Rd:  adapt the \dontshow{} unit test.
225    
226    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * DESCRIPTION (Version): 0.995-14  for CRAN
229    
230            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
231    
232            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
233            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
234    
235            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
236            * R/Tsparse.R (tril, triu, band): methods
237            * R/dgRMatrix.R (tril, ...):    ditto
238            * man/band.Rd:                  ditto
239    
240    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Matrix.R (head, tail): directly use utils:::head.matrix
243                    to be up-to-date automatically.
244    
245    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
248    
249            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
250            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
251            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
252            such that the S4 objects are always created by the current version
253            of R and 'Matrix' class definitions.
254    
255    2006-08-01  Douglas Bates  <bates@R-project.org>
256    
257            * R/lmer.R (LMEoptimize method), tests/lmer.R,
258            inst/external/test3comp.rda: Added warnings for convergence on
259            boundary and test cases.
260    
261            * src/lmer.c (mer_postVar): Modified to return the variances that
262            are marginal to the fixed effects, not conditional on them (which
263            is what the bVar slot contents represent).
264    
265    2006-07-31  Douglas Bates  <bates@R-project.org>
266    
267            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
268            function which calls the C function mer_hat_trace2.
269    
270            * man/ranef.Rd: Include description of "postVar" argument and
271            producing a caterpillar plot.
272    
273    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * NAMESPACE:    change  "correlation" to "corMatrix"
276            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
277            * R/dpoMatrix.R: ditto
278            * R/lmer.R:      ditto
279    
280    2006-07-28  Douglas Bates  <bates@R-project.org>
281    
282            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
283            RZXinv slot's contents into a separate internal function that can
284            be used in mer_hat_trace.
285    
286    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
289            via new smart
290            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
291            utility functions.
292    
293    
294    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/Csparse.R (tril, triu, band): do return *triangular* classed
297            matrices when appropriate; band() even symmetric ones.
298            (replCmat): extend to potentially all "CsparseMatrix"
299            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
300            allow subassignment for special sparse matrices.
301    
302            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
303    
304            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
305            argument; in glmer_*(): print only if(verbose).
306    
307            speed-optimize a few places by moving REAL(.) out of loops.
308    
309            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
310    
311    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
314                    since that wrongly triggers also for M[ logi , ]
315    
316            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
317            a symmetric matrix that results in a non-symmetric one.
318            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
319    
320            * R/dMatrix.R: make round(M) work as round(M, 0)
321    
322            * R/dgTMatrix.R (image): coordinate system and axis now use
323            1-based indices, not 0-based ones.
324    
325            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
326            * tests/indexing.R: test it.
327    
328            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
329            * man/isSymmetric-methods.Rd: and document it.
330    
331            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
332            * man/SparseM-conv.Rd: docu them
333    
334            * tests/other-pkgs.R: renamed from tests/graph.R and add example
335                    for 'SparseM' conversions
336    
337    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
338    
339            * R/Matrix.R (head): added head() and tail() methods.
340    
341    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * DESCRIPTION (Version): 0.995-12 released to CRAN
344    
345    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * tests/simple.R: add check for correct dsT -> dgT coercion;
348                    add check for correct printing of symmetric sparse matrices.
349    
350            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
351            for sparse symmetric matrices.
352    
353            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
354            diagonal twice.
355    
356    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
357    
358            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
359            being applied to the x slot (detected by Brian Ripley).
360    
361    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
364    
365            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
366    
367    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * src/lgCMatrix.c (lgCMatrix_diag): new function
370            * R/lgCMatrix.R (diag): for new method
371    
372            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
373                 ==> construction of illegal "*gTMatrix" via new() should
374                 now be much less easy:
375            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
376    
377            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
378                    directly.
379            * man/Matrix.Rd: documents it.
380    
381    2006-07-06  Douglas Bates  <bates@R-project.org>
382    
383            * src/pedigree.c (pedigree_inbreeding): Correction in
384            initialization.  This function is not currently being used and is
385            not fully tested.
386    
387            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
388            Introduced the glmer class.  Added code for mcmcmsamp on glmer
389            objects.  Modified validity check on pedigree objects to account
390            for nonparallel patterns of missingness of parents.
391    
392            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
393            class.
394    
395    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/pMatrix.R: coercion pMatrix -> Tsparse
398    
399    2006-06-12  Douglas Bates  <bates@R-project.org>
400    
401            * DESCRIPTION (Version): 0.995-11 released to CRAN
402    
403            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
404            the output from mcmcsamp.
405    
406  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
407    
408          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
409            of the hat matrix.
410    
411  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
414          classes.          classes.
415            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
416    
417  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
# Line 43  Line 450 
450    
451          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
452          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.
453          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
454    
455    
456  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 573 
573          * 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)
574          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
575          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
576          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
577    
578  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
# Line 370  Line 777 
777  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
780          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
781          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
782    
783  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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