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revision 1342, Tue Aug 1 20:26:45 2006 UTC revision 1624, Wed Oct 11 15:00:11 2006 UTC
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1    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
4            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
5    
6    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/dgCMatrix.R: deprecate the writeHB function.  Use writeMM instead.
9    
10    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * DESCRIPTION (Version): 0.9975-3
13    
14            * R/diagMatrix.R (bdiag): new function constructing block diagonal
15            (sparse) matrices.
16            * man/bdiag.Rd: docu + examples
17    
18            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
19    
20            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
21            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
22    
23            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
24            that result is sparse or diagonal (and not dense).
25    
26            * man/Subassign-methods.Rd: fix examples
27    
28            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
29            should always return a sparse (and not sometimes a diagonal) matrix.
30    
31    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
34    
35    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * DESCRIPTION (Version): 0.9975-2
38    
39            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
40    
41    2006-10-02  Douglas Bates  <bates@R-project.org>
42    
43            * tests/dg_Matrix.R: Simplify test taking into account new code.
44    
45    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
48    
49            * R/lsTMatrix.R: new files w/ missing methods
50            * R/nsTMatrix.R:  "  'for completeness'
51    
52            * tests/Class+Meth.R: a bit less 'not.ok.classes'
53    
54            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
55    
56    
57    2006-09-28  Douglas Bates  <bates@R-project.org>
58    
59            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
60            included.
61    
62            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
63            Export C-callable functions used in Zt_create in lme4.
64    
65    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * DESCRIPTION (Version): 0.9975-1
68    
69            * tests/simple.R: less checks fail; using NA, found that our
70                    kronecker() is not base-compatible with NA's.
71    
72            * R/dMatrix.R: "Compare" method now implemented for all cases
73    
74            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
75    
76            * man/dtpMatrix-class.Rd: mention length of 'x' slot
77    
78            * src/dtpMatrix.c (dtpMatrix_validate): fix check
79            * src/dspMatrix.c (dspMatrix_validate): ditto
80    
81            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
82              including coercion to [nl]tTMatrix.
83    
84            * R/diagMatrix.R (show): print a header line as for other classes.
85    
86    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * src/Makefile.win (SUBDIRS): fix typo
89    
90    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
93    
94    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
97            symmetric and y missing in R code using %*% (cholmod_aat doesn't
98            accept a symmetric matrix).
99            * tests/group-methods.R: Uncomment test of crossprod applied to
100            lsCMatrix objects.
101    
102    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/AllClass.R (symmetricMatrix): add validity method (available
105            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
106    
107            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
108    
109            * tests/indexing.Rout.save:
110            * tests/indexing.R: additions, mainly for 'lsparse'
111    
112            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
113            case.
114    
115            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
116    
117    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
120                    as 'N' (1-letter - Ok?)
121    
122            * tests/group-methods.R: add test for logical + NAs
123    
124            * R/dMatrix.R ("Compare"): fix to work with NA's
125    
126            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
127    
128            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
129                    which is implemented.
130    
131    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * src/chm_common.c: coerce logical <-> double instead of
134            typecasting;  needed for "l" matrix handling in cholmod.
135    
136            * tests/other-pkgs.R (graph): small extension in "graph" checks.
137    
138            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
139            (Tsp2grNEL): other fixes needed
140    
141    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
144                    Matrices, since "lMatrix", also "lsparseM" can have NA
145            * R/ndenseMatrix.R, etc: new source files
146            * man/nsparseMatrix-classes.Rd, etc: new help files
147            * tests/: adaptions
148            * src/chm_common.c (chm_dense_to_SEXP): and others:
149                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
150            * src/Csparse.c, etc: ditto
151    
152    2006-09-11  Douglas Bates  <bates@R-project.org>
153    
154            * src/Mutils.[ch],init.c inst/include/*.h: Move the
155            alloc_d**Matrix functions to the lme4 package.
156    
157    2006-09-09  Douglas Bates  <bates@R-project.org>
158    
159            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
160            fixed
161    
162    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/lMatrix.R: new
165    
166            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
167    
168            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
169            * man/tcrossprod.Rd: ditto
170    
171    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
172    
173            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
174            for exported functions
175            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
176            Remove partitioning algorithms for sparse matrix reordering.  The
177            copyright on the Metis code was problematic and the methods were
178            rarely used.
179            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
180            operations are now done entirely in CHOLMOD code.
181    
182    2006-09-06  Douglas Bates  <bates@R-project.org>
183    
184            * src/Mutils.h: Remove functions that are no longer used.
185    
186    2006-09-04  Douglas Bates  <bates@R-project.org>
187    
188            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
189            * src/DEPS.mkf: update
190    
191    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * created branches/Matrix-for-R-2.3.x;  on trunk: do
194            * DESCRIPTION (Version): 0.9975-0
195            (Depends): R (>= 2.4.0)
196    
197    2006-09-01  Douglas Bates  <bates@R-project.org>
198    
199            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
200    
201    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
204            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
205    
206            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
207    
208    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
211            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
212            * R/dsparseMatrix.R: ditto
213            * R/Csparse.R: ditto
214    
215    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/dMatrix.R (Compare): improve availability of "<", etc
218            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
219    
220    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
223            of a 0-index which was used as 1-index (..hmm)
224    
225            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
226    
227            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
228            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
229            (.is.diagonal): ditto
230    
231            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
232    
233            * R/Matrix.R (Matrix): also work for NA data
234    
235    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
238            in all cases.
239    
240    2006-08-27  Douglas Bates  <bates@R-project.org>
241    
242            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
243            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
244    
245    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
248            subclasses of "ddenseMatrix"
249            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
250            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
251            instead of half dozen specialized ones.
252    
253    2006-08-25  Douglas Bates  <bates@R-project.org>
254    
255            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
256            <tillard@cirad.fr> - ordering standard errors to match effects.
257    
258    2006-08-24  Douglas Bates  <bates@R-project.org>
259    
260            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
261            on R_ldl.
262            * R/lCholCMatrix.R,
263            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
264            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
265            * many files in ./R and ./src: Use more general version of
266            dup_mMatrix_as_dgeMatrix to simplify method definitions.
267            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
268            dtpMatrix, dspMatrix and dppMatrix conversions.
269    
270    
271    2006-08-23  Douglas Bates  <bates@R-project.org>
272    
273            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
274            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
275            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
276            dgeMatrix_crossprod (may need to do this in other places).
277            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
278            generic and method for dsCMatrix.  Use CHOLMOD for chol().
279    
280    2006-08-22  Douglas Bates  <bates@R-project.org>
281    
282            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
283            types of classed Matrices, matrices or numeric or logical vectors.
284            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
285            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
286            to Mutils.h (as an inline) and change name to Matrix_check_class;
287            fixes in as_cholmod_factor and chm_factor_to_SEXP.
288            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
289            dsCMatrix_matrix_solve.  Comment out vestigial functions.
290            * src/Csparse.c: use diag_P and uplo_P macros.
291    
292    2006-08-21  Douglas Bates  <bates@R-project.org>
293    
294            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
295            valgrind.
296            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
297            inverses.
298            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
299            -Wall warnings.
300            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
301            Use dup_mMatrix_as_dgeMatrix.
302    
303    2006-08-20  Douglas Bates  <bates@R-project.org>
304    
305            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
306            * tests/sparseQR.R: Added
307            * man/sparseQR-class.Rd: Document methods for qr.* generics
308            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
309    
310    2006-08-19  Douglas Bates  <bates@R-project.org>
311    
312            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
313            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
314            and qr.fitted.
315            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
316            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
317    
318    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
321            the base version has no "..." argument.
322    
323            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
324    
325            * R/Matrix.R: define and
326            * NAMESPACE: export as.numeric() and as.logical() methods.
327                    Let's hope these do not badly slow down something...
328            Finally export the zapsmall() method.
329    
330    2006-08-17  Douglas Bates  <bates@R-project.org>
331    
332            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
333            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
334            * src/dtCMatrix.c :Remove code that is no longer used
335            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
336    
337    2006-08-14  Douglas Bates  <bates@R-project.org>
338    
339            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
340            Csparse_to_logical and Csparse_symmetric_to_general.
341            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
342            coercion methods between CsparseMatrix and TsparseMatrix.
343    
344    2006-08-14  Douglas Bates  <bates@R-project.org>
345    
346            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
347            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
348            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
349            possible.
350    
351    2006-08-12  Douglas Bates  <bates@R-project.org>
352    
353            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
354              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
355              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
356              generalize conversions between TsparseMatrix, CsparseMatrix,
357              denseMatrix and matrix.  Preserve triangularity property and
358              propagate Dimnames in the easy cases.
359    
360    2006-08-10  Douglas Bates  <bates@R-project.org>
361    
362            * src/lmer.c: adjust checks in glmer_init for S4SXP
363            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
364            before S4SXP but for the wrong reasons.
365    
366    2006-08-08  Douglas Bates  <bates@R-project.org>
367    
368            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
369            Later modified to return the upper triangle only.
370            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
371    
372    2006-08-07  Douglas Bates  <bates@R-project.org>
373    
374            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
375            R-level conversion to a sparse symmetric class.
376            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
377            Remove conversion to sparse symmetric classes (now done in C code).
378    
379    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
382            * man/band.Rd:  adapt the \dontshow{} unit test.
383    
384    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * DESCRIPTION (Version): 0.995-14  for CRAN
387    
388            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
389    
390            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
391            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
392    
393            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
394            * R/Tsparse.R (tril, triu, band): methods
395            * R/dgRMatrix.R (tril, ...):    ditto
396            * man/band.Rd:                  ditto
397    
398    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Matrix.R (head, tail): directly use utils:::head.matrix
401                    to be up-to-date automatically.
402    
403    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
406    
407            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
408            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
409            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
410            such that the S4 objects are always created by the current version
411            of R and 'Matrix' class definitions.
412    
413  2006-08-01  Douglas Bates  <bates@R-project.org>  2006-08-01  Douglas Bates  <bates@R-project.org>
414    
415          * R/lmer.R (LMEoptimize method), tests/lmer.R,          * R/lmer.R (LMEoptimize method), tests/lmer.R,
# Line 20  Line 432 
432    
433          * NAMESPACE:    change  "correlation" to "corMatrix"          * NAMESPACE:    change  "correlation" to "corMatrix"
434          * R/AllClass.R: to avoid clash with S3 class in 'nlme'.          * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
435          * R/dpoMatrix.R: dito          * R/dpoMatrix.R: ditto
436          * R/lmer.R:      dito          * R/lmer.R:      ditto
437    
438  2006-07-28  Douglas Bates  <bates@R-project.org>  2006-07-28  Douglas Bates  <bates@R-project.org>
439    
# Line 196  Line 608 
608    
609          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
610          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.
611          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
612    
613    
614  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 319  Line 731 
731          * 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)
732          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
733          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
734          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
735    
736  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
# Line 523  Line 935 
935  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
936    
937          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
938          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
939          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
940    
941  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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