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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1481, Sat Sep 2 16:43:22 2006 UTC
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1    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * created branches/Matrix-for-R-2.3.x;  on trunk: do
4            * DESCRIPTION (Version): 0.9975-0
5            (Depends): R (>= 2.4.0)
6    
7    2006-09-01  Douglas Bates  <bates@R-project.org>
8    
9            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
10    
11    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
14            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
15    
16            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
17    
18    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
21            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
22            * R/dsparseMatrix.R: dito
23            * R/Csparse.R: dito
24    
25    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/dMatrix.R (Compare): improve availability of "<", etc
28            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
29    
30    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
33            of a 0-index which was used as 1-index (..hmm)
34    
35            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
36    
37            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
38            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
39            (.is.diagonal): dito
40    
41            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
42    
43            * R/Matrix.R (Matrix): also work for NA data
44    
45    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
48            in all cases.
49    
50    2006-08-27  Douglas Bates  <bates@R-project.org>
51    
52            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
53            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
54    
55    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
58            subclasses of "ddenseMatrix"
59            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
60            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
61            instead of half dozen specialized ones.
62    
63    2006-08-25  Douglas Bates  <bates@R-project.org>
64    
65            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
66            <tillard@cirad.fr> - ordering standard errors to match effects.
67    
68    2006-08-24  Douglas Bates  <bates@R-project.org>
69    
70            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
71            on R_ldl.
72            * R/lCholCMatrix.R,
73            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
74            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
75            * many files in ./R and ./src: Use more general version of
76            dup_mMatrix_as_dgeMatrix to simplify method definitions.
77            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
78            dtpMatrix, dspMatrix and dppMatrix conversions.
79    
80    
81    2006-08-23  Douglas Bates  <bates@R-project.org>
82    
83            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
84            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
85            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
86            dgeMatrix_crossprod (may need to do this in other places).
87            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
88            generic and method for dsCMatrix.  Use CHOLMOD for chol().
89    
90    2006-08-22  Douglas Bates  <bates@R-project.org>
91    
92            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
93            types of classed Matrices, matrices or numeric or logical vectors.
94            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
95            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
96            to Mutils.h (as an inline) and change name to Matrix_check_class;
97            fixes in as_cholmod_factor and chm_factor_to_SEXP.
98            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
99            dsCMatrix_matrix_solve.  Comment out vestigial functions.
100            * src/Csparse.c: use diag_P and uplo_P macros.
101    
102    2006-08-21  Douglas Bates  <bates@R-project.org>
103    
104            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
105            valgrind.
106            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
107            inverses.
108            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
109            -Wall warnings.
110            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
111            Use dup_mMatrix_as_dgeMatrix.
112    
113    2006-08-20  Douglas Bates  <bates@R-project.org>
114    
115            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
116            * tests/sparseQR.R: Added
117            * man/sparseQR-class.Rd: Document methods for qr.* generics
118            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
119    
120    2006-08-19  Douglas Bates  <bates@R-project.org>
121    
122            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
123            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
124            and qr.fitted.
125            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
126            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
127    
128    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
131            the base version has no "..." argument.
132    
133            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
134    
135            * R/Matrix.R: define and
136            * NAMESPACE: export as.numeric() and as.logical() methods.
137                    Let's hope these do not badly slow down something...
138            Finally export the zapsmall() method.
139    
140    2006-08-17  Douglas Bates  <bates@R-project.org>
141    
142            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
143            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
144            * src/dtCMatrix.c :Remove code that is no longer used
145            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
146    
147    2006-08-14  Douglas Bates  <bates@R-project.org>
148    
149            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
150            Csparse_to_logical and Csparse_symmetric_to_general.
151            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
152            coercion methods between CsparseMatrix and TsparseMatrix.
153    
154    2006-08-14  Douglas Bates  <bates@R-project.org>
155    
156            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
157            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
158            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
159            possible.
160    
161    2006-08-12  Douglas Bates  <bates@R-project.org>
162    
163            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
164              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
165              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
166              generalize conversions between TsparseMatrix, CsparseMatrix,
167              denseMatrix and matrix.  Preserve triangularity property and
168              propagate Dimnames in the easy cases.
169    
170    2006-08-10  Douglas Bates  <bates@R-project.org>
171    
172            * src/lmer.c: adjust checks in glmer_init for S4SXP
173            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
174            before S4SXP but for the wrong reasons.
175    
176    2006-08-08  Douglas Bates  <bates@R-project.org>
177    
178            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
179            Later modified to return the upper triangle only.
180            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
181    
182    2006-08-07  Douglas Bates  <bates@R-project.org>
183    
184            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
185            R-level conversion to a sparse symmetric class.
186            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
187            Remove conversion to sparse symmetric classes (now done in C code).
188    
189    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
192            * man/band.Rd:  adapt the \dontshow{} unit test.
193    
194    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * DESCRIPTION (Version): 0.995-14  for CRAN
197    
198            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
199    
200            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
201            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
202    
203            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
204            * R/Tsparse.R (tril, triu, band): methods
205            * R/dgRMatrix.R (tril, ...):    ditto
206            * man/band.Rd:                  ditto
207    
208    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Matrix.R (head, tail): directly use utils:::head.matrix
211                    to be up-to-date automatically.
212    
213    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
216    
217            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
218            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
219            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
220            such that the S4 objects are always created by the current version
221            of R and 'Matrix' class definitions.
222    
223    2006-08-01  Douglas Bates  <bates@R-project.org>
224    
225            * R/lmer.R (LMEoptimize method), tests/lmer.R,
226            inst/external/test3comp.rda: Added warnings for convergence on
227            boundary and test cases.
228    
229            * src/lmer.c (mer_postVar): Modified to return the variances that
230            are marginal to the fixed effects, not conditional on them (which
231            is what the bVar slot contents represent).
232    
233    2006-07-31  Douglas Bates  <bates@R-project.org>
234    
235            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
236            function which calls the C function mer_hat_trace2.
237    
238            * man/ranef.Rd: Include description of "postVar" argument and
239            producing a caterpillar plot.
240    
241    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * NAMESPACE:    change  "correlation" to "corMatrix"
244            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
245            * R/dpoMatrix.R: ditto
246            * R/lmer.R:      ditto
247    
248    2006-07-28  Douglas Bates  <bates@R-project.org>
249    
250            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
251            RZXinv slot's contents into a separate internal function that can
252            be used in mer_hat_trace.
253    
254    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
257            via new smart
258            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
259            utility functions.
260    
261    
262    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Csparse.R (tril, triu, band): do return *triangular* classed
265            matrices when appropriate; band() even symmetric ones.
266            (replCmat): extend to potentially all "CsparseMatrix"
267            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
268            allow subassignment for special sparse matrices.
269    
270            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
271    
272            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
273            argument; in glmer_*(): print only if(verbose).
274    
275            speed-optimize a few places by moving REAL(.) out of loops.
276    
277            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
278    
279    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
282                    since that wrongly triggers also for M[ logi , ]
283    
284            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
285            a symmetric matrix that results in a non-symmetric one.
286            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
287    
288            * R/dMatrix.R: make round(M) work as round(M, 0)
289    
290            * R/dgTMatrix.R (image): coordinate system and axis now use
291            1-based indices, not 0-based ones.
292    
293            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
294            * tests/indexing.R: test it.
295    
296            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
297            * man/isSymmetric-methods.Rd: and document it.
298    
299            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
300            * man/SparseM-conv.Rd: docu them
301    
302            * tests/other-pkgs.R: renamed from tests/graph.R and add example
303                    for 'SparseM' conversions
304    
305    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
306    
307            * R/Matrix.R (head): added head() and tail() methods.
308    
309    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * DESCRIPTION (Version): 0.995-12 released to CRAN
312    
313    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * tests/simple.R: add check for correct dsT -> dgT coercion;
316                    add check for correct printing of symmetric sparse matrices.
317    
318            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
319            for sparse symmetric matrices.
320    
321            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
322            diagonal twice.
323    
324    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
325    
326            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
327            being applied to the x slot (detected by Brian Ripley).
328    
329    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
332    
333            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
334    
335    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * src/lgCMatrix.c (lgCMatrix_diag): new function
338            * R/lgCMatrix.R (diag): for new method
339    
340            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
341                 ==> construction of illegal "*gTMatrix" via new() should
342                 now be much less easy:
343            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
344    
345            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
346                    directly.
347            * man/Matrix.Rd: documents it.
348    
349    2006-07-06  Douglas Bates  <bates@R-project.org>
350    
351            * src/pedigree.c (pedigree_inbreeding): Correction in
352            initialization.  This function is not currently being used and is
353            not fully tested.
354    
355            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
356            Introduced the glmer class.  Added code for mcmcmsamp on glmer
357            objects.  Modified validity check on pedigree objects to account
358            for nonparallel patterns of missingness of parents.
359    
360            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
361            class.
362    
363    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/pMatrix.R: coercion pMatrix -> Tsparse
366    
367    2006-06-12  Douglas Bates  <bates@R-project.org>
368    
369            * DESCRIPTION (Version): 0.995-11 released to CRAN
370    
371            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
372            the output from mcmcsamp.
373    
374    2006-06-10  Douglas Bates  <bates@R-project.org>
375    
376            * R/lmer.R (simulestimate): added C code for calculating the trace
377            of the hat matrix.
378    
379    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
382            classes.
383            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
384    
385    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/dgTMatrix.R (colSums): etc. All four of
388            colSums(), rowSums(), colMeans(), rowMeans() now should work for
389            all "Matrices".
390    
391  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
392    
393          * R/lmer.R (panel.ci): Add a reference line at zero and a          * R/lmer.R (panel.ci): Add a reference line at zero and a
# Line 28  Line 418 
418    
419          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
420          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.
421          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
422    
423    
424  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 541 
541          * 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)
542          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
543          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
544          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
545    
546  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
# Line 355  Line 745 
745  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
748          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
749          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
750    
751  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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