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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1475, Fri Sep 1 22:35:59 2006 UTC
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1    2006-09-01  Douglas Bates  <bates@R-project.org>
2    
3            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
4    
5    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
8            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
9    
10            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
11    
12    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
15            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
16            * R/dsparseMatrix.R: dito
17            * R/Csparse.R: dito
18    
19    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/dMatrix.R (Compare): improve availability of "<", etc
22            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
23    
24    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
27            of a 0-index which was used as 1-index (..hmm)
28    
29            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
30    
31            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
32            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
33            (.is.diagonal): dito
34    
35            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
36    
37            * R/Matrix.R (Matrix): also work for NA data
38    
39    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
42            in all cases.
43    
44    2006-08-27  Douglas Bates  <bates@R-project.org>
45    
46            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
47            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
48    
49    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
52            subclasses of "ddenseMatrix"
53            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
54            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
55            instead of half dozen specialized ones.
56    
57    2006-08-25  Douglas Bates  <bates@R-project.org>
58    
59            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
60            <tillard@cirad.fr> - ordering standard errors to match effects.
61    
62    2006-08-24  Douglas Bates  <bates@R-project.org>
63    
64            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
65            on R_ldl.
66            * R/lCholCMatrix.R,
67            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
68            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
69            * many files in ./R and ./src: Use more general version of
70            dup_mMatrix_as_dgeMatrix to simplify method definitions.
71            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
72            dtpMatrix, dspMatrix and dppMatrix conversions.
73    
74    
75    2006-08-23  Douglas Bates  <bates@R-project.org>
76    
77            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
78            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
79            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
80            dgeMatrix_crossprod (may need to do this in other places).
81            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
82            generic and method for dsCMatrix.  Use CHOLMOD for chol().
83    
84    2006-08-22  Douglas Bates  <bates@R-project.org>
85    
86            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
87            types of classed Matrices, matrices or numeric or logical vectors.
88            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
89            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
90            to Mutils.h (as an inline) and change name to Matrix_check_class;
91            fixes in as_cholmod_factor and chm_factor_to_SEXP.
92            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
93            dsCMatrix_matrix_solve.  Comment out vestigial functions.
94            * src/Csparse.c: use diag_P and uplo_P macros.
95    
96    2006-08-21  Douglas Bates  <bates@R-project.org>
97    
98            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
99            valgrind.
100            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
101            inverses.
102            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
103            -Wall warnings.
104            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
105            Use dup_mMatrix_as_dgeMatrix.
106    
107    2006-08-20  Douglas Bates  <bates@R-project.org>
108    
109            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
110            * tests/sparseQR.R: Added
111            * man/sparseQR-class.Rd: Document methods for qr.* generics
112            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
113    
114    2006-08-19  Douglas Bates  <bates@R-project.org>
115    
116            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
117            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
118            and qr.fitted.
119            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
120            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
121    
122    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
125            the base version has no "..." argument.
126    
127            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
128    
129            * R/Matrix.R: define and
130            * NAMESPACE: export as.numeric() and as.logical() methods.
131                    Let's hope these do not badly slow down something...
132            Finally export the zapsmall() method.
133    
134    2006-08-17  Douglas Bates  <bates@R-project.org>
135    
136            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
137            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
138            * src/dtCMatrix.c :Remove code that is no longer used
139            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
140    
141    2006-08-14  Douglas Bates  <bates@R-project.org>
142    
143            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
144            Csparse_to_logical and Csparse_symmetric_to_general.
145            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
146            coercion methods between CsparseMatrix and TsparseMatrix.
147    
148    2006-08-14  Douglas Bates  <bates@R-project.org>
149    
150            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
151            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
152            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
153            possible.
154    
155    2006-08-12  Douglas Bates  <bates@R-project.org>
156    
157            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
158              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
159              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
160              generalize conversions between TsparseMatrix, CsparseMatrix,
161              denseMatrix and matrix.  Preserve triangularity property and
162              propagate Dimnames in the easy cases.
163    
164    2006-08-10  Douglas Bates  <bates@R-project.org>
165    
166            * src/lmer.c: adjust checks in glmer_init for S4SXP
167            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
168            before S4SXP but for the wrong reasons.
169    
170    2006-08-08  Douglas Bates  <bates@R-project.org>
171    
172            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
173            Later modified to return the upper triangle only.
174            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
175    
176    2006-08-07  Douglas Bates  <bates@R-project.org>
177    
178            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
179            R-level conversion to a sparse symmetric class.
180            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
181            Remove conversion to sparse symmetric classes (now done in C code).
182    
183    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
186            * man/band.Rd:  adapt the \dontshow{} unit test.
187    
188    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * DESCRIPTION (Version): 0.995-14  for CRAN
191    
192            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
193    
194            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
195            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
196    
197            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
198            * R/Tsparse.R (tril, triu, band): methods
199            * R/dgRMatrix.R (tril, ...):    ditto
200            * man/band.Rd:                  ditto
201    
202    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/Matrix.R (head, tail): directly use utils:::head.matrix
205                    to be up-to-date automatically.
206    
207    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
210    
211            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
212            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
213            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
214            such that the S4 objects are always created by the current version
215            of R and 'Matrix' class definitions.
216    
217    2006-08-01  Douglas Bates  <bates@R-project.org>
218    
219            * R/lmer.R (LMEoptimize method), tests/lmer.R,
220            inst/external/test3comp.rda: Added warnings for convergence on
221            boundary and test cases.
222    
223            * src/lmer.c (mer_postVar): Modified to return the variances that
224            are marginal to the fixed effects, not conditional on them (which
225            is what the bVar slot contents represent).
226    
227    2006-07-31  Douglas Bates  <bates@R-project.org>
228    
229            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
230            function which calls the C function mer_hat_trace2.
231    
232            * man/ranef.Rd: Include description of "postVar" argument and
233            producing a caterpillar plot.
234    
235    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * NAMESPACE:    change  "correlation" to "corMatrix"
238            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
239            * R/dpoMatrix.R: ditto
240            * R/lmer.R:      ditto
241    
242    2006-07-28  Douglas Bates  <bates@R-project.org>
243    
244            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
245            RZXinv slot's contents into a separate internal function that can
246            be used in mer_hat_trace.
247    
248    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
251            via new smart
252            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
253            utility functions.
254    
255    
256    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/Csparse.R (tril, triu, band): do return *triangular* classed
259            matrices when appropriate; band() even symmetric ones.
260            (replCmat): extend to potentially all "CsparseMatrix"
261            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
262            allow subassignment for special sparse matrices.
263    
264            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
265    
266            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
267            argument; in glmer_*(): print only if(verbose).
268    
269            speed-optimize a few places by moving REAL(.) out of loops.
270    
271            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
272    
273    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
276                    since that wrongly triggers also for M[ logi , ]
277    
278            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
279            a symmetric matrix that results in a non-symmetric one.
280            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
281    
282            * R/dMatrix.R: make round(M) work as round(M, 0)
283    
284            * R/dgTMatrix.R (image): coordinate system and axis now use
285            1-based indices, not 0-based ones.
286    
287            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
288            * tests/indexing.R: test it.
289    
290            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
291            * man/isSymmetric-methods.Rd: and document it.
292    
293            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
294            * man/SparseM-conv.Rd: docu them
295    
296            * tests/other-pkgs.R: renamed from tests/graph.R and add example
297                    for 'SparseM' conversions
298    
299    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
300    
301            * R/Matrix.R (head): added head() and tail() methods.
302    
303    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * DESCRIPTION (Version): 0.995-12 released to CRAN
306    
307    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * tests/simple.R: add check for correct dsT -> dgT coercion;
310                    add check for correct printing of symmetric sparse matrices.
311    
312            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
313            for sparse symmetric matrices.
314    
315            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
316            diagonal twice.
317    
318    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
319    
320            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
321            being applied to the x slot (detected by Brian Ripley).
322    
323    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
326    
327            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
328    
329    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * src/lgCMatrix.c (lgCMatrix_diag): new function
332            * R/lgCMatrix.R (diag): for new method
333    
334            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
335                 ==> construction of illegal "*gTMatrix" via new() should
336                 now be much less easy:
337            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
338    
339            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
340                    directly.
341            * man/Matrix.Rd: documents it.
342    
343    2006-07-06  Douglas Bates  <bates@R-project.org>
344    
345            * src/pedigree.c (pedigree_inbreeding): Correction in
346            initialization.  This function is not currently being used and is
347            not fully tested.
348    
349            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
350            Introduced the glmer class.  Added code for mcmcmsamp on glmer
351            objects.  Modified validity check on pedigree objects to account
352            for nonparallel patterns of missingness of parents.
353    
354            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
355            class.
356    
357    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/pMatrix.R: coercion pMatrix -> Tsparse
360    
361    2006-06-12  Douglas Bates  <bates@R-project.org>
362    
363            * DESCRIPTION (Version): 0.995-11 released to CRAN
364    
365            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
366            the output from mcmcsamp.
367    
368  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
369    
370          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
371            of the hat matrix.
372    
373  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
376          classes.          classes.
377            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
378    
379  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
# Line 43  Line 412 
412    
413          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
414          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.
415          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
416    
417    
418  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 535 
535          * 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)
536          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
537          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
538          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
539    
540  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
# Line 370  Line 739 
739  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
742          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
743          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
744    
745  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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