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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1517, Wed Sep 6 13:34:03 2006 UTC
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1    2006-09-06  Douglas Bates  <bates@R-project.org>
2    
3            * src/Mutils.h: Remove functions that are no longer used.
4    
5    2006-09-04  Douglas Bates  <bates@R-project.org>
6    
7            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
8            * src/DEPS.mkf: update
9    
10    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * created branches/Matrix-for-R-2.3.x;  on trunk: do
13            * DESCRIPTION (Version): 0.9975-0
14            (Depends): R (>= 2.4.0)
15    
16    2006-09-01  Douglas Bates  <bates@R-project.org>
17    
18            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
19    
20    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
23            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
24    
25            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
26    
27    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
30            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
31            * R/dsparseMatrix.R: dito
32            * R/Csparse.R: dito
33    
34    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/dMatrix.R (Compare): improve availability of "<", etc
37            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
38    
39    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
42            of a 0-index which was used as 1-index (..hmm)
43    
44            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
45    
46            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
47            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
48            (.is.diagonal): dito
49    
50            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
51    
52            * R/Matrix.R (Matrix): also work for NA data
53    
54    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
57            in all cases.
58    
59    2006-08-27  Douglas Bates  <bates@R-project.org>
60    
61            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
62            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
63    
64    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
67            subclasses of "ddenseMatrix"
68            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
69            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
70            instead of half dozen specialized ones.
71    
72    2006-08-25  Douglas Bates  <bates@R-project.org>
73    
74            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
75            <tillard@cirad.fr> - ordering standard errors to match effects.
76    
77    2006-08-24  Douglas Bates  <bates@R-project.org>
78    
79            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
80            on R_ldl.
81            * R/lCholCMatrix.R,
82            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
83            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
84            * many files in ./R and ./src: Use more general version of
85            dup_mMatrix_as_dgeMatrix to simplify method definitions.
86            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
87            dtpMatrix, dspMatrix and dppMatrix conversions.
88    
89    
90    2006-08-23  Douglas Bates  <bates@R-project.org>
91    
92            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
93            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
94            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
95            dgeMatrix_crossprod (may need to do this in other places).
96            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
97            generic and method for dsCMatrix.  Use CHOLMOD for chol().
98    
99    2006-08-22  Douglas Bates  <bates@R-project.org>
100    
101            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
102            types of classed Matrices, matrices or numeric or logical vectors.
103            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
104            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
105            to Mutils.h (as an inline) and change name to Matrix_check_class;
106            fixes in as_cholmod_factor and chm_factor_to_SEXP.
107            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
108            dsCMatrix_matrix_solve.  Comment out vestigial functions.
109            * src/Csparse.c: use diag_P and uplo_P macros.
110    
111    2006-08-21  Douglas Bates  <bates@R-project.org>
112    
113            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
114            valgrind.
115            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
116            inverses.
117            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
118            -Wall warnings.
119            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
120            Use dup_mMatrix_as_dgeMatrix.
121    
122    2006-08-20  Douglas Bates  <bates@R-project.org>
123    
124            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
125            * tests/sparseQR.R: Added
126            * man/sparseQR-class.Rd: Document methods for qr.* generics
127            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
128    
129    2006-08-19  Douglas Bates  <bates@R-project.org>
130    
131            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
132            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
133            and qr.fitted.
134            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
135            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
136    
137    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
140            the base version has no "..." argument.
141    
142            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
143    
144            * R/Matrix.R: define and
145            * NAMESPACE: export as.numeric() and as.logical() methods.
146                    Let's hope these do not badly slow down something...
147            Finally export the zapsmall() method.
148    
149    2006-08-17  Douglas Bates  <bates@R-project.org>
150    
151            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
152            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
153            * src/dtCMatrix.c :Remove code that is no longer used
154            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
155    
156    2006-08-14  Douglas Bates  <bates@R-project.org>
157    
158            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
159            Csparse_to_logical and Csparse_symmetric_to_general.
160            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
161            coercion methods between CsparseMatrix and TsparseMatrix.
162    
163    2006-08-14  Douglas Bates  <bates@R-project.org>
164    
165            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
166            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
167            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
168            possible.
169    
170    2006-08-12  Douglas Bates  <bates@R-project.org>
171    
172            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
173              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
174              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
175              generalize conversions between TsparseMatrix, CsparseMatrix,
176              denseMatrix and matrix.  Preserve triangularity property and
177              propagate Dimnames in the easy cases.
178    
179    2006-08-10  Douglas Bates  <bates@R-project.org>
180    
181            * src/lmer.c: adjust checks in glmer_init for S4SXP
182            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
183            before S4SXP but for the wrong reasons.
184    
185    2006-08-08  Douglas Bates  <bates@R-project.org>
186    
187            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
188            Later modified to return the upper triangle only.
189            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
190    
191    2006-08-07  Douglas Bates  <bates@R-project.org>
192    
193            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
194            R-level conversion to a sparse symmetric class.
195            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
196            Remove conversion to sparse symmetric classes (now done in C code).
197    
198    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
201            * man/band.Rd:  adapt the \dontshow{} unit test.
202    
203    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * DESCRIPTION (Version): 0.995-14  for CRAN
206    
207            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
208    
209            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
210            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
211    
212            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
213            * R/Tsparse.R (tril, triu, band): methods
214            * R/dgRMatrix.R (tril, ...):    ditto
215            * man/band.Rd:                  ditto
216    
217    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Matrix.R (head, tail): directly use utils:::head.matrix
220                    to be up-to-date automatically.
221    
222    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
225    
226            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
227            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
228            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
229            such that the S4 objects are always created by the current version
230            of R and 'Matrix' class definitions.
231    
232    2006-08-01  Douglas Bates  <bates@R-project.org>
233    
234            * R/lmer.R (LMEoptimize method), tests/lmer.R,
235            inst/external/test3comp.rda: Added warnings for convergence on
236            boundary and test cases.
237    
238            * src/lmer.c (mer_postVar): Modified to return the variances that
239            are marginal to the fixed effects, not conditional on them (which
240            is what the bVar slot contents represent).
241    
242    2006-07-31  Douglas Bates  <bates@R-project.org>
243    
244            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
245            function which calls the C function mer_hat_trace2.
246    
247            * man/ranef.Rd: Include description of "postVar" argument and
248            producing a caterpillar plot.
249    
250    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * NAMESPACE:    change  "correlation" to "corMatrix"
253            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
254            * R/dpoMatrix.R: ditto
255            * R/lmer.R:      ditto
256    
257    2006-07-28  Douglas Bates  <bates@R-project.org>
258    
259            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
260            RZXinv slot's contents into a separate internal function that can
261            be used in mer_hat_trace.
262    
263    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
266            via new smart
267            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
268            utility functions.
269    
270    
271    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/Csparse.R (tril, triu, band): do return *triangular* classed
274            matrices when appropriate; band() even symmetric ones.
275            (replCmat): extend to potentially all "CsparseMatrix"
276            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
277            allow subassignment for special sparse matrices.
278    
279            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
280    
281            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
282            argument; in glmer_*(): print only if(verbose).
283    
284            speed-optimize a few places by moving REAL(.) out of loops.
285    
286            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
287    
288    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
291                    since that wrongly triggers also for M[ logi , ]
292    
293            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
294            a symmetric matrix that results in a non-symmetric one.
295            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
296    
297            * R/dMatrix.R: make round(M) work as round(M, 0)
298    
299            * R/dgTMatrix.R (image): coordinate system and axis now use
300            1-based indices, not 0-based ones.
301    
302            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
303            * tests/indexing.R: test it.
304    
305            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
306            * man/isSymmetric-methods.Rd: and document it.
307    
308            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
309            * man/SparseM-conv.Rd: docu them
310    
311            * tests/other-pkgs.R: renamed from tests/graph.R and add example
312                    for 'SparseM' conversions
313    
314    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
315    
316            * R/Matrix.R (head): added head() and tail() methods.
317    
318    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * DESCRIPTION (Version): 0.995-12 released to CRAN
321    
322    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * tests/simple.R: add check for correct dsT -> dgT coercion;
325                    add check for correct printing of symmetric sparse matrices.
326    
327            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
328            for sparse symmetric matrices.
329    
330            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
331            diagonal twice.
332    
333    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
334    
335            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
336            being applied to the x slot (detected by Brian Ripley).
337    
338    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
341    
342            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
343    
344    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * src/lgCMatrix.c (lgCMatrix_diag): new function
347            * R/lgCMatrix.R (diag): for new method
348    
349            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
350                 ==> construction of illegal "*gTMatrix" via new() should
351                 now be much less easy:
352            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
353    
354            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
355                    directly.
356            * man/Matrix.Rd: documents it.
357    
358    2006-07-06  Douglas Bates  <bates@R-project.org>
359    
360            * src/pedigree.c (pedigree_inbreeding): Correction in
361            initialization.  This function is not currently being used and is
362            not fully tested.
363    
364            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
365            Introduced the glmer class.  Added code for mcmcmsamp on glmer
366            objects.  Modified validity check on pedigree objects to account
367            for nonparallel patterns of missingness of parents.
368    
369            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
370            class.
371    
372    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * R/pMatrix.R: coercion pMatrix -> Tsparse
375    
376    2006-06-12  Douglas Bates  <bates@R-project.org>
377    
378            * DESCRIPTION (Version): 0.995-11 released to CRAN
379    
380            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
381            the output from mcmcsamp.
382    
383    2006-06-10  Douglas Bates  <bates@R-project.org>
384    
385            * R/lmer.R (simulestimate): added C code for calculating the trace
386            of the hat matrix.
387    
388    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
391            classes.
392            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
393    
394    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/dgTMatrix.R (colSums): etc. All four of
397            colSums(), rowSums(), colMeans(), rowMeans() now should work for
398            all "Matrices".
399    
400    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
401    
402            * R/lmer.R (panel.ci): Add a reference line at zero and a
403            background grid to the qqmath plot of ranef.lmer.
404    
405    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
406    
407            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
408            grouping factors to be specified in the formula as (1|foo/bar).
409    
410    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
411    
412            * R/lmer.R (findbars and others): Change check of is.numeric to
413            !is.language to resolve the bug reported by Jacob Wegelin.
414    
415            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
416            code to evaluate inbreeding coefficients without calculating T,
417            based on code in Sargolzaei and Iwaisaki's paper.
418    
419    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
420    
421            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
422            generic and mer methods for isNested and denomDF. This denomDF was
423            an attempt to emulate that in lme but I don't think that makes
424            sense.  Use the trace of the hat matrix instead.
425    
426  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
429          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.
430          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
431    
432    
433  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 550 
550          * 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)
551          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
552          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
553          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
554    
555  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
# Line 329  Line 754 
754  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
757          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
758          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
759    
760  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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