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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1447, Fri Aug 25 20:38:36 2006 UTC
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1    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
4            subclasses of "ddenseMatrix"
5            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
6            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
7            instead of half dozen specialized ones.
8    
9    2006-08-25  Douglas Bates  <bates@R-project.org>
10    
11            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
12            <tillard@cirad.fr> - ordering standard errors to match effects.
13    
14    2006-08-24  Douglas Bates  <bates@R-project.org>
15    
16            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
17            on R_ldl.
18            * R/lCholCMatrix.R,
19            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
20            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
21            * many files in ./R and ./src: Use more general version of
22            dup_mMatrix_as_dgeMatrix to simplify method definitions.
23            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
24            dtpMatrix, dspMatrix and dppMatrix conversions.
25    
26    
27    2006-08-23  Douglas Bates  <bates@R-project.org>
28    
29            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
30            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
31            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
32            dgeMatrix_crossprod (may need to do this in other places).
33            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
34            generic and method for dsCMatrix.  Use CHOLMOD for chol().
35    
36    2006-08-22  Douglas Bates  <bates@R-project.org>
37    
38            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
39            types of classed Matrices, matrices or numeric or logical vectors.
40            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
41            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
42            to Mutils.h (as an inline) and change name to Matrix_check_class;
43            fixes in as_cholmod_factor and chm_factor_to_SEXP.
44            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
45            dsCMatrix_matrix_solve.  Comment out vestigial functions.
46            * src/Csparse.c: use diag_P and uplo_P macros.
47    
48    2006-08-21  Douglas Bates  <bates@R-project.org>
49    
50            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
51            valgrind.
52            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
53            inverses.
54            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
55            -Wall warnings.
56            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
57            Use dup_mMatrix_as_dgeMatrix.
58    
59    2006-08-20  Douglas Bates  <bates@R-project.org>
60    
61            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
62            * tests/sparseQR.R: Added
63            * man/sparseQR-class.Rd: Document methods for qr.* generics
64            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
65    
66    2006-08-19  Douglas Bates  <bates@R-project.org>
67    
68            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
69            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
70            and qr.fitted.
71            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
72            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
73    
74    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
77            the base version has no "..." argument.
78    
79            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
80    
81            * R/Matrix.R: define and
82            * NAMESPACE: export as.numeric() and as.logical() methods.
83                    Let's hope these do not badly slow down something...
84            Finally export the zapsmall() method.
85    
86    2006-08-17  Douglas Bates  <bates@R-project.org>
87    
88            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
89            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
90            * src/dtCMatrix.c :Remove code that is no longer used
91            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
92    
93    2006-08-14  Douglas Bates  <bates@R-project.org>
94    
95            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
96            Csparse_to_logical and Csparse_symmetric_to_general.
97            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
98            coercion methods between CsparseMatrix and TsparseMatrix.
99    
100    2006-08-14  Douglas Bates  <bates@R-project.org>
101    
102            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
103            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
104            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
105            possible.
106    
107    2006-08-12  Douglas Bates  <bates@R-project.org>
108    
109            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
110              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
111              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
112              generalize conversions between TsparseMatrix, CsparseMatrix,
113              denseMatrix and matrix.  Preserve triangularity property and
114              propagate Dimnames in the easy cases.
115    
116    2006-08-10  Douglas Bates  <bates@R-project.org>
117    
118            * src/lmer.c: adjust checks in glmer_init for S4SXP
119            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
120            before S4SXP but for the wrong reasons.
121    
122    2006-08-08  Douglas Bates  <bates@R-project.org>
123    
124            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
125            Later modified to return the upper triangle only.
126            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
127    
128    2006-08-07  Douglas Bates  <bates@R-project.org>
129    
130            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
131            R-level conversion to a sparse symmetric class.
132            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
133            Remove conversion to sparse symmetric classes (now done in C code).
134    
135    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
138            * man/band.Rd:  adapt the \dontshow{} unit test.
139    
140    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * DESCRIPTION (Version): 0.995-14  for CRAN
143    
144            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
145    
146            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
147            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
148    
149            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
150            * R/Tsparse.R (tril, triu, band): methods
151            * R/dgRMatrix.R (tril, ...):    ditto
152            * man/band.Rd:                  ditto
153    
154    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/Matrix.R (head, tail): directly use utils:::head.matrix
157                    to be up-to-date automatically.
158    
159    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
162    
163            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
164            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
165            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
166            such that the S4 objects are always created by the current version
167            of R and 'Matrix' class definitions.
168    
169    2006-08-01  Douglas Bates  <bates@R-project.org>
170    
171            * R/lmer.R (LMEoptimize method), tests/lmer.R,
172            inst/external/test3comp.rda: Added warnings for convergence on
173            boundary and test cases.
174    
175            * src/lmer.c (mer_postVar): Modified to return the variances that
176            are marginal to the fixed effects, not conditional on them (which
177            is what the bVar slot contents represent).
178    
179    2006-07-31  Douglas Bates  <bates@R-project.org>
180    
181            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
182            function which calls the C function mer_hat_trace2.
183    
184            * man/ranef.Rd: Include description of "postVar" argument and
185            producing a caterpillar plot.
186    
187    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * NAMESPACE:    change  "correlation" to "corMatrix"
190            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
191            * R/dpoMatrix.R: ditto
192            * R/lmer.R:      ditto
193    
194    2006-07-28  Douglas Bates  <bates@R-project.org>
195    
196            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
197            RZXinv slot's contents into a separate internal function that can
198            be used in mer_hat_trace.
199    
200    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
203            via new smart
204            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
205            utility functions.
206    
207    
208    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Csparse.R (tril, triu, band): do return *triangular* classed
211            matrices when appropriate; band() even symmetric ones.
212            (replCmat): extend to potentially all "CsparseMatrix"
213            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
214            allow subassignment for special sparse matrices.
215    
216            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
217    
218            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
219            argument; in glmer_*(): print only if(verbose).
220    
221            speed-optimize a few places by moving REAL(.) out of loops.
222    
223            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
224    
225    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
228                    since that wrongly triggers also for M[ logi , ]
229    
230            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
231            a symmetric matrix that results in a non-symmetric one.
232            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
233    
234            * R/dMatrix.R: make round(M) work as round(M, 0)
235    
236            * R/dgTMatrix.R (image): coordinate system and axis now use
237            1-based indices, not 0-based ones.
238    
239            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
240            * tests/indexing.R: test it.
241    
242            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
243            * man/isSymmetric-methods.Rd: and document it.
244    
245            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
246            * man/SparseM-conv.Rd: docu them
247    
248            * tests/other-pkgs.R: renamed from tests/graph.R and add example
249                    for 'SparseM' conversions
250    
251    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
252    
253            * R/Matrix.R (head): added head() and tail() methods.
254    
255    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * DESCRIPTION (Version): 0.995-12 released to CRAN
258    
259    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * tests/simple.R: add check for correct dsT -> dgT coercion;
262                    add check for correct printing of symmetric sparse matrices.
263    
264            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
265            for sparse symmetric matrices.
266    
267            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
268            diagonal twice.
269    
270    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
271    
272            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
273            being applied to the x slot (detected by Brian Ripley).
274    
275    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
278    
279            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
280    
281    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * src/lgCMatrix.c (lgCMatrix_diag): new function
284            * R/lgCMatrix.R (diag): for new method
285    
286            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
287                 ==> construction of illegal "*gTMatrix" via new() should
288                 now be much less easy:
289            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
290    
291            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
292                    directly.
293            * man/Matrix.Rd: documents it.
294    
295    2006-07-06  Douglas Bates  <bates@R-project.org>
296    
297            * src/pedigree.c (pedigree_inbreeding): Correction in
298            initialization.  This function is not currently being used and is
299            not fully tested.
300    
301            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
302            Introduced the glmer class.  Added code for mcmcmsamp on glmer
303            objects.  Modified validity check on pedigree objects to account
304            for nonparallel patterns of missingness of parents.
305    
306            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
307            class.
308    
309    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/pMatrix.R: coercion pMatrix -> Tsparse
312    
313    2006-06-12  Douglas Bates  <bates@R-project.org>
314    
315            * DESCRIPTION (Version): 0.995-11 released to CRAN
316    
317            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
318            the output from mcmcsamp.
319    
320  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
321    
322          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
323            of the hat matrix.
324    
325  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
328          classes.          classes.
329            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
330    
331  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
# Line 43  Line 364 
364    
365          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
366          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.
367          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
368    
369    
370  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 487 
487          * 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)
488          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
489          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
490          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
491    
492  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
# Line 370  Line 691 
691  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
694          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
695          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
696    
697  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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