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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1423, Tue Aug 22 22:51:56 2006 UTC
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1    2006-08-22  Douglas Bates  <bates@R-project.org>
2    
3            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
4            types of classed Matrices, matrices or numeric or logical vectors.
5            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
6            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
7            to Mutils.h (as an inline) and change name to Matrix_check_class;
8            fixes in as_cholmod_factor and chm_factor_to_SEXP.
9            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
10            dsCMatrix_matrix_solve.  Comment out vestigial functions.
11            * src/Csparse.c: use diag_P and uplo_P macros.
12    
13    2006-08-21  Douglas Bates  <bates@R-project.org>
14    
15            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
16            valgrind.
17            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
18            inverses.
19            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
20            -Wall warnings.
21            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
22            Use dup_mMatrix_as_dgeMatrix.
23    
24    2006-08-20  Douglas Bates  <bates@R-project.org>
25    
26            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
27            * tests/sparseQR.R: Added
28            * man/sparseQR-class.Rd: Document methods for qr.* generics
29            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
30    
31    2006-08-19  Douglas Bates  <bates@R-project.org>
32    
33            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
34            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
35            and qr.fitted.
36            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
37            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
38    
39    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
42            the base version has no "..." argument.
43    
44            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
45    
46            * R/Matrix.R: define and
47            * NAMESPACE: export as.numeric() and as.logical() methods.
48                    Let's hope these do not badly slow down something...
49            Finally export the zapsmall() method.
50    
51    2006-08-17  Douglas Bates  <bates@R-project.org>
52    
53            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
54            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
55            * src/dtCMatrix.c :Remove code that is no longer used
56            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
57    
58    2006-08-14  Douglas Bates  <bates@R-project.org>
59    
60            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
61            Csparse_to_logical and Csparse_symmetric_to_general.
62            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
63            coercion methods between CsparseMatrix and TsparseMatrix.
64    
65    2006-08-14  Douglas Bates  <bates@R-project.org>
66    
67            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
68            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
69            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
70            possible.
71    
72    2006-08-12  Douglas Bates  <bates@R-project.org>
73    
74            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
75              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
76              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
77              generalize conversions between TsparseMatrix, CsparseMatrix,
78              denseMatrix and matrix.  Preserve triangularity property and
79              propagate Dimnames in the easy cases.
80    
81    2006-08-10  Douglas Bates  <bates@R-project.org>
82    
83            * src/lmer.c: adjust checks in glmer_init for S4SXP
84            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
85            before S4SXP but for the wrong reasons.
86    
87    2006-08-08  Douglas Bates  <bates@R-project.org>
88    
89            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
90            Later modified to return the upper triangle only.
91            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
92    
93    2006-08-07  Douglas Bates  <bates@R-project.org>
94    
95            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
96            R-level conversion to a sparse symmetric class.
97            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
98            Remove conversion to sparse symmetric classes (now done in C code).
99    
100    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
103            * man/band.Rd:  adapt the \dontshow{} unit test.
104    
105    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * DESCRIPTION (Version): 0.995-14  for CRAN
108    
109            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
110    
111            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
112            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
113    
114            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
115            * R/Tsparse.R (tril, triu, band): methods
116            * R/dgRMatrix.R (tril, ...):    ditto
117            * man/band.Rd:                  ditto
118    
119    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/Matrix.R (head, tail): directly use utils:::head.matrix
122                    to be up-to-date automatically.
123    
124    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
127    
128            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
129            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
130            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
131            such that the S4 objects are always created by the current version
132            of R and 'Matrix' class definitions.
133    
134    2006-08-01  Douglas Bates  <bates@R-project.org>
135    
136            * R/lmer.R (LMEoptimize method), tests/lmer.R,
137            inst/external/test3comp.rda: Added warnings for convergence on
138            boundary and test cases.
139    
140            * src/lmer.c (mer_postVar): Modified to return the variances that
141            are marginal to the fixed effects, not conditional on them (which
142            is what the bVar slot contents represent).
143    
144    2006-07-31  Douglas Bates  <bates@R-project.org>
145    
146            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
147            function which calls the C function mer_hat_trace2.
148    
149            * man/ranef.Rd: Include description of "postVar" argument and
150            producing a caterpillar plot.
151    
152    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * NAMESPACE:    change  "correlation" to "corMatrix"
155            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
156            * R/dpoMatrix.R: ditto
157            * R/lmer.R:      ditto
158    
159    2006-07-28  Douglas Bates  <bates@R-project.org>
160    
161            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
162            RZXinv slot's contents into a separate internal function that can
163            be used in mer_hat_trace.
164    
165    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
168            via new smart
169            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
170            utility functions.
171    
172    
173    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/Csparse.R (tril, triu, band): do return *triangular* classed
176            matrices when appropriate; band() even symmetric ones.
177            (replCmat): extend to potentially all "CsparseMatrix"
178            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
179            allow subassignment for special sparse matrices.
180    
181            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
182    
183            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
184            argument; in glmer_*(): print only if(verbose).
185    
186            speed-optimize a few places by moving REAL(.) out of loops.
187    
188            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
189    
190    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
193                    since that wrongly triggers also for M[ logi , ]
194    
195            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
196            a symmetric matrix that results in a non-symmetric one.
197            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
198    
199            * R/dMatrix.R: make round(M) work as round(M, 0)
200    
201            * R/dgTMatrix.R (image): coordinate system and axis now use
202            1-based indices, not 0-based ones.
203    
204            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
205            * tests/indexing.R: test it.
206    
207            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
208            * man/isSymmetric-methods.Rd: and document it.
209    
210            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
211            * man/SparseM-conv.Rd: docu them
212    
213            * tests/other-pkgs.R: renamed from tests/graph.R and add example
214                    for 'SparseM' conversions
215    
216    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
217    
218            * R/Matrix.R (head): added head() and tail() methods.
219    
220    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * DESCRIPTION (Version): 0.995-12 released to CRAN
223    
224    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * tests/simple.R: add check for correct dsT -> dgT coercion;
227                    add check for correct printing of symmetric sparse matrices.
228    
229            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
230            for sparse symmetric matrices.
231    
232            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
233            diagonal twice.
234    
235    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
236    
237            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
238            being applied to the x slot (detected by Brian Ripley).
239    
240    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
243    
244            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
245    
246    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * src/lgCMatrix.c (lgCMatrix_diag): new function
249            * R/lgCMatrix.R (diag): for new method
250    
251            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
252                 ==> construction of illegal "*gTMatrix" via new() should
253                 now be much less easy:
254            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
255    
256            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
257                    directly.
258            * man/Matrix.Rd: documents it.
259    
260  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
261    
262          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 268 
268          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
269          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
270    
271            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
272            class.
273    
274    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/pMatrix.R: coercion pMatrix -> Tsparse
277    
278  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
279    
280            * DESCRIPTION (Version): 0.995-11 released to CRAN
281    
282          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
283          the output from mcmcsamp.          the output from mcmcsamp.
284    
# Line 23  Line 291 
291    
292          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
293          classes.          classes.
294            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
295    
296  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
# Line 60  Line 329 
329    
330          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
331          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.
332          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
333    
334    
335  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 452 
452          * 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)
453          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
454          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
455          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
456    
457  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
# Line 387  Line 656 
656  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
659          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
660          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
661    
662  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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