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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1431, Wed Aug 23 22:13:53 2006 UTC
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1    2006-08-23  Douglas Bates  <bates@dyn-51-128.uwnet.wisc.edu>
2    
3            * R/AllClass.R,src/SOURCES_C.mkf,init.c,NAMESPACE: Remove classes
4            lCholCMatrix and dCholCMatrix based on R_ldl code.
5            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
6            dgeMatrix_crossprod (may need to do this in other places).
7            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
8            generic and method for dsCMatrix.  Use CHOLMOD for chol().
9    
10    2006-08-22  Douglas Bates  <bates@R-project.org>
11    
12            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
13            types of classed Matrices, matrices or numeric or logical vectors.
14            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
15            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
16            to Mutils.h (as an inline) and change name to Matrix_check_class;
17            fixes in as_cholmod_factor and chm_factor_to_SEXP.
18            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
19            dsCMatrix_matrix_solve.  Comment out vestigial functions.
20            * src/Csparse.c: use diag_P and uplo_P macros.
21    
22    2006-08-21  Douglas Bates  <bates@R-project.org>
23    
24            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
25            valgrind.
26            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
27            inverses.
28            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
29            -Wall warnings.
30            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
31            Use dup_mMatrix_as_dgeMatrix.
32    
33    2006-08-20  Douglas Bates  <bates@R-project.org>
34    
35            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
36            * tests/sparseQR.R: Added
37            * man/sparseQR-class.Rd: Document methods for qr.* generics
38            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
39    
40    2006-08-19  Douglas Bates  <bates@R-project.org>
41    
42            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
43            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
44            and qr.fitted.
45            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
46            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
47    
48    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
51            the base version has no "..." argument.
52    
53            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
54    
55            * R/Matrix.R: define and
56            * NAMESPACE: export as.numeric() and as.logical() methods.
57                    Let's hope these do not badly slow down something...
58            Finally export the zapsmall() method.
59    
60    2006-08-17  Douglas Bates  <bates@R-project.org>
61    
62            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
63            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
64            * src/dtCMatrix.c :Remove code that is no longer used
65            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
66    
67    2006-08-14  Douglas Bates  <bates@R-project.org>
68    
69            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
70            Csparse_to_logical and Csparse_symmetric_to_general.
71            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
72            coercion methods between CsparseMatrix and TsparseMatrix.
73    
74    2006-08-14  Douglas Bates  <bates@R-project.org>
75    
76            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
77            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
78            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
79            possible.
80    
81    2006-08-12  Douglas Bates  <bates@R-project.org>
82    
83            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
84              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
85              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
86              generalize conversions between TsparseMatrix, CsparseMatrix,
87              denseMatrix and matrix.  Preserve triangularity property and
88              propagate Dimnames in the easy cases.
89    
90    2006-08-10  Douglas Bates  <bates@R-project.org>
91    
92            * src/lmer.c: adjust checks in glmer_init for S4SXP
93            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
94            before S4SXP but for the wrong reasons.
95    
96    2006-08-08  Douglas Bates  <bates@R-project.org>
97    
98            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
99            Later modified to return the upper triangle only.
100            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
101    
102    2006-08-07  Douglas Bates  <bates@R-project.org>
103    
104            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
105            R-level conversion to a sparse symmetric class.
106            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
107            Remove conversion to sparse symmetric classes (now done in C code).
108    
109    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
112            * man/band.Rd:  adapt the \dontshow{} unit test.
113    
114    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * DESCRIPTION (Version): 0.995-14  for CRAN
117    
118            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
119    
120            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
121            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
122    
123            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
124            * R/Tsparse.R (tril, triu, band): methods
125            * R/dgRMatrix.R (tril, ...):    ditto
126            * man/band.Rd:                  ditto
127    
128    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/Matrix.R (head, tail): directly use utils:::head.matrix
131                    to be up-to-date automatically.
132    
133    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
136    
137            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
138            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
139            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
140            such that the S4 objects are always created by the current version
141            of R and 'Matrix' class definitions.
142    
143    2006-08-01  Douglas Bates  <bates@R-project.org>
144    
145            * R/lmer.R (LMEoptimize method), tests/lmer.R,
146            inst/external/test3comp.rda: Added warnings for convergence on
147            boundary and test cases.
148    
149            * src/lmer.c (mer_postVar): Modified to return the variances that
150            are marginal to the fixed effects, not conditional on them (which
151            is what the bVar slot contents represent).
152    
153    2006-07-31  Douglas Bates  <bates@R-project.org>
154    
155            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
156            function which calls the C function mer_hat_trace2.
157    
158            * man/ranef.Rd: Include description of "postVar" argument and
159            producing a caterpillar plot.
160    
161    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * NAMESPACE:    change  "correlation" to "corMatrix"
164            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
165            * R/dpoMatrix.R: ditto
166            * R/lmer.R:      ditto
167    
168    2006-07-28  Douglas Bates  <bates@R-project.org>
169    
170            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
171            RZXinv slot's contents into a separate internal function that can
172            be used in mer_hat_trace.
173    
174    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
177            via new smart
178            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
179            utility functions.
180    
181    
182    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/Csparse.R (tril, triu, band): do return *triangular* classed
185            matrices when appropriate; band() even symmetric ones.
186            (replCmat): extend to potentially all "CsparseMatrix"
187            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
188            allow subassignment for special sparse matrices.
189    
190            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
191    
192            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
193            argument; in glmer_*(): print only if(verbose).
194    
195            speed-optimize a few places by moving REAL(.) out of loops.
196    
197            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
198    
199    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
202                    since that wrongly triggers also for M[ logi , ]
203    
204            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
205            a symmetric matrix that results in a non-symmetric one.
206            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
207    
208            * R/dMatrix.R: make round(M) work as round(M, 0)
209    
210            * R/dgTMatrix.R (image): coordinate system and axis now use
211            1-based indices, not 0-based ones.
212    
213            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
214            * tests/indexing.R: test it.
215    
216            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
217            * man/isSymmetric-methods.Rd: and document it.
218    
219            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
220            * man/SparseM-conv.Rd: docu them
221    
222            * tests/other-pkgs.R: renamed from tests/graph.R and add example
223                    for 'SparseM' conversions
224    
225    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
226    
227            * R/Matrix.R (head): added head() and tail() methods.
228    
229    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * DESCRIPTION (Version): 0.995-12 released to CRAN
232    
233    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * tests/simple.R: add check for correct dsT -> dgT coercion;
236                    add check for correct printing of symmetric sparse matrices.
237    
238            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
239            for sparse symmetric matrices.
240    
241            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
242            diagonal twice.
243    
244    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
245    
246            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
247            being applied to the x slot (detected by Brian Ripley).
248    
249    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
252    
253            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
254    
255    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * src/lgCMatrix.c (lgCMatrix_diag): new function
258            * R/lgCMatrix.R (diag): for new method
259    
260            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
261                 ==> construction of illegal "*gTMatrix" via new() should
262                 now be much less easy:
263            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
264    
265            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
266                    directly.
267            * man/Matrix.Rd: documents it.
268    
269  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
270    
271          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 277 
277          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
278          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
279    
280            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
281            class.
282    
283    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/pMatrix.R: coercion pMatrix -> Tsparse
286    
287  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
288    
289            * DESCRIPTION (Version): 0.995-11 released to CRAN
290    
291          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
292          the output from mcmcsamp.          the output from mcmcsamp.
293    
# Line 23  Line 300 
300    
301          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
302          classes.          classes.
303            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
304    
305  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
# Line 60  Line 338 
338    
339          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
340          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.
341          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
342    
343    
344  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 461 
461          * 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)
462          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
463          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
464          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
465    
466  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
# Line 387  Line 665 
665  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
668          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
669          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
670    
671  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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