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revision 1331, Sat Jul 22 17:59:53 2006 UTC revision 1507, Mon Sep 4 18:41:34 2006 UTC
# Line 1  Line 1 
1    2006-09-04  Douglas Bates  <bates@R-project.org>
2    
3            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
4            * src/DEPS.mkf: update
5    
6    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * created branches/Matrix-for-R-2.3.x;  on trunk: do
9            * DESCRIPTION (Version): 0.9975-0
10            (Depends): R (>= 2.4.0)
11    
12    2006-09-01  Douglas Bates  <bates@R-project.org>
13    
14            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
15    
16    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
19            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
20    
21            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
22    
23    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
26            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
27            * R/dsparseMatrix.R: dito
28            * R/Csparse.R: dito
29    
30    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dMatrix.R (Compare): improve availability of "<", etc
33            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
34    
35    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
38            of a 0-index which was used as 1-index (..hmm)
39    
40            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
41    
42            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
43            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
44            (.is.diagonal): dito
45    
46            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
47    
48            * R/Matrix.R (Matrix): also work for NA data
49    
50    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
53            in all cases.
54    
55    2006-08-27  Douglas Bates  <bates@R-project.org>
56    
57            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
58            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
59    
60    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
63            subclasses of "ddenseMatrix"
64            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
65            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
66            instead of half dozen specialized ones.
67    
68    2006-08-25  Douglas Bates  <bates@R-project.org>
69    
70            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
71            <tillard@cirad.fr> - ordering standard errors to match effects.
72    
73    2006-08-24  Douglas Bates  <bates@R-project.org>
74    
75            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
76            on R_ldl.
77            * R/lCholCMatrix.R,
78            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
79            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
80            * many files in ./R and ./src: Use more general version of
81            dup_mMatrix_as_dgeMatrix to simplify method definitions.
82            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
83            dtpMatrix, dspMatrix and dppMatrix conversions.
84    
85    
86    2006-08-23  Douglas Bates  <bates@R-project.org>
87    
88            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
89            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
90            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
91            dgeMatrix_crossprod (may need to do this in other places).
92            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
93            generic and method for dsCMatrix.  Use CHOLMOD for chol().
94    
95    2006-08-22  Douglas Bates  <bates@R-project.org>
96    
97            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
98            types of classed Matrices, matrices or numeric or logical vectors.
99            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
100            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
101            to Mutils.h (as an inline) and change name to Matrix_check_class;
102            fixes in as_cholmod_factor and chm_factor_to_SEXP.
103            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
104            dsCMatrix_matrix_solve.  Comment out vestigial functions.
105            * src/Csparse.c: use diag_P and uplo_P macros.
106    
107    2006-08-21  Douglas Bates  <bates@R-project.org>
108    
109            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
110            valgrind.
111            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
112            inverses.
113            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
114            -Wall warnings.
115            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
116            Use dup_mMatrix_as_dgeMatrix.
117    
118    2006-08-20  Douglas Bates  <bates@R-project.org>
119    
120            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
121            * tests/sparseQR.R: Added
122            * man/sparseQR-class.Rd: Document methods for qr.* generics
123            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
124    
125    2006-08-19  Douglas Bates  <bates@R-project.org>
126    
127            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
128            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
129            and qr.fitted.
130            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
131            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
132    
133    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
136            the base version has no "..." argument.
137    
138            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
139    
140            * R/Matrix.R: define and
141            * NAMESPACE: export as.numeric() and as.logical() methods.
142                    Let's hope these do not badly slow down something...
143            Finally export the zapsmall() method.
144    
145    2006-08-17  Douglas Bates  <bates@R-project.org>
146    
147            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
148            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
149            * src/dtCMatrix.c :Remove code that is no longer used
150            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
151    
152    2006-08-14  Douglas Bates  <bates@R-project.org>
153    
154            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
155            Csparse_to_logical and Csparse_symmetric_to_general.
156            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
157            coercion methods between CsparseMatrix and TsparseMatrix.
158    
159    2006-08-14  Douglas Bates  <bates@R-project.org>
160    
161            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
162            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
163            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
164            possible.
165    
166    2006-08-12  Douglas Bates  <bates@R-project.org>
167    
168            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
169              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
170              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
171              generalize conversions between TsparseMatrix, CsparseMatrix,
172              denseMatrix and matrix.  Preserve triangularity property and
173              propagate Dimnames in the easy cases.
174    
175    2006-08-10  Douglas Bates  <bates@R-project.org>
176    
177            * src/lmer.c: adjust checks in glmer_init for S4SXP
178            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
179            before S4SXP but for the wrong reasons.
180    
181    2006-08-08  Douglas Bates  <bates@R-project.org>
182    
183            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
184            Later modified to return the upper triangle only.
185            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
186    
187    2006-08-07  Douglas Bates  <bates@R-project.org>
188    
189            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
190            R-level conversion to a sparse symmetric class.
191            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
192            Remove conversion to sparse symmetric classes (now done in C code).
193    
194    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
197            * man/band.Rd:  adapt the \dontshow{} unit test.
198    
199    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * DESCRIPTION (Version): 0.995-14  for CRAN
202    
203            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
204    
205            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
206            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
207    
208            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
209            * R/Tsparse.R (tril, triu, band): methods
210            * R/dgRMatrix.R (tril, ...):    ditto
211            * man/band.Rd:                  ditto
212    
213    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Matrix.R (head, tail): directly use utils:::head.matrix
216                    to be up-to-date automatically.
217    
218    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
221    
222            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
223            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
224            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
225            such that the S4 objects are always created by the current version
226            of R and 'Matrix' class definitions.
227    
228    2006-08-01  Douglas Bates  <bates@R-project.org>
229    
230            * R/lmer.R (LMEoptimize method), tests/lmer.R,
231            inst/external/test3comp.rda: Added warnings for convergence on
232            boundary and test cases.
233    
234            * src/lmer.c (mer_postVar): Modified to return the variances that
235            are marginal to the fixed effects, not conditional on them (which
236            is what the bVar slot contents represent).
237    
238    2006-07-31  Douglas Bates  <bates@R-project.org>
239    
240            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
241            function which calls the C function mer_hat_trace2.
242    
243            * man/ranef.Rd: Include description of "postVar" argument and
244            producing a caterpillar plot.
245    
246    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * NAMESPACE:    change  "correlation" to "corMatrix"
249            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
250            * R/dpoMatrix.R: ditto
251            * R/lmer.R:      ditto
252    
253    2006-07-28  Douglas Bates  <bates@R-project.org>
254    
255            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
256            RZXinv slot's contents into a separate internal function that can
257            be used in mer_hat_trace.
258    
259  2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261          * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix          * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
# Line 165  Line 423 
423    
424          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
425          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.
426          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
427    
428    
429  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 288  Line 546 
546          * 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)
547          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
548          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
549          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
550    
551  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
# Line 492  Line 750 
750  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
753          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
754          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
755    
756  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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