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revision 1316, Tue Jul 11 22:00:41 2006 UTC revision 1455, Mon Aug 28 15:35:44 2006 UTC
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1    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
4            in all cases.
5    
6    2006-08-27  Douglas Bates  <bates@R-project.org>
7    
8            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
9            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
10    
11    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
14            subclasses of "ddenseMatrix"
15            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
16            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
17            instead of half dozen specialized ones.
18    
19    2006-08-25  Douglas Bates  <bates@R-project.org>
20    
21            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
22            <tillard@cirad.fr> - ordering standard errors to match effects.
23    
24    2006-08-24  Douglas Bates  <bates@R-project.org>
25    
26            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
27            on R_ldl.
28            * R/lCholCMatrix.R,
29            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
30            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
31            * many files in ./R and ./src: Use more general version of
32            dup_mMatrix_as_dgeMatrix to simplify method definitions.
33            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
34            dtpMatrix, dspMatrix and dppMatrix conversions.
35    
36    
37    2006-08-23  Douglas Bates  <bates@R-project.org>
38    
39            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
40            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
41            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
42            dgeMatrix_crossprod (may need to do this in other places).
43            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
44            generic and method for dsCMatrix.  Use CHOLMOD for chol().
45    
46    2006-08-22  Douglas Bates  <bates@R-project.org>
47    
48            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
49            types of classed Matrices, matrices or numeric or logical vectors.
50            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
51            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
52            to Mutils.h (as an inline) and change name to Matrix_check_class;
53            fixes in as_cholmod_factor and chm_factor_to_SEXP.
54            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
55            dsCMatrix_matrix_solve.  Comment out vestigial functions.
56            * src/Csparse.c: use diag_P and uplo_P macros.
57    
58    2006-08-21  Douglas Bates  <bates@R-project.org>
59    
60            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
61            valgrind.
62            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
63            inverses.
64            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
65            -Wall warnings.
66            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
67            Use dup_mMatrix_as_dgeMatrix.
68    
69    2006-08-20  Douglas Bates  <bates@R-project.org>
70    
71            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
72            * tests/sparseQR.R: Added
73            * man/sparseQR-class.Rd: Document methods for qr.* generics
74            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
75    
76    2006-08-19  Douglas Bates  <bates@R-project.org>
77    
78            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
79            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
80            and qr.fitted.
81            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
82            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
83    
84    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
87            the base version has no "..." argument.
88    
89            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
90    
91            * R/Matrix.R: define and
92            * NAMESPACE: export as.numeric() and as.logical() methods.
93                    Let's hope these do not badly slow down something...
94            Finally export the zapsmall() method.
95    
96    2006-08-17  Douglas Bates  <bates@R-project.org>
97    
98            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
99            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
100            * src/dtCMatrix.c :Remove code that is no longer used
101            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
102    
103    2006-08-14  Douglas Bates  <bates@R-project.org>
104    
105            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
106            Csparse_to_logical and Csparse_symmetric_to_general.
107            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
108            coercion methods between CsparseMatrix and TsparseMatrix.
109    
110    2006-08-14  Douglas Bates  <bates@R-project.org>
111    
112            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
113            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
114            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
115            possible.
116    
117    2006-08-12  Douglas Bates  <bates@R-project.org>
118    
119            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
120              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
121              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
122              generalize conversions between TsparseMatrix, CsparseMatrix,
123              denseMatrix and matrix.  Preserve triangularity property and
124              propagate Dimnames in the easy cases.
125    
126    2006-08-10  Douglas Bates  <bates@R-project.org>
127    
128            * src/lmer.c: adjust checks in glmer_init for S4SXP
129            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
130            before S4SXP but for the wrong reasons.
131    
132    2006-08-08  Douglas Bates  <bates@R-project.org>
133    
134            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
135            Later modified to return the upper triangle only.
136            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
137    
138    2006-08-07  Douglas Bates  <bates@R-project.org>
139    
140            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
141            R-level conversion to a sparse symmetric class.
142            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
143            Remove conversion to sparse symmetric classes (now done in C code).
144    
145    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
148            * man/band.Rd:  adapt the \dontshow{} unit test.
149    
150    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * DESCRIPTION (Version): 0.995-14  for CRAN
153    
154            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
155    
156            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
157            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
158    
159            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
160            * R/Tsparse.R (tril, triu, band): methods
161            * R/dgRMatrix.R (tril, ...):    ditto
162            * man/band.Rd:                  ditto
163    
164    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Matrix.R (head, tail): directly use utils:::head.matrix
167                    to be up-to-date automatically.
168    
169    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
172    
173            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
174            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
175            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
176            such that the S4 objects are always created by the current version
177            of R and 'Matrix' class definitions.
178    
179    2006-08-01  Douglas Bates  <bates@R-project.org>
180    
181            * R/lmer.R (LMEoptimize method), tests/lmer.R,
182            inst/external/test3comp.rda: Added warnings for convergence on
183            boundary and test cases.
184    
185            * src/lmer.c (mer_postVar): Modified to return the variances that
186            are marginal to the fixed effects, not conditional on them (which
187            is what the bVar slot contents represent).
188    
189    2006-07-31  Douglas Bates  <bates@R-project.org>
190    
191            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
192            function which calls the C function mer_hat_trace2.
193    
194            * man/ranef.Rd: Include description of "postVar" argument and
195            producing a caterpillar plot.
196    
197    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * NAMESPACE:    change  "correlation" to "corMatrix"
200            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
201            * R/dpoMatrix.R: ditto
202            * R/lmer.R:      ditto
203    
204    2006-07-28  Douglas Bates  <bates@R-project.org>
205    
206            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
207            RZXinv slot's contents into a separate internal function that can
208            be used in mer_hat_trace.
209    
210    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
213            via new smart
214            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
215            utility functions.
216    
217    
218    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Csparse.R (tril, triu, band): do return *triangular* classed
221            matrices when appropriate; band() even symmetric ones.
222            (replCmat): extend to potentially all "CsparseMatrix"
223            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
224            allow subassignment for special sparse matrices.
225    
226            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
227    
228            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
229            argument; in glmer_*(): print only if(verbose).
230    
231            speed-optimize a few places by moving REAL(.) out of loops.
232    
233            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
234    
235    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
238                    since that wrongly triggers also for M[ logi , ]
239    
240            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
241            a symmetric matrix that results in a non-symmetric one.
242            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
243    
244            * R/dMatrix.R: make round(M) work as round(M, 0)
245    
246            * R/dgTMatrix.R (image): coordinate system and axis now use
247            1-based indices, not 0-based ones.
248    
249            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
250            * tests/indexing.R: test it.
251    
252            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
253            * man/isSymmetric-methods.Rd: and document it.
254    
255            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
256            * man/SparseM-conv.Rd: docu them
257    
258            * tests/other-pkgs.R: renamed from tests/graph.R and add example
259                    for 'SparseM' conversions
260    
261    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
262    
263            * R/Matrix.R (head): added head() and tail() methods.
264    
265    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * DESCRIPTION (Version): 0.995-12 released to CRAN
268    
269    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * tests/simple.R: add check for correct dsT -> dgT coercion;
272                    add check for correct printing of symmetric sparse matrices.
273    
274            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
275            for sparse symmetric matrices.
276    
277            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
278            diagonal twice.
279    
280  2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>  2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
281    
282          * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER          * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
283          being applied to the x slot (detected by Brian Ripley).  Possible          being applied to the x slot (detected by Brian Ripley).
         problem with copying the diagonal elements twice?  
284    
285  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
# Line 44  Line 322 
322    
323  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
324    
325            * DESCRIPTION (Version): 0.995-11 released to CRAN
326    
327          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
328          the output from mcmcsamp.          the output from mcmcsamp.
329    
# Line 94  Line 374 
374    
375          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
376          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.
377          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
378    
379    
380  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 217  Line 497 
497          * 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)
498          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
499          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
500          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
501    
502  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
# Line 421  Line 701 
701  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
704          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
705          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
706    
707  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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