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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1453, Sun Aug 27 16:16:35 2006 UTC
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1    2006-08-27  Douglas Bates  <bates@R-project.org>
2    
3            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
4            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
5    
6    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
9            subclasses of "ddenseMatrix"
10            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
11            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
12            instead of half dozen specialized ones.
13    
14    2006-08-25  Douglas Bates  <bates@R-project.org>
15    
16            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
17            <tillard@cirad.fr> - ordering standard errors to match effects.
18    
19    2006-08-24  Douglas Bates  <bates@R-project.org>
20    
21            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
22            on R_ldl.
23            * R/lCholCMatrix.R,
24            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
25            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
26            * many files in ./R and ./src: Use more general version of
27            dup_mMatrix_as_dgeMatrix to simplify method definitions.
28            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
29            dtpMatrix, dspMatrix and dppMatrix conversions.
30    
31    
32    2006-08-23  Douglas Bates  <bates@R-project.org>
33    
34            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
35            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
36            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
37            dgeMatrix_crossprod (may need to do this in other places).
38            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
39            generic and method for dsCMatrix.  Use CHOLMOD for chol().
40    
41    2006-08-22  Douglas Bates  <bates@R-project.org>
42    
43            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
44            types of classed Matrices, matrices or numeric or logical vectors.
45            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
46            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
47            to Mutils.h (as an inline) and change name to Matrix_check_class;
48            fixes in as_cholmod_factor and chm_factor_to_SEXP.
49            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
50            dsCMatrix_matrix_solve.  Comment out vestigial functions.
51            * src/Csparse.c: use diag_P and uplo_P macros.
52    
53    2006-08-21  Douglas Bates  <bates@R-project.org>
54    
55            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
56            valgrind.
57            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
58            inverses.
59            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
60            -Wall warnings.
61            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
62            Use dup_mMatrix_as_dgeMatrix.
63    
64    2006-08-20  Douglas Bates  <bates@R-project.org>
65    
66            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
67            * tests/sparseQR.R: Added
68            * man/sparseQR-class.Rd: Document methods for qr.* generics
69            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
70    
71    2006-08-19  Douglas Bates  <bates@R-project.org>
72    
73            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
74            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
75            and qr.fitted.
76            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
77            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
78    
79    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
82            the base version has no "..." argument.
83    
84            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
85    
86            * R/Matrix.R: define and
87            * NAMESPACE: export as.numeric() and as.logical() methods.
88                    Let's hope these do not badly slow down something...
89            Finally export the zapsmall() method.
90    
91    2006-08-17  Douglas Bates  <bates@R-project.org>
92    
93            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
94            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
95            * src/dtCMatrix.c :Remove code that is no longer used
96            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
97    
98    2006-08-14  Douglas Bates  <bates@R-project.org>
99    
100            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
101            Csparse_to_logical and Csparse_symmetric_to_general.
102            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
103            coercion methods between CsparseMatrix and TsparseMatrix.
104    
105    2006-08-14  Douglas Bates  <bates@R-project.org>
106    
107            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
108            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
109            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
110            possible.
111    
112    2006-08-12  Douglas Bates  <bates@R-project.org>
113    
114            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
115              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
116              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
117              generalize conversions between TsparseMatrix, CsparseMatrix,
118              denseMatrix and matrix.  Preserve triangularity property and
119              propagate Dimnames in the easy cases.
120    
121    2006-08-10  Douglas Bates  <bates@R-project.org>
122    
123            * src/lmer.c: adjust checks in glmer_init for S4SXP
124            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
125            before S4SXP but for the wrong reasons.
126    
127    2006-08-08  Douglas Bates  <bates@R-project.org>
128    
129            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
130            Later modified to return the upper triangle only.
131            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
132    
133    2006-08-07  Douglas Bates  <bates@R-project.org>
134    
135            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
136            R-level conversion to a sparse symmetric class.
137            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
138            Remove conversion to sparse symmetric classes (now done in C code).
139    
140    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
143            * man/band.Rd:  adapt the \dontshow{} unit test.
144    
145    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * DESCRIPTION (Version): 0.995-14  for CRAN
148    
149            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
150    
151            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
152            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
153    
154            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
155            * R/Tsparse.R (tril, triu, band): methods
156            * R/dgRMatrix.R (tril, ...):    ditto
157            * man/band.Rd:                  ditto
158    
159    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/Matrix.R (head, tail): directly use utils:::head.matrix
162                    to be up-to-date automatically.
163    
164    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
167    
168            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
169            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
170            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
171            such that the S4 objects are always created by the current version
172            of R and 'Matrix' class definitions.
173    
174    2006-08-01  Douglas Bates  <bates@R-project.org>
175    
176            * R/lmer.R (LMEoptimize method), tests/lmer.R,
177            inst/external/test3comp.rda: Added warnings for convergence on
178            boundary and test cases.
179    
180            * src/lmer.c (mer_postVar): Modified to return the variances that
181            are marginal to the fixed effects, not conditional on them (which
182            is what the bVar slot contents represent).
183    
184    2006-07-31  Douglas Bates  <bates@R-project.org>
185    
186            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
187            function which calls the C function mer_hat_trace2.
188    
189            * man/ranef.Rd: Include description of "postVar" argument and
190            producing a caterpillar plot.
191    
192    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * NAMESPACE:    change  "correlation" to "corMatrix"
195            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
196            * R/dpoMatrix.R: ditto
197            * R/lmer.R:      ditto
198    
199    2006-07-28  Douglas Bates  <bates@R-project.org>
200    
201            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
202            RZXinv slot's contents into a separate internal function that can
203            be used in mer_hat_trace.
204    
205    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
208            via new smart
209            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
210            utility functions.
211    
212    
213    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Csparse.R (tril, triu, band): do return *triangular* classed
216            matrices when appropriate; band() even symmetric ones.
217            (replCmat): extend to potentially all "CsparseMatrix"
218            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
219            allow subassignment for special sparse matrices.
220    
221            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
222    
223            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
224            argument; in glmer_*(): print only if(verbose).
225    
226            speed-optimize a few places by moving REAL(.) out of loops.
227    
228            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
229    
230    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
233                    since that wrongly triggers also for M[ logi , ]
234    
235            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
236            a symmetric matrix that results in a non-symmetric one.
237            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
238    
239            * R/dMatrix.R: make round(M) work as round(M, 0)
240    
241            * R/dgTMatrix.R (image): coordinate system and axis now use
242            1-based indices, not 0-based ones.
243    
244            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
245            * tests/indexing.R: test it.
246    
247            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
248            * man/isSymmetric-methods.Rd: and document it.
249    
250            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
251            * man/SparseM-conv.Rd: docu them
252    
253            * tests/other-pkgs.R: renamed from tests/graph.R and add example
254                    for 'SparseM' conversions
255    
256    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
257    
258            * R/Matrix.R (head): added head() and tail() methods.
259    
260    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * DESCRIPTION (Version): 0.995-12 released to CRAN
263    
264    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * tests/simple.R: add check for correct dsT -> dgT coercion;
267                    add check for correct printing of symmetric sparse matrices.
268    
269            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
270            for sparse symmetric matrices.
271    
272            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
273            diagonal twice.
274    
275    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
276    
277            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
278            being applied to the x slot (detected by Brian Ripley).
279    
280    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
283    
284            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
285    
286    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * src/lgCMatrix.c (lgCMatrix_diag): new function
289            * R/lgCMatrix.R (diag): for new method
290    
291            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
292                 ==> construction of illegal "*gTMatrix" via new() should
293                 now be much less easy:
294            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
295    
296            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
297                    directly.
298            * man/Matrix.Rd: documents it.
299    
300  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
301    
302          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 308 
308          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
309          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
310    
311            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
312            class.
313    
314    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/pMatrix.R: coercion pMatrix -> Tsparse
317    
318  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
319    
320            * DESCRIPTION (Version): 0.995-11 released to CRAN
321    
322          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
323          the output from mcmcsamp.          the output from mcmcsamp.
324    
# Line 23  Line 331 
331    
332          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
333          classes.          classes.
334            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
335    
336  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
# Line 60  Line 369 
369    
370          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
371          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.
372          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
373    
374    
375  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 492 
492          * 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)
493          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
494          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
495          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
496    
497  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
# Line 387  Line 696 
696  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
699          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
700          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
701    
702  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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