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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1467, Wed Aug 30 21:35:09 2006 UTC
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1    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
4            of a 0-index which was used as 1-index (..hmm)
5    
6            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
7    
8            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
9            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
10            (.is.diagonal): dito
11    
12            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
13    
14            * R/Matrix.R (Matrix): also work for NA data
15    
16    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
19            in all cases.
20    
21    2006-08-27  Douglas Bates  <bates@R-project.org>
22    
23            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
24            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
25    
26    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
29            subclasses of "ddenseMatrix"
30            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
31            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
32            instead of half dozen specialized ones.
33    
34    2006-08-25  Douglas Bates  <bates@R-project.org>
35    
36            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
37            <tillard@cirad.fr> - ordering standard errors to match effects.
38    
39    2006-08-24  Douglas Bates  <bates@R-project.org>
40    
41            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
42            on R_ldl.
43            * R/lCholCMatrix.R,
44            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
45            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
46            * many files in ./R and ./src: Use more general version of
47            dup_mMatrix_as_dgeMatrix to simplify method definitions.
48            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
49            dtpMatrix, dspMatrix and dppMatrix conversions.
50    
51    
52    2006-08-23  Douglas Bates  <bates@R-project.org>
53    
54            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
55            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
56            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
57            dgeMatrix_crossprod (may need to do this in other places).
58            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
59            generic and method for dsCMatrix.  Use CHOLMOD for chol().
60    
61    2006-08-22  Douglas Bates  <bates@R-project.org>
62    
63            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
64            types of classed Matrices, matrices or numeric or logical vectors.
65            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
66            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
67            to Mutils.h (as an inline) and change name to Matrix_check_class;
68            fixes in as_cholmod_factor and chm_factor_to_SEXP.
69            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
70            dsCMatrix_matrix_solve.  Comment out vestigial functions.
71            * src/Csparse.c: use diag_P and uplo_P macros.
72    
73    2006-08-21  Douglas Bates  <bates@R-project.org>
74    
75            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
76            valgrind.
77            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
78            inverses.
79            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
80            -Wall warnings.
81            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
82            Use dup_mMatrix_as_dgeMatrix.
83    
84    2006-08-20  Douglas Bates  <bates@R-project.org>
85    
86            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
87            * tests/sparseQR.R: Added
88            * man/sparseQR-class.Rd: Document methods for qr.* generics
89            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
90    
91    2006-08-19  Douglas Bates  <bates@R-project.org>
92    
93            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
94            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
95            and qr.fitted.
96            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
97            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
98    
99    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
102            the base version has no "..." argument.
103    
104            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
105    
106            * R/Matrix.R: define and
107            * NAMESPACE: export as.numeric() and as.logical() methods.
108                    Let's hope these do not badly slow down something...
109            Finally export the zapsmall() method.
110    
111    2006-08-17  Douglas Bates  <bates@R-project.org>
112    
113            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
114            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
115            * src/dtCMatrix.c :Remove code that is no longer used
116            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
117    
118    2006-08-14  Douglas Bates  <bates@R-project.org>
119    
120            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
121            Csparse_to_logical and Csparse_symmetric_to_general.
122            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
123            coercion methods between CsparseMatrix and TsparseMatrix.
124    
125    2006-08-14  Douglas Bates  <bates@R-project.org>
126    
127            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
128            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
129            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
130            possible.
131    
132    2006-08-12  Douglas Bates  <bates@R-project.org>
133    
134            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
135              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
136              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
137              generalize conversions between TsparseMatrix, CsparseMatrix,
138              denseMatrix and matrix.  Preserve triangularity property and
139              propagate Dimnames in the easy cases.
140    
141    2006-08-10  Douglas Bates  <bates@R-project.org>
142    
143            * src/lmer.c: adjust checks in glmer_init for S4SXP
144            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
145            before S4SXP but for the wrong reasons.
146    
147    2006-08-08  Douglas Bates  <bates@R-project.org>
148    
149            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
150            Later modified to return the upper triangle only.
151            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
152    
153    2006-08-07  Douglas Bates  <bates@R-project.org>
154    
155            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
156            R-level conversion to a sparse symmetric class.
157            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
158            Remove conversion to sparse symmetric classes (now done in C code).
159    
160    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
163            * man/band.Rd:  adapt the \dontshow{} unit test.
164    
165    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * DESCRIPTION (Version): 0.995-14  for CRAN
168    
169            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
170    
171            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
172            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
173    
174            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
175            * R/Tsparse.R (tril, triu, band): methods
176            * R/dgRMatrix.R (tril, ...):    ditto
177            * man/band.Rd:                  ditto
178    
179    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/Matrix.R (head, tail): directly use utils:::head.matrix
182                    to be up-to-date automatically.
183    
184    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
187    
188            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
189            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
190            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
191            such that the S4 objects are always created by the current version
192            of R and 'Matrix' class definitions.
193    
194    2006-08-01  Douglas Bates  <bates@R-project.org>
195    
196            * R/lmer.R (LMEoptimize method), tests/lmer.R,
197            inst/external/test3comp.rda: Added warnings for convergence on
198            boundary and test cases.
199    
200            * src/lmer.c (mer_postVar): Modified to return the variances that
201            are marginal to the fixed effects, not conditional on them (which
202            is what the bVar slot contents represent).
203    
204    2006-07-31  Douglas Bates  <bates@R-project.org>
205    
206            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
207            function which calls the C function mer_hat_trace2.
208    
209            * man/ranef.Rd: Include description of "postVar" argument and
210            producing a caterpillar plot.
211    
212    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * NAMESPACE:    change  "correlation" to "corMatrix"
215            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
216            * R/dpoMatrix.R: ditto
217            * R/lmer.R:      ditto
218    
219    2006-07-28  Douglas Bates  <bates@R-project.org>
220    
221            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
222            RZXinv slot's contents into a separate internal function that can
223            be used in mer_hat_trace.
224    
225    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
228            via new smart
229            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
230            utility functions.
231    
232    
233    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/Csparse.R (tril, triu, band): do return *triangular* classed
236            matrices when appropriate; band() even symmetric ones.
237            (replCmat): extend to potentially all "CsparseMatrix"
238            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
239            allow subassignment for special sparse matrices.
240    
241            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
242    
243            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
244            argument; in glmer_*(): print only if(verbose).
245    
246            speed-optimize a few places by moving REAL(.) out of loops.
247    
248            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
249    
250    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
253                    since that wrongly triggers also for M[ logi , ]
254    
255            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
256            a symmetric matrix that results in a non-symmetric one.
257            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
258    
259            * R/dMatrix.R: make round(M) work as round(M, 0)
260    
261            * R/dgTMatrix.R (image): coordinate system and axis now use
262            1-based indices, not 0-based ones.
263    
264            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
265            * tests/indexing.R: test it.
266    
267            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
268            * man/isSymmetric-methods.Rd: and document it.
269    
270            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
271            * man/SparseM-conv.Rd: docu them
272    
273            * tests/other-pkgs.R: renamed from tests/graph.R and add example
274                    for 'SparseM' conversions
275    
276    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
277    
278            * R/Matrix.R (head): added head() and tail() methods.
279    
280    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * DESCRIPTION (Version): 0.995-12 released to CRAN
283    
284    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * tests/simple.R: add check for correct dsT -> dgT coercion;
287                    add check for correct printing of symmetric sparse matrices.
288    
289            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
290            for sparse symmetric matrices.
291    
292            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
293            diagonal twice.
294    
295    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
296    
297            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
298            being applied to the x slot (detected by Brian Ripley).
299    
300    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
303    
304            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
305    
306    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * src/lgCMatrix.c (lgCMatrix_diag): new function
309            * R/lgCMatrix.R (diag): for new method
310    
311            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
312                 ==> construction of illegal "*gTMatrix" via new() should
313                 now be much less easy:
314            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
315    
316            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
317                    directly.
318            * man/Matrix.Rd: documents it.
319    
320    2006-07-06  Douglas Bates  <bates@R-project.org>
321    
322            * src/pedigree.c (pedigree_inbreeding): Correction in
323            initialization.  This function is not currently being used and is
324            not fully tested.
325    
326            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
327            Introduced the glmer class.  Added code for mcmcmsamp on glmer
328            objects.  Modified validity check on pedigree objects to account
329            for nonparallel patterns of missingness of parents.
330    
331            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
332            class.
333    
334    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/pMatrix.R: coercion pMatrix -> Tsparse
337    
338    2006-06-12  Douglas Bates  <bates@R-project.org>
339    
340            * DESCRIPTION (Version): 0.995-11 released to CRAN
341    
342            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
343            the output from mcmcsamp.
344    
345    2006-06-10  Douglas Bates  <bates@R-project.org>
346    
347            * R/lmer.R (simulestimate): added C code for calculating the trace
348            of the hat matrix.
349    
350    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
353            classes.
354            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
355    
356    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/dgTMatrix.R (colSums): etc. All four of
359            colSums(), rowSums(), colMeans(), rowMeans() now should work for
360            all "Matrices".
361    
362  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
363    
364          * R/lmer.R (panel.ci): Add a reference line at zero and a          * R/lmer.R (panel.ci): Add a reference line at zero and a
# Line 28  Line 389 
389    
390          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
391          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.
392          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
393    
394    
395  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 512 
512          * 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)
513          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
514          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
515          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
516    
517  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
# Line 355  Line 716 
716  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
719          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
720          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
721    
722  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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