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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1472, Fri Sep 1 15:31:04 2006 UTC
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1    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
4            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
5    
6            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
7    
8    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
11            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
12            * R/dsparseMatrix.R: dito
13            * R/Csparse.R: dito
14    
15    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/dMatrix.R (Compare): improve availability of "<", etc
18            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
19    
20    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
23            of a 0-index which was used as 1-index (..hmm)
24    
25            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
26    
27            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
28            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
29            (.is.diagonal): dito
30    
31            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
32    
33            * R/Matrix.R (Matrix): also work for NA data
34    
35    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
38            in all cases.
39    
40    2006-08-27  Douglas Bates  <bates@R-project.org>
41    
42            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
43            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
44    
45    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
48            subclasses of "ddenseMatrix"
49            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
50            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
51            instead of half dozen specialized ones.
52    
53    2006-08-25  Douglas Bates  <bates@R-project.org>
54    
55            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
56            <tillard@cirad.fr> - ordering standard errors to match effects.
57    
58    2006-08-24  Douglas Bates  <bates@R-project.org>
59    
60            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
61            on R_ldl.
62            * R/lCholCMatrix.R,
63            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
64            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
65            * many files in ./R and ./src: Use more general version of
66            dup_mMatrix_as_dgeMatrix to simplify method definitions.
67            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
68            dtpMatrix, dspMatrix and dppMatrix conversions.
69    
70    
71    2006-08-23  Douglas Bates  <bates@R-project.org>
72    
73            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
74            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
75            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
76            dgeMatrix_crossprod (may need to do this in other places).
77            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
78            generic and method for dsCMatrix.  Use CHOLMOD for chol().
79    
80    2006-08-22  Douglas Bates  <bates@R-project.org>
81    
82            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
83            types of classed Matrices, matrices or numeric or logical vectors.
84            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
85            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
86            to Mutils.h (as an inline) and change name to Matrix_check_class;
87            fixes in as_cholmod_factor and chm_factor_to_SEXP.
88            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
89            dsCMatrix_matrix_solve.  Comment out vestigial functions.
90            * src/Csparse.c: use diag_P and uplo_P macros.
91    
92    2006-08-21  Douglas Bates  <bates@R-project.org>
93    
94            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
95            valgrind.
96            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
97            inverses.
98            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
99            -Wall warnings.
100            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
101            Use dup_mMatrix_as_dgeMatrix.
102    
103    2006-08-20  Douglas Bates  <bates@R-project.org>
104    
105            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
106            * tests/sparseQR.R: Added
107            * man/sparseQR-class.Rd: Document methods for qr.* generics
108            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
109    
110    2006-08-19  Douglas Bates  <bates@R-project.org>
111    
112            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
113            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
114            and qr.fitted.
115            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
116            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
117    
118    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
121            the base version has no "..." argument.
122    
123            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
124    
125            * R/Matrix.R: define and
126            * NAMESPACE: export as.numeric() and as.logical() methods.
127                    Let's hope these do not badly slow down something...
128            Finally export the zapsmall() method.
129    
130    2006-08-17  Douglas Bates  <bates@R-project.org>
131    
132            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
133            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
134            * src/dtCMatrix.c :Remove code that is no longer used
135            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
136    
137    2006-08-14  Douglas Bates  <bates@R-project.org>
138    
139            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
140            Csparse_to_logical and Csparse_symmetric_to_general.
141            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
142            coercion methods between CsparseMatrix and TsparseMatrix.
143    
144    2006-08-14  Douglas Bates  <bates@R-project.org>
145    
146            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
147            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
148            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
149            possible.
150    
151    2006-08-12  Douglas Bates  <bates@R-project.org>
152    
153            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
154              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
155              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
156              generalize conversions between TsparseMatrix, CsparseMatrix,
157              denseMatrix and matrix.  Preserve triangularity property and
158              propagate Dimnames in the easy cases.
159    
160    2006-08-10  Douglas Bates  <bates@R-project.org>
161    
162            * src/lmer.c: adjust checks in glmer_init for S4SXP
163            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
164            before S4SXP but for the wrong reasons.
165    
166    2006-08-08  Douglas Bates  <bates@R-project.org>
167    
168            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
169            Later modified to return the upper triangle only.
170            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
171    
172    2006-08-07  Douglas Bates  <bates@R-project.org>
173    
174            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
175            R-level conversion to a sparse symmetric class.
176            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
177            Remove conversion to sparse symmetric classes (now done in C code).
178    
179    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
182            * man/band.Rd:  adapt the \dontshow{} unit test.
183    
184    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * DESCRIPTION (Version): 0.995-14  for CRAN
187    
188            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
189    
190            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
191            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
192    
193            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
194            * R/Tsparse.R (tril, triu, band): methods
195            * R/dgRMatrix.R (tril, ...):    ditto
196            * man/band.Rd:                  ditto
197    
198    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/Matrix.R (head, tail): directly use utils:::head.matrix
201                    to be up-to-date automatically.
202    
203    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
206    
207            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
208            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
209            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
210            such that the S4 objects are always created by the current version
211            of R and 'Matrix' class definitions.
212    
213    2006-08-01  Douglas Bates  <bates@R-project.org>
214    
215            * R/lmer.R (LMEoptimize method), tests/lmer.R,
216            inst/external/test3comp.rda: Added warnings for convergence on
217            boundary and test cases.
218    
219            * src/lmer.c (mer_postVar): Modified to return the variances that
220            are marginal to the fixed effects, not conditional on them (which
221            is what the bVar slot contents represent).
222    
223    2006-07-31  Douglas Bates  <bates@R-project.org>
224    
225            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
226            function which calls the C function mer_hat_trace2.
227    
228            * man/ranef.Rd: Include description of "postVar" argument and
229            producing a caterpillar plot.
230    
231    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * NAMESPACE:    change  "correlation" to "corMatrix"
234            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
235            * R/dpoMatrix.R: ditto
236            * R/lmer.R:      ditto
237    
238    2006-07-28  Douglas Bates  <bates@R-project.org>
239    
240            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
241            RZXinv slot's contents into a separate internal function that can
242            be used in mer_hat_trace.
243    
244    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
247            via new smart
248            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
249            utility functions.
250    
251    
252    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Csparse.R (tril, triu, band): do return *triangular* classed
255            matrices when appropriate; band() even symmetric ones.
256            (replCmat): extend to potentially all "CsparseMatrix"
257            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
258            allow subassignment for special sparse matrices.
259    
260            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
261    
262            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
263            argument; in glmer_*(): print only if(verbose).
264    
265            speed-optimize a few places by moving REAL(.) out of loops.
266    
267            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
268    
269    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
272                    since that wrongly triggers also for M[ logi , ]
273    
274            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
275            a symmetric matrix that results in a non-symmetric one.
276            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
277    
278            * R/dMatrix.R: make round(M) work as round(M, 0)
279    
280            * R/dgTMatrix.R (image): coordinate system and axis now use
281            1-based indices, not 0-based ones.
282    
283            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
284            * tests/indexing.R: test it.
285    
286            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
287            * man/isSymmetric-methods.Rd: and document it.
288    
289            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
290            * man/SparseM-conv.Rd: docu them
291    
292            * tests/other-pkgs.R: renamed from tests/graph.R and add example
293                    for 'SparseM' conversions
294    
295    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
296    
297            * R/Matrix.R (head): added head() and tail() methods.
298    
299    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * DESCRIPTION (Version): 0.995-12 released to CRAN
302    
303    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * tests/simple.R: add check for correct dsT -> dgT coercion;
306                    add check for correct printing of symmetric sparse matrices.
307    
308            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
309            for sparse symmetric matrices.
310    
311            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
312            diagonal twice.
313    
314    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
315    
316            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
317            being applied to the x slot (detected by Brian Ripley).
318    
319    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
322    
323            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
324    
325    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * src/lgCMatrix.c (lgCMatrix_diag): new function
328            * R/lgCMatrix.R (diag): for new method
329    
330            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
331                 ==> construction of illegal "*gTMatrix" via new() should
332                 now be much less easy:
333            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
334    
335            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
336                    directly.
337            * man/Matrix.Rd: documents it.
338    
339    2006-07-06  Douglas Bates  <bates@R-project.org>
340    
341            * src/pedigree.c (pedigree_inbreeding): Correction in
342            initialization.  This function is not currently being used and is
343            not fully tested.
344    
345            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
346            Introduced the glmer class.  Added code for mcmcmsamp on glmer
347            objects.  Modified validity check on pedigree objects to account
348            for nonparallel patterns of missingness of parents.
349    
350            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
351            class.
352    
353    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/pMatrix.R: coercion pMatrix -> Tsparse
356    
357    2006-06-12  Douglas Bates  <bates@R-project.org>
358    
359            * DESCRIPTION (Version): 0.995-11 released to CRAN
360    
361            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
362            the output from mcmcsamp.
363    
364  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
365    
366          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
367            of the hat matrix.
368    
369  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
372          classes.          classes.
373            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
374    
375  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
# Line 43  Line 408 
408    
409          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
410          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.
411          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
412    
413    
414  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 531 
531          * 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)
532          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
533          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
534          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
535    
536  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
# Line 370  Line 735 
735  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
738          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
739          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
740    
741  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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