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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1389, Fri Aug 18 13:53:33 2006 UTC
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1    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
4            the base version has no "..." argument.
5    
6            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
7    
8            * R/Matrix.R: define and
9            * NAMESPACE: export as.numeric() and as.logical() methods.
10                    Let's hope these do not badly slow down something...
11            Finally export the zapsmall() method.
12    
13    2006-08-17  Douglas Bates  <bates@R-project.org>
14    
15            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
16            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
17            * src/dtCMatrix.c :Remove code that is no longer used
18            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
19    
20    2006-08-14  Douglas Bates  <bates@R-project.org>
21    
22            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
23            Csparse_to_logical and Csparse_symmetric_to_general.
24            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
25            coercion methods between CsparseMatrix and TsparseMatrix.
26    
27    2006-08-14  Douglas Bates  <bates@R-project.org>
28    
29            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
30            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
31            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
32            possible.
33    
34    2006-08-12  Douglas Bates  <bates@R-project.org>
35    
36            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
37              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
38              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
39              generalize conversions between TsparseMatrix, CsparseMatrix,
40              denseMatrix and matrix.  Preserve triangularity property and
41              propagate Dimnames in the easy cases.
42    
43    2006-08-10  Douglas Bates  <bates@R-project.org>
44    
45            * src/lmer.c: adjust checks in glmer_init for S4SXP
46            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
47            before S4SXP but for the wrong reasons.
48    
49    2006-08-08  Douglas Bates  <bates@R-project.org>
50    
51            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
52            Later modified to return the upper triangle only.
53            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
54    
55    2006-08-07  Douglas Bates  <bates@R-project.org>
56    
57            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
58            R-level conversion to a sparse symmetric class.
59            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
60            Remove conversion to sparse symmetric classes (now done in C code).
61    
62    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
65            * man/band.Rd:  adapt the \dontshow{} unit test.
66    
67    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * DESCRIPTION (Version): 0.995-14  for CRAN
70    
71            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
72    
73            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
74            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
75    
76            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
77            * R/Tsparse.R (tril, triu, band): methods
78            * R/dgRMatrix.R (tril, ...):    ditto
79            * man/band.Rd:                  ditto
80    
81    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/Matrix.R (head, tail): directly use utils:::head.matrix
84                    to be up-to-date automatically.
85    
86    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
89    
90            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
91            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
92            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
93            such that the S4 objects are always created by the current version
94            of R and 'Matrix' class definitions.
95    
96    2006-08-01  Douglas Bates  <bates@R-project.org>
97    
98            * R/lmer.R (LMEoptimize method), tests/lmer.R,
99            inst/external/test3comp.rda: Added warnings for convergence on
100            boundary and test cases.
101    
102            * src/lmer.c (mer_postVar): Modified to return the variances that
103            are marginal to the fixed effects, not conditional on them (which
104            is what the bVar slot contents represent).
105    
106    2006-07-31  Douglas Bates  <bates@R-project.org>
107    
108            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
109            function which calls the C function mer_hat_trace2.
110    
111            * man/ranef.Rd: Include description of "postVar" argument and
112            producing a caterpillar plot.
113    
114    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * NAMESPACE:    change  "correlation" to "corMatrix"
117            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
118            * R/dpoMatrix.R: ditto
119            * R/lmer.R:      ditto
120    
121    2006-07-28  Douglas Bates  <bates@R-project.org>
122    
123            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
124            RZXinv slot's contents into a separate internal function that can
125            be used in mer_hat_trace.
126    
127    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
130            via new smart
131            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
132            utility functions.
133    
134    
135    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Csparse.R (tril, triu, band): do return *triangular* classed
138            matrices when appropriate; band() even symmetric ones.
139            (replCmat): extend to potentially all "CsparseMatrix"
140            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
141            allow subassignment for special sparse matrices.
142    
143            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
144    
145            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
146            argument; in glmer_*(): print only if(verbose).
147    
148            speed-optimize a few places by moving REAL(.) out of loops.
149    
150            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
151    
152    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
155                    since that wrongly triggers also for M[ logi , ]
156    
157            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
158            a symmetric matrix that results in a non-symmetric one.
159            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
160    
161            * R/dMatrix.R: make round(M) work as round(M, 0)
162    
163            * R/dgTMatrix.R (image): coordinate system and axis now use
164            1-based indices, not 0-based ones.
165    
166            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
167            * tests/indexing.R: test it.
168    
169            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
170            * man/isSymmetric-methods.Rd: and document it.
171    
172            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
173            * man/SparseM-conv.Rd: docu them
174    
175            * tests/other-pkgs.R: renamed from tests/graph.R and add example
176                    for 'SparseM' conversions
177    
178    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
179    
180            * R/Matrix.R (head): added head() and tail() methods.
181    
182    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * DESCRIPTION (Version): 0.995-12 released to CRAN
185    
186    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * tests/simple.R: add check for correct dsT -> dgT coercion;
189                    add check for correct printing of symmetric sparse matrices.
190    
191            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
192            for sparse symmetric matrices.
193    
194            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
195            diagonal twice.
196    
197    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
198    
199            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
200            being applied to the x slot (detected by Brian Ripley).
201    
202    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
205    
206            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
207    
208    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * src/lgCMatrix.c (lgCMatrix_diag): new function
211            * R/lgCMatrix.R (diag): for new method
212    
213            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
214                 ==> construction of illegal "*gTMatrix" via new() should
215                 now be much less easy:
216            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
217    
218            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
219                    directly.
220            * man/Matrix.Rd: documents it.
221    
222  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
223    
224          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 230 
230          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
231          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
232    
233            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
234            class.
235    
236    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/pMatrix.R: coercion pMatrix -> Tsparse
239    
240  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
241    
242            * DESCRIPTION (Version): 0.995-11 released to CRAN
243    
244          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
245          the output from mcmcsamp.          the output from mcmcsamp.
246    
# Line 23  Line 253 
253    
254          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
255          classes.          classes.
256            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
257    
258  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
# Line 60  Line 291 
291    
292          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
293          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.
294          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
295    
296    
297  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 414 
414          * 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)
415          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
416          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
417          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
418    
419  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
# Line 387  Line 618 
618  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
621          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
622          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
623    
624  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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