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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1388, Thu Aug 17 22:37:19 2006 UTC
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1    2006-08-17  Douglas Bates  <bates@R-project.org>
2    
3            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
4            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
5            * src/dtCMatrix.c :Remove code that is no longer used
6            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
7    
8    2006-08-14  Douglas Bates  <bates@R-project.org>
9    
10            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
11            Csparse_to_logical and Csparse_symmetric_to_general.
12            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
13            coercion methods between CsparseMatrix and TsparseMatrix.
14    
15    2006-08-14  Douglas Bates  <bates@R-project.org>
16    
17            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
18            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
19            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
20            possible.
21    
22    2006-08-12  Douglas Bates  <bates@R-project.org>
23    
24            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
25              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
26              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
27              generalize conversions between TsparseMatrix, CsparseMatrix,
28              denseMatrix and matrix.  Preserve triangularity property and
29              propagate Dimnames in the easy cases.
30    
31    2006-08-10  Douglas Bates  <bates@R-project.org>
32    
33            * src/lmer.c: adjust checks in glmer_init for S4SXP
34            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
35            before S4SXP but for the wrong reasons.
36    
37    2006-08-08  Douglas Bates  <bates@R-project.org>
38    
39            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
40            Later modified to return the upper triangle only.
41            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
42    
43    2006-08-07  Douglas Bates  <bates@R-project.org>
44    
45            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
46            R-level conversion to a sparse symmetric class.
47            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
48            Remove conversion to sparse symmetric classes (now done in C code).
49    
50    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
53            * man/band.Rd:  adapt the \dontshow{} unit test.
54    
55    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * DESCRIPTION (Version): 0.995-14  for CRAN
58    
59            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
60    
61            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
62            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
63    
64            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
65            * R/Tsparse.R (tril, triu, band): methods
66            * R/dgRMatrix.R (tril, ...):    ditto
67            * man/band.Rd:                  ditto
68    
69    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/Matrix.R (head, tail): directly use utils:::head.matrix
72                    to be up-to-date automatically.
73    
74    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
77    
78            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
79            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
80            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
81            such that the S4 objects are always created by the current version
82            of R and 'Matrix' class definitions.
83    
84    2006-08-01  Douglas Bates  <bates@R-project.org>
85    
86            * R/lmer.R (LMEoptimize method), tests/lmer.R,
87            inst/external/test3comp.rda: Added warnings for convergence on
88            boundary and test cases.
89    
90            * src/lmer.c (mer_postVar): Modified to return the variances that
91            are marginal to the fixed effects, not conditional on them (which
92            is what the bVar slot contents represent).
93    
94    2006-07-31  Douglas Bates  <bates@R-project.org>
95    
96            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
97            function which calls the C function mer_hat_trace2.
98    
99            * man/ranef.Rd: Include description of "postVar" argument and
100            producing a caterpillar plot.
101    
102    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * NAMESPACE:    change  "correlation" to "corMatrix"
105            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
106            * R/dpoMatrix.R: ditto
107            * R/lmer.R:      ditto
108    
109    2006-07-28  Douglas Bates  <bates@R-project.org>
110    
111            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
112            RZXinv slot's contents into a separate internal function that can
113            be used in mer_hat_trace.
114    
115    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
118            via new smart
119            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
120            utility functions.
121    
122    
123    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Csparse.R (tril, triu, band): do return *triangular* classed
126            matrices when appropriate; band() even symmetric ones.
127            (replCmat): extend to potentially all "CsparseMatrix"
128            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
129            allow subassignment for special sparse matrices.
130    
131            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
132    
133            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
134            argument; in glmer_*(): print only if(verbose).
135    
136            speed-optimize a few places by moving REAL(.) out of loops.
137    
138            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
139    
140    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
143                    since that wrongly triggers also for M[ logi , ]
144    
145            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
146            a symmetric matrix that results in a non-symmetric one.
147            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
148    
149            * R/dMatrix.R: make round(M) work as round(M, 0)
150    
151            * R/dgTMatrix.R (image): coordinate system and axis now use
152            1-based indices, not 0-based ones.
153    
154            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
155            * tests/indexing.R: test it.
156    
157            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
158            * man/isSymmetric-methods.Rd: and document it.
159    
160            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
161            * man/SparseM-conv.Rd: docu them
162    
163            * tests/other-pkgs.R: renamed from tests/graph.R and add example
164                    for 'SparseM' conversions
165    
166    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
167    
168            * R/Matrix.R (head): added head() and tail() methods.
169    
170    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * DESCRIPTION (Version): 0.995-12 released to CRAN
173    
174    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * tests/simple.R: add check for correct dsT -> dgT coercion;
177                    add check for correct printing of symmetric sparse matrices.
178    
179            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
180            for sparse symmetric matrices.
181    
182            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
183            diagonal twice.
184    
185    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
186    
187            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
188            being applied to the x slot (detected by Brian Ripley).
189    
190    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
193    
194            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
195    
196    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * src/lgCMatrix.c (lgCMatrix_diag): new function
199            * R/lgCMatrix.R (diag): for new method
200    
201            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
202                 ==> construction of illegal "*gTMatrix" via new() should
203                 now be much less easy:
204            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
205    
206            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
207                    directly.
208            * man/Matrix.Rd: documents it.
209    
210    2006-07-06  Douglas Bates  <bates@R-project.org>
211    
212            * src/pedigree.c (pedigree_inbreeding): Correction in
213            initialization.  This function is not currently being used and is
214            not fully tested.
215    
216            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
217            Introduced the glmer class.  Added code for mcmcmsamp on glmer
218            objects.  Modified validity check on pedigree objects to account
219            for nonparallel patterns of missingness of parents.
220    
221            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
222            class.
223    
224    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/pMatrix.R: coercion pMatrix -> Tsparse
227    
228    2006-06-12  Douglas Bates  <bates@R-project.org>
229    
230            * DESCRIPTION (Version): 0.995-11 released to CRAN
231    
232            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
233            the output from mcmcsamp.
234    
235    2006-06-10  Douglas Bates  <bates@R-project.org>
236    
237            * R/lmer.R (simulestimate): added C code for calculating the trace
238            of the hat matrix.
239    
240    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
243            classes.
244            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
245    
246    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dgTMatrix.R (colSums): etc. All four of
249            colSums(), rowSums(), colMeans(), rowMeans() now should work for
250            all "Matrices".
251    
252  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
253    
254          * 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 279 
279    
280          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
281          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.
282          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
283    
284    
285  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 402 
402          * 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)
403          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
404          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
405          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
406    
407  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
# Line 355  Line 606 
606  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
609          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
610          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
611    
612  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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