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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1373, Mon Aug 14 21:15:38 2006 UTC
# Line 1  Line 1 
1    2006-08-14  Douglas Bates  <bates@R-project.org>
2    
3            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
4            Csparse_to_logical and Csparse_symmetric_to_general.
5            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
6            coercion methods between CsparseMatrix and TsparseMatrix.
7    
8    2006-08-14  Douglas Bates  <bates@R-project.org>
9    
10            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
11            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
12            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
13            possible.
14    
15    2006-08-12  Douglas Bates  <bates@R-project.org>
16    
17            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
18              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
19              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
20              generalize conversions between TsparseMatrix, CsparseMatrix,
21              denseMatrix and matrix.  Preserve triangularity property and
22              propagate Dimnames in the easy cases.
23    
24    2006-08-10  Douglas Bates  <bates@R-project.org>
25    
26            * src/lmer.c: adjust checks in glmer_init for S4SXP
27            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
28            before S4SXP but for the wrong reasons.
29    
30    2006-08-08  Douglas Bates  <bates@R-project.org>
31    
32            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
33            Later modified to return the upper triangle only.
34            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
35    
36    2006-08-07  Douglas Bates  <bates@R-project.org>
37    
38            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
39            R-level conversion to a sparse symmetric class.
40            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
41            Remove conversion to sparse symmetric classes (now done in C code).
42    
43    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
46            * man/band.Rd:  adapt the \dontshow{} unit test.
47    
48    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * DESCRIPTION (Version): 0.995-14  for CRAN
51    
52            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
53    
54            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
55            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
56    
57            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
58            * R/Tsparse.R (tril, triu, band): methods
59            * R/dgRMatrix.R (tril, ...):    ditto
60            * man/band.Rd:                  ditto
61    
62    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/Matrix.R (head, tail): directly use utils:::head.matrix
65                    to be up-to-date automatically.
66    
67    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
70    
71            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
72            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
73            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
74            such that the S4 objects are always created by the current version
75            of R and 'Matrix' class definitions.
76    
77    2006-08-01  Douglas Bates  <bates@R-project.org>
78    
79            * R/lmer.R (LMEoptimize method), tests/lmer.R,
80            inst/external/test3comp.rda: Added warnings for convergence on
81            boundary and test cases.
82    
83            * src/lmer.c (mer_postVar): Modified to return the variances that
84            are marginal to the fixed effects, not conditional on them (which
85            is what the bVar slot contents represent).
86    
87    2006-07-31  Douglas Bates  <bates@R-project.org>
88    
89            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
90            function which calls the C function mer_hat_trace2.
91    
92            * man/ranef.Rd: Include description of "postVar" argument and
93            producing a caterpillar plot.
94    
95    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * NAMESPACE:    change  "correlation" to "corMatrix"
98            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
99            * R/dpoMatrix.R: ditto
100            * R/lmer.R:      ditto
101    
102    2006-07-28  Douglas Bates  <bates@R-project.org>
103    
104            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
105            RZXinv slot's contents into a separate internal function that can
106            be used in mer_hat_trace.
107    
108    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
111            via new smart
112            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
113            utility functions.
114    
115    
116    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Csparse.R (tril, triu, band): do return *triangular* classed
119            matrices when appropriate; band() even symmetric ones.
120            (replCmat): extend to potentially all "CsparseMatrix"
121            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
122            allow subassignment for special sparse matrices.
123    
124            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
125    
126            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
127            argument; in glmer_*(): print only if(verbose).
128    
129            speed-optimize a few places by moving REAL(.) out of loops.
130    
131            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
132    
133    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
136                    since that wrongly triggers also for M[ logi , ]
137    
138            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
139            a symmetric matrix that results in a non-symmetric one.
140            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
141    
142            * R/dMatrix.R: make round(M) work as round(M, 0)
143    
144            * R/dgTMatrix.R (image): coordinate system and axis now use
145            1-based indices, not 0-based ones.
146    
147            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
148            * tests/indexing.R: test it.
149    
150            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
151            * man/isSymmetric-methods.Rd: and document it.
152    
153            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
154            * man/SparseM-conv.Rd: docu them
155    
156            * tests/other-pkgs.R: renamed from tests/graph.R and add example
157                    for 'SparseM' conversions
158    
159    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
160    
161            * R/Matrix.R (head): added head() and tail() methods.
162    
163    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * DESCRIPTION (Version): 0.995-12 released to CRAN
166    
167    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * tests/simple.R: add check for correct dsT -> dgT coercion;
170                    add check for correct printing of symmetric sparse matrices.
171    
172            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
173            for sparse symmetric matrices.
174    
175            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
176            diagonal twice.
177    
178    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
179    
180            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
181            being applied to the x slot (detected by Brian Ripley).
182    
183    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
186    
187            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
188    
189    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/lgCMatrix.c (lgCMatrix_diag): new function
192            * R/lgCMatrix.R (diag): for new method
193    
194            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
195                 ==> construction of illegal "*gTMatrix" via new() should
196                 now be much less easy:
197            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
198    
199            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
200                    directly.
201            * man/Matrix.Rd: documents it.
202    
203    2006-07-06  Douglas Bates  <bates@R-project.org>
204    
205            * src/pedigree.c (pedigree_inbreeding): Correction in
206            initialization.  This function is not currently being used and is
207            not fully tested.
208    
209            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
210            Introduced the glmer class.  Added code for mcmcmsamp on glmer
211            objects.  Modified validity check on pedigree objects to account
212            for nonparallel patterns of missingness of parents.
213    
214            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
215            class.
216    
217    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/pMatrix.R: coercion pMatrix -> Tsparse
220    
221    2006-06-12  Douglas Bates  <bates@R-project.org>
222    
223            * DESCRIPTION (Version): 0.995-11 released to CRAN
224    
225            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
226            the output from mcmcsamp.
227    
228  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
229    
230          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
231            of the hat matrix.
232    
233  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
236          classes.          classes.
237            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
238    
239  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
# Line 43  Line 272 
272    
273          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
274          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.
275          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
276    
277    
278  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 395 
395          * 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)
396          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
397          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
398          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
399    
400  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
# Line 370  Line 599 
599  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
602          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
603          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
604    
605  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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