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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1354, Tue Aug 8 14:54:43 2006 UTC
# Line 1  Line 1 
1    2006-08-08  Douglas Bates  <bates@R-project.org>
2    
3            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1
4    
5    2006-08-07  Douglas Bates  <bates@R-project.org>
6    
7            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
8            R-level conversion to a sparse symmetric class.
9            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
10            Remove conversion to sparse symmetric classes (now done in C code).
11    
12    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
15            * man/band.Rd:  adapt the \dontshow{} unit test.
16    
17    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * DESCRIPTION (Version): 0.995-14  for CRAN
20    
21            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
22    
23            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
24            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
25    
26            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
27            * R/Tsparse.R (tril, triu, band): methods
28            * R/dgRMatrix.R (tril, ...):    ditto
29            * man/band.Rd:                  ditto
30    
31    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Matrix.R (head, tail): directly use utils:::head.matrix
34                    to be up-to-date automatically.
35    
36    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
39    
40            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
41            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
42            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
43            such that the S4 objects are always created by the current version
44            of R and 'Matrix' class definitions.
45    
46    2006-08-01  Douglas Bates  <bates@R-project.org>
47    
48            * R/lmer.R (LMEoptimize method), tests/lmer.R,
49            inst/external/test3comp.rda: Added warnings for convergence on
50            boundary and test cases.
51    
52            * src/lmer.c (mer_postVar): Modified to return the variances that
53            are marginal to the fixed effects, not conditional on them (which
54            is what the bVar slot contents represent).
55    
56    2006-07-31  Douglas Bates  <bates@R-project.org>
57    
58            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
59            function which calls the C function mer_hat_trace2.
60    
61            * man/ranef.Rd: Include description of "postVar" argument and
62            producing a caterpillar plot.
63    
64    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * NAMESPACE:    change  "correlation" to "corMatrix"
67            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
68            * R/dpoMatrix.R: ditto
69            * R/lmer.R:      ditto
70    
71    2006-07-28  Douglas Bates  <bates@R-project.org>
72    
73            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
74            RZXinv slot's contents into a separate internal function that can
75            be used in mer_hat_trace.
76    
77    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
80            via new smart
81            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
82            utility functions.
83    
84    
85    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Csparse.R (tril, triu, band): do return *triangular* classed
88            matrices when appropriate; band() even symmetric ones.
89            (replCmat): extend to potentially all "CsparseMatrix"
90            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
91            allow subassignment for special sparse matrices.
92    
93            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
94    
95            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
96            argument; in glmer_*(): print only if(verbose).
97    
98            speed-optimize a few places by moving REAL(.) out of loops.
99    
100            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
101    
102    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
105                    since that wrongly triggers also for M[ logi , ]
106    
107            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
108            a symmetric matrix that results in a non-symmetric one.
109            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
110    
111            * R/dMatrix.R: make round(M) work as round(M, 0)
112    
113            * R/dgTMatrix.R (image): coordinate system and axis now use
114            1-based indices, not 0-based ones.
115    
116            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
117            * tests/indexing.R: test it.
118    
119            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
120            * man/isSymmetric-methods.Rd: and document it.
121    
122            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
123            * man/SparseM-conv.Rd: docu them
124    
125            * tests/other-pkgs.R: renamed from tests/graph.R and add example
126                    for 'SparseM' conversions
127    
128    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
129    
130            * R/Matrix.R (head): added head() and tail() methods.
131    
132    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * DESCRIPTION (Version): 0.995-12 released to CRAN
135    
136    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * tests/simple.R: add check for correct dsT -> dgT coercion;
139                    add check for correct printing of symmetric sparse matrices.
140    
141            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
142            for sparse symmetric matrices.
143    
144            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
145            diagonal twice.
146    
147    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
148    
149            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
150            being applied to the x slot (detected by Brian Ripley).
151    
152    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
155    
156            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
157    
158    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * src/lgCMatrix.c (lgCMatrix_diag): new function
161            * R/lgCMatrix.R (diag): for new method
162    
163            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
164                 ==> construction of illegal "*gTMatrix" via new() should
165                 now be much less easy:
166            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
167    
168            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
169                    directly.
170            * man/Matrix.Rd: documents it.
171    
172  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
173    
174          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 180 
180          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
181          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
182    
183            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
184            class.
185    
186    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/pMatrix.R: coercion pMatrix -> Tsparse
189    
190  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
191    
192            * DESCRIPTION (Version): 0.995-11 released to CRAN
193    
194          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
195          the output from mcmcsamp.          the output from mcmcsamp.
196    
# Line 23  Line 203 
203    
204          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
205          classes.          classes.
206            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
207    
208  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
# Line 60  Line 241 
241    
242          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
243          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.
244          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
245    
246    
247  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 364 
364          * 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)
365          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
366          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
367          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
368    
369  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
# Line 387  Line 568 
568  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
571          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
572          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
573    
574  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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