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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1349, Mon Aug 7 09:05:42 2006 UTC
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1    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.995-14  for CRAN
4    
5            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
6    
7            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
8            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
9    
10            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
11            * R/Tsparse.R (tril, triu, band): methods
12            * R/dgRMatrix.R (tril, ...):    dito
13            * man/band.Rd:                  dito
14    
15    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Matrix.R (head, tail): directly use utils:::head.matrix
18                    to be up-to-date automatically.
19    
20    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
23    
24            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
25            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
26            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
27            such that the S4 objects are always created by the current version
28            of R and 'Matrix' class definitions.
29    
30    2006-08-01  Douglas Bates  <bates@R-project.org>
31    
32            * R/lmer.R (LMEoptimize method), tests/lmer.R,
33            inst/external/test3comp.rda: Added warnings for convergence on
34            boundary and test cases.
35    
36            * src/lmer.c (mer_postVar): Modified to return the variances that
37            are marginal to the fixed effects, not conditional on them (which
38            is what the bVar slot contents represent).
39    
40    2006-07-31  Douglas Bates  <bates@R-project.org>
41    
42            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
43            function which calls the C function mer_hat_trace2.
44    
45            * man/ranef.Rd: Include description of "postVar" argument and
46            producing a caterpillar plot.
47    
48    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * NAMESPACE:    change  "correlation" to "corMatrix"
51            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
52            * R/dpoMatrix.R: dito
53            * R/lmer.R:      dito
54    
55    2006-07-28  Douglas Bates  <bates@R-project.org>
56    
57            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
58            RZXinv slot's contents into a separate internal function that can
59            be used in mer_hat_trace.
60    
61    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
64            via new smart
65            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
66            utility functions.
67    
68    
69    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/Csparse.R (tril, triu, band): do return *triangular* classed
72            matrices when appropriate; band() even symmetric ones.
73            (replCmat): extend to potentially all "CsparseMatrix"
74            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
75            allow subassignment for special sparse matrices.
76    
77            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
78    
79            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
80            argument; in glmer_*(): print only if(verbose).
81    
82            speed-optimize a few places by moving REAL(.) out of loops.
83    
84            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
85    
86    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
89                    since that wrongly triggers also for M[ logi , ]
90    
91            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
92            a symmetric matrix that results in a non-symmetric one.
93            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
94    
95            * R/dMatrix.R: make round(M) work as round(M, 0)
96    
97            * R/dgTMatrix.R (image): coordinate system and axis now use
98            1-based indices, not 0-based ones.
99    
100            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
101            * tests/indexing.R: test it.
102    
103            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
104            * man/isSymmetric-methods.Rd: and document it.
105    
106            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
107            * man/SparseM-conv.Rd: docu them
108    
109            * tests/other-pkgs.R: renamed from tests/graph.R and add example
110                    for 'SparseM' conversions
111    
112    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
113    
114            * R/Matrix.R (head): added head() and tail() methods.
115    
116    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * DESCRIPTION (Version): 0.995-12 released to CRAN
119    
120    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * tests/simple.R: add check for correct dsT -> dgT coercion;
123                    add check for correct printing of symmetric sparse matrices.
124    
125            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
126            for sparse symmetric matrices.
127    
128            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
129            diagonal twice.
130    
131    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
132    
133            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
134            being applied to the x slot (detected by Brian Ripley).
135    
136    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
139    
140            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
141    
142    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * src/lgCMatrix.c (lgCMatrix_diag): new function
145            * R/lgCMatrix.R (diag): for new method
146    
147            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
148                 ==> construction of illegal "*gTMatrix" via new() should
149                 now be much less easy:
150            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
151    
152            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
153                    directly.
154            * man/Matrix.Rd: documents it.
155    
156  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
157    
158          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 164 
164          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
165          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
166    
167            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
168            class.
169    
170    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/pMatrix.R: coercion pMatrix -> Tsparse
173    
174  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
175    
176            * DESCRIPTION (Version): 0.995-11 released to CRAN
177    
178          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
179          the output from mcmcsamp.          the output from mcmcsamp.
180    
# Line 23  Line 187 
187    
188          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
189          classes.          classes.
190            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
191    
192  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
193    

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