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Diff of /pkg/ChangeLog

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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1338, Mon Jul 31 23:06:01 2006 UTC
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1    2006-07-31  Douglas Bates  <bates@R-project.org>
2    
3            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
4            function which calls the C function mer_hat_trace2.
5    
6            * man/ranef.Rd: Include description of "postVar" argument.
7    
8    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * NAMESPACE:    change  "correlation" to "corMatrix"
11            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
12            * R/dpoMatrix.R: dito
13            * R/lmer.R:      dito
14    
15    2006-07-28  Douglas Bates  <bates@R-project.org>
16    
17            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
18            RZXinv slot's contents into a separate internal function that can
19            be used in mer_hat_trace.
20    
21    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
24            via new smart
25            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
26            utility functions.
27    
28    
29    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/Csparse.R (tril, triu, band): do return *triangular* classed
32            matrices when appropriate; band() even symmetric ones.
33            (replCmat): extend to potentially all "CsparseMatrix"
34            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
35            allow subassignment for special sparse matrices.
36    
37            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
38    
39            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
40            argument; in glmer_*(): print only if(verbose).
41    
42            speed-optimize a few places by moving REAL(.) out of loops.
43    
44            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
45    
46    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
49                    since that wrongly triggers also for M[ logi , ]
50    
51            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
52            a symmetric matrix that results in a non-symmetric one.
53            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
54    
55            * R/dMatrix.R: make round(M) work as round(M, 0)
56    
57            * R/dgTMatrix.R (image): coordinate system and axis now use
58            1-based indices, not 0-based ones.
59    
60            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
61            * tests/indexing.R: test it.
62    
63            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
64            * man/isSymmetric-methods.Rd: and document it.
65    
66            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
67            * man/SparseM-conv.Rd: docu them
68    
69            * tests/other-pkgs.R: renamed from tests/graph.R and add example
70                    for 'SparseM' conversions
71    
72    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
73    
74            * R/Matrix.R (head): added head() and tail() methods.
75    
76    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * DESCRIPTION (Version): 0.995-12 released to CRAN
79    
80    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * tests/simple.R: add check for correct dsT -> dgT coercion;
83                    add check for correct printing of symmetric sparse matrices.
84    
85            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
86            for sparse symmetric matrices.
87    
88            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
89            diagonal twice.
90    
91    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
92    
93            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
94            being applied to the x slot (detected by Brian Ripley).
95    
96    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
99    
100            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
101    
102    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * src/lgCMatrix.c (lgCMatrix_diag): new function
105            * R/lgCMatrix.R (diag): for new method
106    
107            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
108                 ==> construction of illegal "*gTMatrix" via new() should
109                 now be much less easy:
110            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
111    
112            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
113                    directly.
114            * man/Matrix.Rd: documents it.
115    
116    2006-07-06  Douglas Bates  <bates@R-project.org>
117    
118            * src/pedigree.c (pedigree_inbreeding): Correction in
119            initialization.  This function is not currently being used and is
120            not fully tested.
121    
122            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
123            Introduced the glmer class.  Added code for mcmcmsamp on glmer
124            objects.  Modified validity check on pedigree objects to account
125            for nonparallel patterns of missingness of parents.
126    
127            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
128            class.
129    
130    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/pMatrix.R: coercion pMatrix -> Tsparse
133    
134    2006-06-12  Douglas Bates  <bates@R-project.org>
135    
136            * DESCRIPTION (Version): 0.995-11 released to CRAN
137    
138            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
139            the output from mcmcsamp.
140    
141  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
142    
143          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
144            of the hat matrix.
145    
146  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
149          classes.          classes.
150            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
151    
152  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
153    

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