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Diff of /pkg/ChangeLog

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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1329, Fri Jul 21 06:47:06 2006 UTC
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1    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
4                    since that wrongly triggers also for M[ logi , ]
5    
6            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
7            a symmetric matrix that results in a non-symmetric one.
8            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
9    
10            * R/dMatrix.R: make round(M) work as round(M, 0)
11    
12            * R/dgTMatrix.R (image): coordinate system and axis now use
13            1-based indices, not 0-based ones.
14    
15            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
16            * tests/indexing.R: test it.
17    
18            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
19            * man/isSymmetric-methods.Rd: and document it.
20    
21            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
22            * man/SparseM-conv.Rd: docu them
23    
24            * tests/other-pkgs.R: renamed from tests/graph.R and add example
25                    for 'SparseM' conversions
26    
27    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
28    
29            * R/Matrix.R (head): added head() and tail() methods.
30    
31    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * DESCRIPTION (Version): 0.995-12 released to CRAN
34    
35    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * tests/simple.R: add check for correct dsT -> dgT coercion;
38                    add check for correct printing of symmetric sparse matrices.
39    
40            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
41            for sparse symmetric matrices.
42    
43            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
44            diagonal twice.
45    
46    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
47    
48            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
49            being applied to the x slot (detected by Brian Ripley).
50    
51    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
54    
55            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
56    
57    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * src/lgCMatrix.c (lgCMatrix_diag): new function
60            * R/lgCMatrix.R (diag): for new method
61    
62            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
63                 ==> construction of illegal "*gTMatrix" via new() should
64                 now be much less easy:
65            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
66    
67            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
68                    directly.
69            * man/Matrix.Rd: documents it.
70    
71    2006-07-06  Douglas Bates  <bates@R-project.org>
72    
73            * src/pedigree.c (pedigree_inbreeding): Correction in
74            initialization.  This function is not currently being used and is
75            not fully tested.
76    
77            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
78            Introduced the glmer class.  Added code for mcmcmsamp on glmer
79            objects.  Modified validity check on pedigree objects to account
80            for nonparallel patterns of missingness of parents.
81    
82            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
83            class.
84    
85    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/pMatrix.R: coercion pMatrix -> Tsparse
88    
89    2006-06-12  Douglas Bates  <bates@R-project.org>
90    
91            * DESCRIPTION (Version): 0.995-11 released to CRAN
92    
93            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
94            the output from mcmcsamp.
95    
96    2006-06-10  Douglas Bates  <bates@R-project.org>
97    
98            * R/lmer.R (simulestimate): added C code for calculating the trace
99            of the hat matrix.
100    
101    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
104            classes.
105            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
106    
107    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/dgTMatrix.R (colSums): etc. All four of
110            colSums(), rowSums(), colMeans(), rowMeans() now should work for
111            all "Matrices".
112    
113    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/lmer.R (panel.ci): Add a reference line at zero and a
116            background grid to the qqmath plot of ranef.lmer.
117    
118    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
121            grouping factors to be specified in the formula as (1|foo/bar).
122    
123    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * R/lmer.R (findbars and others): Change check of is.numeric to
126            !is.language to resolve the bug reported by Jacob Wegelin.
127    
128            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
129            code to evaluate inbreeding coefficients without calculating T,
130            based on code in Sargolzaei and Iwaisaki's paper.
131    
132    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
135            generic and mer methods for isNested and denomDF. This denomDF was
136            an attempt to emulate that in lme but I don't think that makes
137            sense.  Use the trace of the hat matrix instead.
138    
139  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use

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