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Diff of /pkg/ChangeLog

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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1330, Fri Jul 21 08:28:18 2006 UTC
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1    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
4            argument; in glmer_*(): print only if(verbose).
5    
6            speed-optimize a few places by moving REAL(.) out of loops.
7    
8            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
9    
10    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
13                    since that wrongly triggers also for M[ logi , ]
14    
15            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
16            a symmetric matrix that results in a non-symmetric one.
17            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
18    
19            * R/dMatrix.R: make round(M) work as round(M, 0)
20    
21            * R/dgTMatrix.R (image): coordinate system and axis now use
22            1-based indices, not 0-based ones.
23    
24            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
25            * tests/indexing.R: test it.
26    
27            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
28            * man/isSymmetric-methods.Rd: and document it.
29    
30            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
31            * man/SparseM-conv.Rd: docu them
32    
33            * tests/other-pkgs.R: renamed from tests/graph.R and add example
34                    for 'SparseM' conversions
35    
36    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
37    
38            * R/Matrix.R (head): added head() and tail() methods.
39    
40    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * DESCRIPTION (Version): 0.995-12 released to CRAN
43    
44    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * tests/simple.R: add check for correct dsT -> dgT coercion;
47                    add check for correct printing of symmetric sparse matrices.
48    
49            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
50            for sparse symmetric matrices.
51    
52            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
53            diagonal twice.
54    
55    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
56    
57            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
58            being applied to the x slot (detected by Brian Ripley).
59    
60    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
63    
64            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
65    
66    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * src/lgCMatrix.c (lgCMatrix_diag): new function
69            * R/lgCMatrix.R (diag): for new method
70    
71            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
72                 ==> construction of illegal "*gTMatrix" via new() should
73                 now be much less easy:
74            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
75    
76            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
77                    directly.
78            * man/Matrix.Rd: documents it.
79    
80    2006-07-06  Douglas Bates  <bates@R-project.org>
81    
82            * src/pedigree.c (pedigree_inbreeding): Correction in
83            initialization.  This function is not currently being used and is
84            not fully tested.
85    
86            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
87            Introduced the glmer class.  Added code for mcmcmsamp on glmer
88            objects.  Modified validity check on pedigree objects to account
89            for nonparallel patterns of missingness of parents.
90    
91            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
92            class.
93    
94    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/pMatrix.R: coercion pMatrix -> Tsparse
97    
98    2006-06-12  Douglas Bates  <bates@R-project.org>
99    
100            * DESCRIPTION (Version): 0.995-11 released to CRAN
101    
102            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
103            the output from mcmcsamp.
104    
105    2006-06-10  Douglas Bates  <bates@R-project.org>
106    
107            * R/lmer.R (simulestimate): added C code for calculating the trace
108            of the hat matrix.
109    
110    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
113            classes.
114            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
115    
116    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/dgTMatrix.R (colSums): etc. All four of
119            colSums(), rowSums(), colMeans(), rowMeans() now should work for
120            all "Matrices".
121    
122    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
123    
124            * R/lmer.R (panel.ci): Add a reference line at zero and a
125            background grid to the qqmath plot of ranef.lmer.
126    
127    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
130            grouping factors to be specified in the formula as (1|foo/bar).
131    
132    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * R/lmer.R (findbars and others): Change check of is.numeric to
135            !is.language to resolve the bug reported by Jacob Wegelin.
136    
137            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
138            code to evaluate inbreeding coefficients without calculating T,
139            based on code in Sargolzaei and Iwaisaki's paper.
140    
141    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
144            generic and mer methods for isNested and denomDF. This denomDF was
145            an attempt to emulate that in lme but I don't think that makes
146            sense.  Use the trace of the hat matrix instead.
147    
148  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use

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