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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1331, Sat Jul 22 17:59:53 2006 UTC
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1    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
4            via new smart
5            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
6            utility functions.
7    
8    
9    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/Csparse.R (tril, triu, band): do return *triangular* classed
12            matrices when appropriate; band() even symmetric ones.
13            (replCmat): extend to potentially all "CsparseMatrix"
14            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
15            allow subassignment for special sparse matrices.
16    
17            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
18    
19            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
20            argument; in glmer_*(): print only if(verbose).
21    
22            speed-optimize a few places by moving REAL(.) out of loops.
23    
24            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
25    
26    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
29                    since that wrongly triggers also for M[ logi , ]
30    
31            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
32            a symmetric matrix that results in a non-symmetric one.
33            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
34    
35            * R/dMatrix.R: make round(M) work as round(M, 0)
36    
37            * R/dgTMatrix.R (image): coordinate system and axis now use
38            1-based indices, not 0-based ones.
39    
40            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
41            * tests/indexing.R: test it.
42    
43            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
44            * man/isSymmetric-methods.Rd: and document it.
45    
46            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
47            * man/SparseM-conv.Rd: docu them
48    
49            * tests/other-pkgs.R: renamed from tests/graph.R and add example
50                    for 'SparseM' conversions
51    
52    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
53    
54            * R/Matrix.R (head): added head() and tail() methods.
55    
56    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Version): 0.995-12 released to CRAN
59    
60    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * tests/simple.R: add check for correct dsT -> dgT coercion;
63                    add check for correct printing of symmetric sparse matrices.
64    
65            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
66            for sparse symmetric matrices.
67    
68            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
69            diagonal twice.
70    
71    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
72    
73            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
74            being applied to the x slot (detected by Brian Ripley).
75    
76    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
79    
80            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
81    
82    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * src/lgCMatrix.c (lgCMatrix_diag): new function
85            * R/lgCMatrix.R (diag): for new method
86    
87            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
88                 ==> construction of illegal "*gTMatrix" via new() should
89                 now be much less easy:
90            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
91    
92            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
93                    directly.
94            * man/Matrix.Rd: documents it.
95    
96    2006-07-06  Douglas Bates  <bates@R-project.org>
97    
98            * src/pedigree.c (pedigree_inbreeding): Correction in
99            initialization.  This function is not currently being used and is
100            not fully tested.
101    
102            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
103            Introduced the glmer class.  Added code for mcmcmsamp on glmer
104            objects.  Modified validity check on pedigree objects to account
105            for nonparallel patterns of missingness of parents.
106    
107            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
108            class.
109    
110    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/pMatrix.R: coercion pMatrix -> Tsparse
113    
114    2006-06-12  Douglas Bates  <bates@R-project.org>
115    
116            * DESCRIPTION (Version): 0.995-11 released to CRAN
117    
118            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
119            the output from mcmcsamp.
120    
121    2006-06-10  Douglas Bates  <bates@R-project.org>
122    
123            * R/lmer.R (simulestimate): added C code for calculating the trace
124            of the hat matrix.
125    
126    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
129            classes.
130            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
131    
132    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/dgTMatrix.R (colSums): etc. All four of
135            colSums(), rowSums(), colMeans(), rowMeans() now should work for
136            all "Matrices".
137    
138    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
139    
140            * R/lmer.R (panel.ci): Add a reference line at zero and a
141            background grid to the qqmath plot of ranef.lmer.
142    
143    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
144    
145            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
146            grouping factors to be specified in the formula as (1|foo/bar).
147    
148    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
149    
150            * R/lmer.R (findbars and others): Change check of is.numeric to
151            !is.language to resolve the bug reported by Jacob Wegelin.
152    
153            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
154            code to evaluate inbreeding coefficients without calculating T,
155            based on code in Sargolzaei and Iwaisaki's paper.
156    
157    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
158    
159            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
160            generic and mer methods for isNested and denomDF. This denomDF was
161            an attempt to emulate that in lme but I don't think that makes
162            sense.  Use the trace of the hat matrix instead.
163    
164  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use

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