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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1335, Mon Jul 31 12:11:35 2006 UTC
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1    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * NAMESPACE:    change  "correlation" to "corMatrix"
4            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
5            * R/dpoMatrix.R: dito
6            * R/lmer.R:      dito
7    
8    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
11            via new smart
12            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
13            utility functions.
14    
15    
16    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Csparse.R (tril, triu, band): do return *triangular* classed
19            matrices when appropriate; band() even symmetric ones.
20            (replCmat): extend to potentially all "CsparseMatrix"
21            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
22            allow subassignment for special sparse matrices.
23    
24            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
25    
26            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
27            argument; in glmer_*(): print only if(verbose).
28    
29            speed-optimize a few places by moving REAL(.) out of loops.
30    
31            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
32    
33    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
36                    since that wrongly triggers also for M[ logi , ]
37    
38            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
39            a symmetric matrix that results in a non-symmetric one.
40            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
41    
42            * R/dMatrix.R: make round(M) work as round(M, 0)
43    
44            * R/dgTMatrix.R (image): coordinate system and axis now use
45            1-based indices, not 0-based ones.
46    
47            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
48            * tests/indexing.R: test it.
49    
50            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
51            * man/isSymmetric-methods.Rd: and document it.
52    
53            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
54            * man/SparseM-conv.Rd: docu them
55    
56            * tests/other-pkgs.R: renamed from tests/graph.R and add example
57                    for 'SparseM' conversions
58    
59    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
60    
61            * R/Matrix.R (head): added head() and tail() methods.
62    
63    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * DESCRIPTION (Version): 0.995-12 released to CRAN
66    
67    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * tests/simple.R: add check for correct dsT -> dgT coercion;
70                    add check for correct printing of symmetric sparse matrices.
71    
72            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
73            for sparse symmetric matrices.
74    
75            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
76            diagonal twice.
77    
78    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
79    
80            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
81            being applied to the x slot (detected by Brian Ripley).
82    
83    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
86    
87            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
88    
89    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * src/lgCMatrix.c (lgCMatrix_diag): new function
92            * R/lgCMatrix.R (diag): for new method
93    
94            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
95                 ==> construction of illegal "*gTMatrix" via new() should
96                 now be much less easy:
97            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
98    
99            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
100                    directly.
101            * man/Matrix.Rd: documents it.
102    
103    2006-07-06  Douglas Bates  <bates@R-project.org>
104    
105            * src/pedigree.c (pedigree_inbreeding): Correction in
106            initialization.  This function is not currently being used and is
107            not fully tested.
108    
109            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
110            Introduced the glmer class.  Added code for mcmcmsamp on glmer
111            objects.  Modified validity check on pedigree objects to account
112            for nonparallel patterns of missingness of parents.
113    
114            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
115            class.
116    
117    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/pMatrix.R: coercion pMatrix -> Tsparse
120    
121    2006-06-12  Douglas Bates  <bates@R-project.org>
122    
123            * DESCRIPTION (Version): 0.995-11 released to CRAN
124    
125            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
126            the output from mcmcsamp.
127    
128    2006-06-10  Douglas Bates  <bates@R-project.org>
129    
130            * R/lmer.R (simulestimate): added C code for calculating the trace
131            of the hat matrix.
132    
133    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
136            classes.
137            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
138    
139    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/dgTMatrix.R (colSums): etc. All four of
142            colSums(), rowSums(), colMeans(), rowMeans() now should work for
143            all "Matrices".
144    
145    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
146    
147            * R/lmer.R (panel.ci): Add a reference line at zero and a
148            background grid to the qqmath plot of ranef.lmer.
149    
150    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
153            grouping factors to be specified in the formula as (1|foo/bar).
154    
155    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
156    
157            * R/lmer.R (findbars and others): Change check of is.numeric to
158            !is.language to resolve the bug reported by Jacob Wegelin.
159    
160            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
161            code to evaluate inbreeding coefficients without calculating T,
162            based on code in Sargolzaei and Iwaisaki's paper.
163    
164    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
167            generic and mer methods for isNested and denomDF. This denomDF was
168            an attempt to emulate that in lme but I don't think that makes
169            sense.  Use the trace of the hat matrix instead.
170    
171  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use

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