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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1342, Tue Aug 1 20:26:45 2006 UTC
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1    2006-08-01  Douglas Bates  <bates@R-project.org>
2    
3            * R/lmer.R (LMEoptimize method), tests/lmer.R,
4            inst/external/test3comp.rda: Added warnings for convergence on
5            boundary and test cases.
6    
7            * src/lmer.c (mer_postVar): Modified to return the variances that
8            are marginal to the fixed effects, not conditional on them (which
9            is what the bVar slot contents represent).
10    
11    2006-07-31  Douglas Bates  <bates@R-project.org>
12    
13            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
14            function which calls the C function mer_hat_trace2.
15    
16            * man/ranef.Rd: Include description of "postVar" argument and
17            producing a caterpillar plot.
18    
19    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * NAMESPACE:    change  "correlation" to "corMatrix"
22            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
23            * R/dpoMatrix.R: dito
24            * R/lmer.R:      dito
25    
26    2006-07-28  Douglas Bates  <bates@R-project.org>
27    
28            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
29            RZXinv slot's contents into a separate internal function that can
30            be used in mer_hat_trace.
31    
32    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
35            via new smart
36            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
37            utility functions.
38    
39    
40    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/Csparse.R (tril, triu, band): do return *triangular* classed
43            matrices when appropriate; band() even symmetric ones.
44            (replCmat): extend to potentially all "CsparseMatrix"
45            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
46            allow subassignment for special sparse matrices.
47    
48            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
49    
50            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
51            argument; in glmer_*(): print only if(verbose).
52    
53            speed-optimize a few places by moving REAL(.) out of loops.
54    
55            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
56    
57    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
60                    since that wrongly triggers also for M[ logi , ]
61    
62            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
63            a symmetric matrix that results in a non-symmetric one.
64            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
65    
66            * R/dMatrix.R: make round(M) work as round(M, 0)
67    
68            * R/dgTMatrix.R (image): coordinate system and axis now use
69            1-based indices, not 0-based ones.
70    
71            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
72            * tests/indexing.R: test it.
73    
74            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
75            * man/isSymmetric-methods.Rd: and document it.
76    
77            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
78            * man/SparseM-conv.Rd: docu them
79    
80            * tests/other-pkgs.R: renamed from tests/graph.R and add example
81                    for 'SparseM' conversions
82    
83    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
84    
85            * R/Matrix.R (head): added head() and tail() methods.
86    
87    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * DESCRIPTION (Version): 0.995-12 released to CRAN
90    
91    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * tests/simple.R: add check for correct dsT -> dgT coercion;
94                    add check for correct printing of symmetric sparse matrices.
95    
96            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
97            for sparse symmetric matrices.
98    
99            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
100            diagonal twice.
101    
102    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
103    
104            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
105            being applied to the x slot (detected by Brian Ripley).
106    
107    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
110    
111            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
112    
113    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * src/lgCMatrix.c (lgCMatrix_diag): new function
116            * R/lgCMatrix.R (diag): for new method
117    
118            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
119                 ==> construction of illegal "*gTMatrix" via new() should
120                 now be much less easy:
121            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
122    
123            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
124                    directly.
125            * man/Matrix.Rd: documents it.
126    
127    2006-07-06  Douglas Bates  <bates@R-project.org>
128    
129            * src/pedigree.c (pedigree_inbreeding): Correction in
130            initialization.  This function is not currently being used and is
131            not fully tested.
132    
133            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
134            Introduced the glmer class.  Added code for mcmcmsamp on glmer
135            objects.  Modified validity check on pedigree objects to account
136            for nonparallel patterns of missingness of parents.
137    
138            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
139            class.
140    
141    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/pMatrix.R: coercion pMatrix -> Tsparse
144    
145    2006-06-12  Douglas Bates  <bates@R-project.org>
146    
147            * DESCRIPTION (Version): 0.995-11 released to CRAN
148    
149            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
150            the output from mcmcsamp.
151    
152  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
153    
154          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
155            of the hat matrix.
156    
157  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
160          classes.          classes.
161            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
162    
163  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
164    

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