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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1346, Thu Aug 3 17:17:55 2006 UTC
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1    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
4    
5            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
6            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
7            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
8            such that the S4 objects are always created by the current version
9            of R and 'Matrix' class definitions.
10    
11    2006-08-01  Douglas Bates  <bates@R-project.org>
12    
13            * R/lmer.R (LMEoptimize method), tests/lmer.R,
14            inst/external/test3comp.rda: Added warnings for convergence on
15            boundary and test cases.
16    
17            * src/lmer.c (mer_postVar): Modified to return the variances that
18            are marginal to the fixed effects, not conditional on them (which
19            is what the bVar slot contents represent).
20    
21    2006-07-31  Douglas Bates  <bates@R-project.org>
22    
23            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
24            function which calls the C function mer_hat_trace2.
25    
26            * man/ranef.Rd: Include description of "postVar" argument and
27            producing a caterpillar plot.
28    
29    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * NAMESPACE:    change  "correlation" to "corMatrix"
32            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
33            * R/dpoMatrix.R: dito
34            * R/lmer.R:      dito
35    
36    2006-07-28  Douglas Bates  <bates@R-project.org>
37    
38            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
39            RZXinv slot's contents into a separate internal function that can
40            be used in mer_hat_trace.
41    
42    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
45            via new smart
46            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
47            utility functions.
48    
49    
50    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Csparse.R (tril, triu, band): do return *triangular* classed
53            matrices when appropriate; band() even symmetric ones.
54            (replCmat): extend to potentially all "CsparseMatrix"
55            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
56            allow subassignment for special sparse matrices.
57    
58            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
59    
60            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
61            argument; in glmer_*(): print only if(verbose).
62    
63            speed-optimize a few places by moving REAL(.) out of loops.
64    
65            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
66    
67    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
70                    since that wrongly triggers also for M[ logi , ]
71    
72            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
73            a symmetric matrix that results in a non-symmetric one.
74            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
75    
76            * R/dMatrix.R: make round(M) work as round(M, 0)
77    
78            * R/dgTMatrix.R (image): coordinate system and axis now use
79            1-based indices, not 0-based ones.
80    
81            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
82            * tests/indexing.R: test it.
83    
84            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
85            * man/isSymmetric-methods.Rd: and document it.
86    
87            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
88            * man/SparseM-conv.Rd: docu them
89    
90            * tests/other-pkgs.R: renamed from tests/graph.R and add example
91                    for 'SparseM' conversions
92    
93    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
94    
95            * R/Matrix.R (head): added head() and tail() methods.
96    
97    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * DESCRIPTION (Version): 0.995-12 released to CRAN
100    
101    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * tests/simple.R: add check for correct dsT -> dgT coercion;
104                    add check for correct printing of symmetric sparse matrices.
105    
106            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
107            for sparse symmetric matrices.
108    
109            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
110            diagonal twice.
111    
112    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
113    
114            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
115            being applied to the x slot (detected by Brian Ripley).
116    
117    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
120    
121            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
122    
123    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * src/lgCMatrix.c (lgCMatrix_diag): new function
126            * R/lgCMatrix.R (diag): for new method
127    
128            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
129                 ==> construction of illegal "*gTMatrix" via new() should
130                 now be much less easy:
131            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
132    
133            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
134                    directly.
135            * man/Matrix.Rd: documents it.
136    
137    2006-07-06  Douglas Bates  <bates@R-project.org>
138    
139            * src/pedigree.c (pedigree_inbreeding): Correction in
140            initialization.  This function is not currently being used and is
141            not fully tested.
142    
143            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
144            Introduced the glmer class.  Added code for mcmcmsamp on glmer
145            objects.  Modified validity check on pedigree objects to account
146            for nonparallel patterns of missingness of parents.
147    
148            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
149            class.
150    
151    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/pMatrix.R: coercion pMatrix -> Tsparse
154    
155    2006-06-12  Douglas Bates  <bates@R-project.org>
156    
157            * DESCRIPTION (Version): 0.995-11 released to CRAN
158    
159            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
160            the output from mcmcsamp.
161    
162    2006-06-10  Douglas Bates  <bates@R-project.org>
163    
164            * R/lmer.R (simulestimate): added C code for calculating the trace
165            of the hat matrix.
166    
167    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
170            classes.
171            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
172    
173    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgTMatrix.R (colSums): etc. All four of
176            colSums(), rowSums(), colMeans(), rowMeans() now should work for
177            all "Matrices".
178    
179    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
180    
181            * R/lmer.R (panel.ci): Add a reference line at zero and a
182            background grid to the qqmath plot of ranef.lmer.
183    
184    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
185    
186            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
187            grouping factors to be specified in the formula as (1|foo/bar).
188    
189    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
190    
191            * R/lmer.R (findbars and others): Change check of is.numeric to
192            !is.language to resolve the bug reported by Jacob Wegelin.
193    
194            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
195            code to evaluate inbreeding coefficients without calculating T,
196            based on code in Sargolzaei and Iwaisaki's paper.
197    
198    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
201            generic and mer methods for isNested and denomDF. This denomDF was
202            an attempt to emulate that in lme but I don't think that makes
203            sense.  Use the trace of the hat matrix instead.
204    
205  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use

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