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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1349, Mon Aug 7 09:05:42 2006 UTC
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1    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.995-14  for CRAN
4    
5            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
6    
7            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
8            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
9    
10            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
11            * R/Tsparse.R (tril, triu, band): methods
12            * R/dgRMatrix.R (tril, ...):    dito
13            * man/band.Rd:                  dito
14    
15    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Matrix.R (head, tail): directly use utils:::head.matrix
18                    to be up-to-date automatically.
19    
20    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
23    
24            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
25            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
26            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
27            such that the S4 objects are always created by the current version
28            of R and 'Matrix' class definitions.
29    
30    2006-08-01  Douglas Bates  <bates@R-project.org>
31    
32            * R/lmer.R (LMEoptimize method), tests/lmer.R,
33            inst/external/test3comp.rda: Added warnings for convergence on
34            boundary and test cases.
35    
36            * src/lmer.c (mer_postVar): Modified to return the variances that
37            are marginal to the fixed effects, not conditional on them (which
38            is what the bVar slot contents represent).
39    
40    2006-07-31  Douglas Bates  <bates@R-project.org>
41    
42            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
43            function which calls the C function mer_hat_trace2.
44    
45            * man/ranef.Rd: Include description of "postVar" argument and
46            producing a caterpillar plot.
47    
48    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * NAMESPACE:    change  "correlation" to "corMatrix"
51            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
52            * R/dpoMatrix.R: dito
53            * R/lmer.R:      dito
54    
55    2006-07-28  Douglas Bates  <bates@R-project.org>
56    
57            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
58            RZXinv slot's contents into a separate internal function that can
59            be used in mer_hat_trace.
60    
61    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
64            via new smart
65            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
66            utility functions.
67    
68    
69    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/Csparse.R (tril, triu, band): do return *triangular* classed
72            matrices when appropriate; band() even symmetric ones.
73            (replCmat): extend to potentially all "CsparseMatrix"
74            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
75            allow subassignment for special sparse matrices.
76    
77            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
78    
79            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
80            argument; in glmer_*(): print only if(verbose).
81    
82            speed-optimize a few places by moving REAL(.) out of loops.
83    
84            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
85    
86    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
89                    since that wrongly triggers also for M[ logi , ]
90    
91            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
92            a symmetric matrix that results in a non-symmetric one.
93            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
94    
95            * R/dMatrix.R: make round(M) work as round(M, 0)
96    
97            * R/dgTMatrix.R (image): coordinate system and axis now use
98            1-based indices, not 0-based ones.
99    
100            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
101            * tests/indexing.R: test it.
102    
103            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
104            * man/isSymmetric-methods.Rd: and document it.
105    
106            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
107            * man/SparseM-conv.Rd: docu them
108    
109            * tests/other-pkgs.R: renamed from tests/graph.R and add example
110                    for 'SparseM' conversions
111    
112    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
113    
114            * R/Matrix.R (head): added head() and tail() methods.
115    
116    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * DESCRIPTION (Version): 0.995-12 released to CRAN
119    
120    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * tests/simple.R: add check for correct dsT -> dgT coercion;
123                    add check for correct printing of symmetric sparse matrices.
124    
125            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
126            for sparse symmetric matrices.
127    
128            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
129            diagonal twice.
130    
131    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
132    
133            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
134            being applied to the x slot (detected by Brian Ripley).
135    
136    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
139    
140            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
141    
142    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * src/lgCMatrix.c (lgCMatrix_diag): new function
145            * R/lgCMatrix.R (diag): for new method
146    
147            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
148                 ==> construction of illegal "*gTMatrix" via new() should
149                 now be much less easy:
150            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
151    
152            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
153                    directly.
154            * man/Matrix.Rd: documents it.
155    
156    2006-07-06  Douglas Bates  <bates@R-project.org>
157    
158            * src/pedigree.c (pedigree_inbreeding): Correction in
159            initialization.  This function is not currently being used and is
160            not fully tested.
161    
162            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
163            Introduced the glmer class.  Added code for mcmcmsamp on glmer
164            objects.  Modified validity check on pedigree objects to account
165            for nonparallel patterns of missingness of parents.
166    
167            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
168            class.
169    
170    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/pMatrix.R: coercion pMatrix -> Tsparse
173    
174    2006-06-12  Douglas Bates  <bates@R-project.org>
175    
176            * DESCRIPTION (Version): 0.995-11 released to CRAN
177    
178            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
179            the output from mcmcsamp.
180    
181    2006-06-10  Douglas Bates  <bates@R-project.org>
182    
183            * R/lmer.R (simulestimate): added C code for calculating the trace
184            of the hat matrix.
185    
186    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
189            classes.
190            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
191    
192    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/dgTMatrix.R (colSums): etc. All four of
195            colSums(), rowSums(), colMeans(), rowMeans() now should work for
196            all "Matrices".
197    
198    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * R/lmer.R (panel.ci): Add a reference line at zero and a
201            background grid to the qqmath plot of ranef.lmer.
202    
203    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
206            grouping factors to be specified in the formula as (1|foo/bar).
207    
208    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * R/lmer.R (findbars and others): Change check of is.numeric to
211            !is.language to resolve the bug reported by Jacob Wegelin.
212    
213            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
214            code to evaluate inbreeding coefficients without calculating T,
215            based on code in Sargolzaei and Iwaisaki's paper.
216    
217    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
218    
219            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
220            generic and mer methods for isNested and denomDF. This denomDF was
221            an attempt to emulate that in lme but I don't think that makes
222            sense.  Use the trace of the hat matrix instead.
223    
224  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use

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