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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1330, Fri Jul 21 08:28:18 2006 UTC
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1    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
4            argument; in glmer_*(): print only if(verbose).
5    
6            speed-optimize a few places by moving REAL(.) out of loops.
7    
8            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
9    
10    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
13                    since that wrongly triggers also for M[ logi , ]
14    
15            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
16            a symmetric matrix that results in a non-symmetric one.
17            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
18    
19            * R/dMatrix.R: make round(M) work as round(M, 0)
20    
21            * R/dgTMatrix.R (image): coordinate system and axis now use
22            1-based indices, not 0-based ones.
23    
24            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
25            * tests/indexing.R: test it.
26    
27            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
28            * man/isSymmetric-methods.Rd: and document it.
29    
30            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
31            * man/SparseM-conv.Rd: docu them
32    
33            * tests/other-pkgs.R: renamed from tests/graph.R and add example
34                    for 'SparseM' conversions
35    
36    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
37    
38            * R/Matrix.R (head): added head() and tail() methods.
39    
40    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * DESCRIPTION (Version): 0.995-12 released to CRAN
43    
44    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * tests/simple.R: add check for correct dsT -> dgT coercion;
47                    add check for correct printing of symmetric sparse matrices.
48    
49            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
50            for sparse symmetric matrices.
51    
52            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
53            diagonal twice.
54    
55    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
56    
57            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
58            being applied to the x slot (detected by Brian Ripley).
59    
60    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
63    
64            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
65    
66    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * src/lgCMatrix.c (lgCMatrix_diag): new function
69            * R/lgCMatrix.R (diag): for new method
70    
71            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
72                 ==> construction of illegal "*gTMatrix" via new() should
73                 now be much less easy:
74            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
75    
76            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
77                    directly.
78            * man/Matrix.Rd: documents it.
79    
80    2006-07-06  Douglas Bates  <bates@R-project.org>
81    
82            * src/pedigree.c (pedigree_inbreeding): Correction in
83            initialization.  This function is not currently being used and is
84            not fully tested.
85    
86            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
87            Introduced the glmer class.  Added code for mcmcmsamp on glmer
88            objects.  Modified validity check on pedigree objects to account
89            for nonparallel patterns of missingness of parents.
90    
91            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
92            class.
93    
94    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/pMatrix.R: coercion pMatrix -> Tsparse
97    
98    2006-06-12  Douglas Bates  <bates@R-project.org>
99    
100            * DESCRIPTION (Version): 0.995-11 released to CRAN
101    
102            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
103            the output from mcmcsamp.
104    
105    2006-06-10  Douglas Bates  <bates@R-project.org>
106    
107            * R/lmer.R (simulestimate): added C code for calculating the trace
108            of the hat matrix.
109    
110    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
113            classes.
114            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
115    
116    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/dgTMatrix.R (colSums): etc. All four of
119            colSums(), rowSums(), colMeans(), rowMeans() now should work for
120            all "Matrices".
121    
122    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
123    
124            * R/lmer.R (panel.ci): Add a reference line at zero and a
125            background grid to the qqmath plot of ranef.lmer.
126    
127    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
130            grouping factors to be specified in the formula as (1|foo/bar).
131    
132    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * R/lmer.R (findbars and others): Change check of is.numeric to
135            !is.language to resolve the bug reported by Jacob Wegelin.
136    
137            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
138            code to evaluate inbreeding coefficients without calculating T,
139            based on code in Sargolzaei and Iwaisaki's paper.
140    
141    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
144            generic and mer methods for isNested and denomDF. This denomDF was
145            an attempt to emulate that in lme but I don't think that makes
146            sense.  Use the trace of the hat matrix instead.
147    
148    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
151            the C code depending on a slot structure that's no longer valid.
152            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
153    
154    
155    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
156    
157            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
158            of lowerTriMatrix generic and methods to tril (also upper to triu)
159            and added a general band extractor.
160    
161    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
162    
163            * R/pedigree.R (pedigree): Replace sire and dam values outside the
164            allowable range with NAs. Added a corresponding check in the
165            validity check for the pedigree class.
166    
167            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
168            crossprod methods now inherits from symmetricMatrix.
169    
170    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
171    
172            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
173            generics lowerTriMatrix and upperTriMatrix along with methods for
174            the Csparse virtual class.  Also added a C function Csparse_band
175            that implements these methods by calling cholmod_band.
176    
177    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
180            erased when it was NULL.  This led to invalid subselections!
181    
182    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
183    
184            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
185            in method for "t" so as not to lose the unit diagonal property.
186    
187    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
188    
189            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
190            and methods.  This is now an option to the ranef method for the
191            mer class.
192    
193            * src/cs_utils.c: Ensure that the nz component is -1 for a
194            compressed column-oriented matrix.  Minor formatting cleanup.
195    
196            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
197            objects.
198    
199    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
202            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
203    
204    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
205    
206            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
207            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
208    
209            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
210            for the dtCMatrix class.
211    
212    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
213    
214            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
215            and methods for it.
216    
217    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
220            arguments, such that M %*% 1:6 now works
221            * Tests/matprod.R: test the above
222    
223    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
224    
225            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
226            the ranef.lmer class.
227    
228            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
229            methods to extract the posterior variances from the bVar slot.
230    
231    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
234            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
235    
236            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
237            * tests/simple: (extended)
238    
239            * R/sparseMatrix.R (isTriangular): now using much improved
240            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
241    
242    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
245            (problem report from Franklin Parlamis).  This should be done
246            generally.
247    
248    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
249    
250            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
251            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
252            update the plot methods.
253    
254    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
255    
256            * R/lmer.R (resid and ranef methods):  Added methods for the
257            "residuals" and "resid" generic but only for linear mixed model
258            fits.  Changed the ranef method to return a list of data frames so
259            that the plot methods now work.
260    
261    2006-03-16  Douglas Bates  <bates@bates2>
262    
263            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
264            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
265    
266            * DESCRIPTION (Date): New release
267    
268    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
271    
272            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
273            * man/KNex.Rd: and other help files
274            * tests/*.R: several ones needed adaption
275            * inst/doc/Comparisons.Rnw: dito
276    
277    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
280    
281            * tests/indexing.R: tests for new [<- methods for sparse matrices.
282    
283    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
286    
287            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
288    
289    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/dMatrix.R: enable things like  M [ M < 10 ]
292            * R/dgeMatrix.R: implement it
293    
294    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/AllClass.R: define "summary.mer" and "*.lmer"
297            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
298            * R/lmer.R (show): now works with summary()
299    
300    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
303            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
304                    support the above
305    
306  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
307    
308          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.

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