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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1338, Mon Jul 31 23:06:01 2006 UTC
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1    2006-07-31  Douglas Bates  <bates@R-project.org>
2    
3            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
4            function which calls the C function mer_hat_trace2.
5    
6            * man/ranef.Rd: Include description of "postVar" argument.
7    
8    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * NAMESPACE:    change  "correlation" to "corMatrix"
11            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
12            * R/dpoMatrix.R: dito
13            * R/lmer.R:      dito
14    
15    2006-07-28  Douglas Bates  <bates@R-project.org>
16    
17            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
18            RZXinv slot's contents into a separate internal function that can
19            be used in mer_hat_trace.
20    
21    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
24            via new smart
25            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
26            utility functions.
27    
28    
29    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/Csparse.R (tril, triu, band): do return *triangular* classed
32            matrices when appropriate; band() even symmetric ones.
33            (replCmat): extend to potentially all "CsparseMatrix"
34            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
35            allow subassignment for special sparse matrices.
36    
37            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
38    
39            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
40            argument; in glmer_*(): print only if(verbose).
41    
42            speed-optimize a few places by moving REAL(.) out of loops.
43    
44            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
45    
46    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
49                    since that wrongly triggers also for M[ logi , ]
50    
51            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
52            a symmetric matrix that results in a non-symmetric one.
53            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
54    
55            * R/dMatrix.R: make round(M) work as round(M, 0)
56    
57            * R/dgTMatrix.R (image): coordinate system and axis now use
58            1-based indices, not 0-based ones.
59    
60            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
61            * tests/indexing.R: test it.
62    
63            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
64            * man/isSymmetric-methods.Rd: and document it.
65    
66            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
67            * man/SparseM-conv.Rd: docu them
68    
69            * tests/other-pkgs.R: renamed from tests/graph.R and add example
70                    for 'SparseM' conversions
71    
72    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
73    
74            * R/Matrix.R (head): added head() and tail() methods.
75    
76    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * DESCRIPTION (Version): 0.995-12 released to CRAN
79    
80    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * tests/simple.R: add check for correct dsT -> dgT coercion;
83                    add check for correct printing of symmetric sparse matrices.
84    
85            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
86            for sparse symmetric matrices.
87    
88            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
89            diagonal twice.
90    
91    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
92    
93            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
94            being applied to the x slot (detected by Brian Ripley).
95    
96    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
99    
100            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
101    
102    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * src/lgCMatrix.c (lgCMatrix_diag): new function
105            * R/lgCMatrix.R (diag): for new method
106    
107            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
108                 ==> construction of illegal "*gTMatrix" via new() should
109                 now be much less easy:
110            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
111    
112            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
113                    directly.
114            * man/Matrix.Rd: documents it.
115    
116    2006-07-06  Douglas Bates  <bates@R-project.org>
117    
118            * src/pedigree.c (pedigree_inbreeding): Correction in
119            initialization.  This function is not currently being used and is
120            not fully tested.
121    
122            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
123            Introduced the glmer class.  Added code for mcmcmsamp on glmer
124            objects.  Modified validity check on pedigree objects to account
125            for nonparallel patterns of missingness of parents.
126    
127            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
128            class.
129    
130    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/pMatrix.R: coercion pMatrix -> Tsparse
133    
134    2006-06-12  Douglas Bates  <bates@R-project.org>
135    
136            * DESCRIPTION (Version): 0.995-11 released to CRAN
137    
138            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
139            the output from mcmcsamp.
140    
141    2006-06-10  Douglas Bates  <bates@R-project.org>
142    
143            * R/lmer.R (simulestimate): added C code for calculating the trace
144            of the hat matrix.
145    
146    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
149            classes.
150            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
151    
152    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/dgTMatrix.R (colSums): etc. All four of
155            colSums(), rowSums(), colMeans(), rowMeans() now should work for
156            all "Matrices".
157    
158    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
159    
160            * R/lmer.R (panel.ci): Add a reference line at zero and a
161            background grid to the qqmath plot of ranef.lmer.
162    
163    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
164    
165            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
166            grouping factors to be specified in the formula as (1|foo/bar).
167    
168    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * R/lmer.R (findbars and others): Change check of is.numeric to
171            !is.language to resolve the bug reported by Jacob Wegelin.
172    
173            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
174            code to evaluate inbreeding coefficients without calculating T,
175            based on code in Sargolzaei and Iwaisaki's paper.
176    
177    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
178    
179            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
180            generic and mer methods for isNested and denomDF. This denomDF was
181            an attempt to emulate that in lme but I don't think that makes
182            sense.  Use the trace of the hat matrix instead.
183    
184    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
187            the C code depending on a slot structure that's no longer valid.
188            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
189    
190    
191    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
192    
193            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
194            of lowerTriMatrix generic and methods to tril (also upper to triu)
195            and added a general band extractor.
196    
197    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
198    
199            * R/pedigree.R (pedigree): Replace sire and dam values outside the
200            allowable range with NAs. Added a corresponding check in the
201            validity check for the pedigree class.
202    
203            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
204            crossprod methods now inherits from symmetricMatrix.
205    
206    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
207    
208            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
209            generics lowerTriMatrix and upperTriMatrix along with methods for
210            the Csparse virtual class.  Also added a C function Csparse_band
211            that implements these methods by calling cholmod_band.
212    
213    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
216            erased when it was NULL.  This led to invalid subselections!
217    
218    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
219    
220            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
221            in method for "t" so as not to lose the unit diagonal property.
222    
223    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
224    
225            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
226            and methods.  This is now an option to the ranef method for the
227            mer class.
228    
229            * src/cs_utils.c: Ensure that the nz component is -1 for a
230            compressed column-oriented matrix.  Minor formatting cleanup.
231    
232            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
233            objects.
234    
235    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
238            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
239    
240    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
241    
242            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
243            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
244    
245            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
246            for the dtCMatrix class.
247    
248    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
249    
250            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
251            and methods for it.
252    
253    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
256            arguments, such that M %*% 1:6 now works
257            * Tests/matprod.R: test the above
258    
259    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
262            the ranef.lmer class.
263    
264            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
265            methods to extract the posterior variances from the bVar slot.
266    
267    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
270            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
271    
272            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
273            * tests/simple: (extended)
274    
275            * R/sparseMatrix.R (isTriangular): now using much improved
276            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
277    
278    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
279    
280            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
281            (problem report from Franklin Parlamis).  This should be done
282            generally.
283    
284    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
287            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
288            update the plot methods.
289    
290    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
291    
292            * R/lmer.R (resid and ranef methods):  Added methods for the
293            "residuals" and "resid" generic but only for linear mixed model
294            fits.  Changed the ranef method to return a list of data frames so
295            that the plot methods now work.
296    
297    2006-03-16  Douglas Bates  <bates@bates2>
298    
299            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
300            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
301    
302            * DESCRIPTION (Date): New release
303    
304    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
307    
308            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
309            * man/KNex.Rd: and other help files
310            * tests/*.R: several ones needed adaption
311            * inst/doc/Comparisons.Rnw: dito
312    
313    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
316    
317            * tests/indexing.R: tests for new [<- methods for sparse matrices.
318    
319    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
322    
323            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
324    
325    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/dMatrix.R: enable things like  M [ M < 10 ]
328            * R/dgeMatrix.R: implement it
329    
330    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/AllClass.R: define "summary.mer" and "*.lmer"
333            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
334            * R/lmer.R (show): now works with summary()
335    
336    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
339            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
340                    support the above
341    
342  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
343    
344          * 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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