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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1351, Mon Aug 7 16:51:14 2006 UTC
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1    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
4            * man/band.Rd:  adapt the \dontshow{} unit test.
5    
6    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * DESCRIPTION (Version): 0.995-14  for CRAN
9    
10            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
11    
12            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
13            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
14    
15            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
16            * R/Tsparse.R (tril, triu, band): methods
17            * R/dgRMatrix.R (tril, ...):    dito
18            * man/band.Rd:                  dito
19    
20    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Matrix.R (head, tail): directly use utils:::head.matrix
23                    to be up-to-date automatically.
24    
25    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
28    
29            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
30            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
31            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
32            such that the S4 objects are always created by the current version
33            of R and 'Matrix' class definitions.
34    
35    2006-08-01  Douglas Bates  <bates@R-project.org>
36    
37            * R/lmer.R (LMEoptimize method), tests/lmer.R,
38            inst/external/test3comp.rda: Added warnings for convergence on
39            boundary and test cases.
40    
41            * src/lmer.c (mer_postVar): Modified to return the variances that
42            are marginal to the fixed effects, not conditional on them (which
43            is what the bVar slot contents represent).
44    
45    2006-07-31  Douglas Bates  <bates@R-project.org>
46    
47            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
48            function which calls the C function mer_hat_trace2.
49    
50            * man/ranef.Rd: Include description of "postVar" argument and
51            producing a caterpillar plot.
52    
53    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * NAMESPACE:    change  "correlation" to "corMatrix"
56            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
57            * R/dpoMatrix.R: dito
58            * R/lmer.R:      dito
59    
60    2006-07-28  Douglas Bates  <bates@R-project.org>
61    
62            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
63            RZXinv slot's contents into a separate internal function that can
64            be used in mer_hat_trace.
65    
66    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
69            via new smart
70            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
71            utility functions.
72    
73    
74    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Csparse.R (tril, triu, band): do return *triangular* classed
77            matrices when appropriate; band() even symmetric ones.
78            (replCmat): extend to potentially all "CsparseMatrix"
79            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
80            allow subassignment for special sparse matrices.
81    
82            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
83    
84            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
85            argument; in glmer_*(): print only if(verbose).
86    
87            speed-optimize a few places by moving REAL(.) out of loops.
88    
89            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
90    
91    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
94                    since that wrongly triggers also for M[ logi , ]
95    
96            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
97            a symmetric matrix that results in a non-symmetric one.
98            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
99    
100            * R/dMatrix.R: make round(M) work as round(M, 0)
101    
102            * R/dgTMatrix.R (image): coordinate system and axis now use
103            1-based indices, not 0-based ones.
104    
105            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
106            * tests/indexing.R: test it.
107    
108            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
109            * man/isSymmetric-methods.Rd: and document it.
110    
111            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
112            * man/SparseM-conv.Rd: docu them
113    
114            * tests/other-pkgs.R: renamed from tests/graph.R and add example
115                    for 'SparseM' conversions
116    
117    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
118    
119            * R/Matrix.R (head): added head() and tail() methods.
120    
121    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * DESCRIPTION (Version): 0.995-12 released to CRAN
124    
125    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * tests/simple.R: add check for correct dsT -> dgT coercion;
128                    add check for correct printing of symmetric sparse matrices.
129    
130            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
131            for sparse symmetric matrices.
132    
133            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
134            diagonal twice.
135    
136    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
137    
138            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
139            being applied to the x slot (detected by Brian Ripley).
140    
141    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
144    
145            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
146    
147    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * src/lgCMatrix.c (lgCMatrix_diag): new function
150            * R/lgCMatrix.R (diag): for new method
151    
152            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
153                 ==> construction of illegal "*gTMatrix" via new() should
154                 now be much less easy:
155            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
156    
157            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
158                    directly.
159            * man/Matrix.Rd: documents it.
160    
161    2006-07-06  Douglas Bates  <bates@R-project.org>
162    
163            * src/pedigree.c (pedigree_inbreeding): Correction in
164            initialization.  This function is not currently being used and is
165            not fully tested.
166    
167            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
168            Introduced the glmer class.  Added code for mcmcmsamp on glmer
169            objects.  Modified validity check on pedigree objects to account
170            for nonparallel patterns of missingness of parents.
171    
172            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
173            class.
174    
175    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/pMatrix.R: coercion pMatrix -> Tsparse
178    
179    2006-06-12  Douglas Bates  <bates@R-project.org>
180    
181            * DESCRIPTION (Version): 0.995-11 released to CRAN
182    
183            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
184            the output from mcmcsamp.
185    
186    2006-06-10  Douglas Bates  <bates@R-project.org>
187    
188            * R/lmer.R (simulestimate): added C code for calculating the trace
189            of the hat matrix.
190    
191    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
194            classes.
195            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
196    
197    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/dgTMatrix.R (colSums): etc. All four of
200            colSums(), rowSums(), colMeans(), rowMeans() now should work for
201            all "Matrices".
202    
203    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * R/lmer.R (panel.ci): Add a reference line at zero and a
206            background grid to the qqmath plot of ranef.lmer.
207    
208    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
211            grouping factors to be specified in the formula as (1|foo/bar).
212    
213    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
214    
215            * R/lmer.R (findbars and others): Change check of is.numeric to
216            !is.language to resolve the bug reported by Jacob Wegelin.
217    
218            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
219            code to evaluate inbreeding coefficients without calculating T,
220            based on code in Sargolzaei and Iwaisaki's paper.
221    
222    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
223    
224            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
225            generic and mer methods for isNested and denomDF. This denomDF was
226            an attempt to emulate that in lme but I don't think that makes
227            sense.  Use the trace of the hat matrix instead.
228    
229    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
232            the C code depending on a slot structure that's no longer valid.
233            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
234    
235    
236    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
237    
238            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
239            of lowerTriMatrix generic and methods to tril (also upper to triu)
240            and added a general band extractor.
241    
242    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * R/pedigree.R (pedigree): Replace sire and dam values outside the
245            allowable range with NAs. Added a corresponding check in the
246            validity check for the pedigree class.
247    
248            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
249            crossprod methods now inherits from symmetricMatrix.
250    
251    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
254            generics lowerTriMatrix and upperTriMatrix along with methods for
255            the Csparse virtual class.  Also added a C function Csparse_band
256            that implements these methods by calling cholmod_band.
257    
258    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
261            erased when it was NULL.  This led to invalid subselections!
262    
263    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
264    
265            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
266            in method for "t" so as not to lose the unit diagonal property.
267    
268    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
269    
270            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
271            and methods.  This is now an option to the ranef method for the
272            mer class.
273    
274            * src/cs_utils.c: Ensure that the nz component is -1 for a
275            compressed column-oriented matrix.  Minor formatting cleanup.
276    
277            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
278            objects.
279    
280    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
283            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
284    
285    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
286    
287            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
288            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
289    
290            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
291            for the dtCMatrix class.
292    
293    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
294    
295            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
296            and methods for it.
297    
298    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
301            arguments, such that M %*% 1:6 now works
302            * Tests/matprod.R: test the above
303    
304    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
305    
306            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
307            the ranef.lmer class.
308    
309            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
310            methods to extract the posterior variances from the bVar slot.
311    
312    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
315            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
316    
317            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
318            * tests/simple: (extended)
319    
320            * R/sparseMatrix.R (isTriangular): now using much improved
321            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
322    
323    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
326            (problem report from Franklin Parlamis).  This should be done
327            generally.
328    
329    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
332            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
333            update the plot methods.
334    
335    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * R/lmer.R (resid and ranef methods):  Added methods for the
338            "residuals" and "resid" generic but only for linear mixed model
339            fits.  Changed the ranef method to return a list of data frames so
340            that the plot methods now work.
341    
342    2006-03-16  Douglas Bates  <bates@bates2>
343    
344            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
345            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
346    
347            * DESCRIPTION (Date): New release
348    
349    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
352    
353            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
354            * man/KNex.Rd: and other help files
355            * tests/*.R: several ones needed adaption
356            * inst/doc/Comparisons.Rnw: dito
357    
358    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
361    
362            * tests/indexing.R: tests for new [<- methods for sparse matrices.
363    
364    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
367    
368            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
369    
370    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/dMatrix.R: enable things like  M [ M < 10 ]
373            * R/dgeMatrix.R: implement it
374    
375    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/AllClass.R: define "summary.mer" and "*.lmer"
378            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
379            * R/lmer.R (show): now works with summary()
380    
381    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
384            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
385                    support the above
386    
387  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
388    
389          * 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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