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revision 1213, Tue Feb 7 23:44:07 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>
225    
226            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
227            the C code depending on a slot structure that's no longer valid.
228            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
229    
230    
231    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
232    
233            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
234            of lowerTriMatrix generic and methods to tril (also upper to triu)
235            and added a general band extractor.
236    
237    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * R/pedigree.R (pedigree): Replace sire and dam values outside the
240            allowable range with NAs. Added a corresponding check in the
241            validity check for the pedigree class.
242    
243            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
244            crossprod methods now inherits from symmetricMatrix.
245    
246    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
249            generics lowerTriMatrix and upperTriMatrix along with methods for
250            the Csparse virtual class.  Also added a C function Csparse_band
251            that implements these methods by calling cholmod_band.
252    
253    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
256            erased when it was NULL.  This led to invalid subselections!
257    
258    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
259    
260            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
261            in method for "t" so as not to lose the unit diagonal property.
262    
263    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
264    
265            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
266            and methods.  This is now an option to the ranef method for the
267            mer class.
268    
269            * src/cs_utils.c: Ensure that the nz component is -1 for a
270            compressed column-oriented matrix.  Minor formatting cleanup.
271    
272            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
273            objects.
274    
275    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
278            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
279    
280    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
281    
282            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
283            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
284    
285            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
286            for the dtCMatrix class.
287    
288    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
289    
290            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
291            and methods for it.
292    
293    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
296            arguments, such that M %*% 1:6 now works
297            * Tests/matprod.R: test the above
298    
299    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
300    
301            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
302            the ranef.lmer class.
303    
304            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
305            methods to extract the posterior variances from the bVar slot.
306    
307    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
310            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
311    
312            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
313            * tests/simple: (extended)
314    
315            * R/sparseMatrix.R (isTriangular): now using much improved
316            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
317    
318    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
319    
320            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
321            (problem report from Franklin Parlamis).  This should be done
322            generally.
323    
324    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
325    
326            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
327            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
328            update the plot methods.
329    
330    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
331    
332            * R/lmer.R (resid and ranef methods):  Added methods for the
333            "residuals" and "resid" generic but only for linear mixed model
334            fits.  Changed the ranef method to return a list of data frames so
335            that the plot methods now work.
336    
337    2006-03-16  Douglas Bates  <bates@bates2>
338    
339            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
340            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
341    
342            * DESCRIPTION (Date): New release
343    
344    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
347    
348            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
349            * man/KNex.Rd: and other help files
350            * tests/*.R: several ones needed adaption
351            * inst/doc/Comparisons.Rnw: dito
352    
353    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
356    
357            * tests/indexing.R: tests for new [<- methods for sparse matrices.
358    
359    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
362    
363            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
364    
365    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/dMatrix.R: enable things like  M [ M < 10 ]
368            * R/dgeMatrix.R: implement it
369    
370    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/AllClass.R: define "summary.mer" and "*.lmer"
373            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
374            * R/lmer.R (show): now works with summary()
375    
376    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
379            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
380                    support the above
381    
382  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
383    
384          * 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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