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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1352, Mon Aug 7 18:31:12 2006 UTC
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1    2006-08-07  Douglas Bates  <bates@R-project.org>
2    
3            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
4            R-level conversion to a sparse symmetric class.
5            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
6            Remove conversion to sparse symmetric classes (now done in C code).
7    
8    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
11            * man/band.Rd:  adapt the \dontshow{} unit test.
12    
13    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * DESCRIPTION (Version): 0.995-14  for CRAN
16    
17            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
18    
19            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
20            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
21    
22            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
23            * R/Tsparse.R (tril, triu, band): methods
24            * R/dgRMatrix.R (tril, ...):    ditto
25            * man/band.Rd:                  ditto
26    
27    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Matrix.R (head, tail): directly use utils:::head.matrix
30                    to be up-to-date automatically.
31    
32    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
35    
36            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
37            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
38            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
39            such that the S4 objects are always created by the current version
40            of R and 'Matrix' class definitions.
41    
42    2006-08-01  Douglas Bates  <bates@R-project.org>
43    
44            * R/lmer.R (LMEoptimize method), tests/lmer.R,
45            inst/external/test3comp.rda: Added warnings for convergence on
46            boundary and test cases.
47    
48            * src/lmer.c (mer_postVar): Modified to return the variances that
49            are marginal to the fixed effects, not conditional on them (which
50            is what the bVar slot contents represent).
51    
52    2006-07-31  Douglas Bates  <bates@R-project.org>
53    
54            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
55            function which calls the C function mer_hat_trace2.
56    
57            * man/ranef.Rd: Include description of "postVar" argument and
58            producing a caterpillar plot.
59    
60    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * NAMESPACE:    change  "correlation" to "corMatrix"
63            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
64            * R/dpoMatrix.R: ditto
65            * R/lmer.R:      ditto
66    
67    2006-07-28  Douglas Bates  <bates@R-project.org>
68    
69            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
70            RZXinv slot's contents into a separate internal function that can
71            be used in mer_hat_trace.
72    
73    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
76            via new smart
77            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
78            utility functions.
79    
80    
81    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/Csparse.R (tril, triu, band): do return *triangular* classed
84            matrices when appropriate; band() even symmetric ones.
85            (replCmat): extend to potentially all "CsparseMatrix"
86            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
87            allow subassignment for special sparse matrices.
88    
89            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
90    
91            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
92            argument; in glmer_*(): print only if(verbose).
93    
94            speed-optimize a few places by moving REAL(.) out of loops.
95    
96            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
97    
98    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
101                    since that wrongly triggers also for M[ logi , ]
102    
103            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
104            a symmetric matrix that results in a non-symmetric one.
105            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
106    
107            * R/dMatrix.R: make round(M) work as round(M, 0)
108    
109            * R/dgTMatrix.R (image): coordinate system and axis now use
110            1-based indices, not 0-based ones.
111    
112            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
113            * tests/indexing.R: test it.
114    
115            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
116            * man/isSymmetric-methods.Rd: and document it.
117    
118            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
119            * man/SparseM-conv.Rd: docu them
120    
121            * tests/other-pkgs.R: renamed from tests/graph.R and add example
122                    for 'SparseM' conversions
123    
124    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
125    
126            * R/Matrix.R (head): added head() and tail() methods.
127    
128    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * DESCRIPTION (Version): 0.995-12 released to CRAN
131    
132    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * tests/simple.R: add check for correct dsT -> dgT coercion;
135                    add check for correct printing of symmetric sparse matrices.
136    
137            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
138            for sparse symmetric matrices.
139    
140            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
141            diagonal twice.
142    
143    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
144    
145            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
146            being applied to the x slot (detected by Brian Ripley).
147    
148    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
151    
152            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
153    
154    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/lgCMatrix.c (lgCMatrix_diag): new function
157            * R/lgCMatrix.R (diag): for new method
158    
159            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
160                 ==> construction of illegal "*gTMatrix" via new() should
161                 now be much less easy:
162            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
163    
164            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
165                    directly.
166            * man/Matrix.Rd: documents it.
167    
168    2006-07-06  Douglas Bates  <bates@R-project.org>
169    
170            * src/pedigree.c (pedigree_inbreeding): Correction in
171            initialization.  This function is not currently being used and is
172            not fully tested.
173    
174            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
175            Introduced the glmer class.  Added code for mcmcmsamp on glmer
176            objects.  Modified validity check on pedigree objects to account
177            for nonparallel patterns of missingness of parents.
178    
179            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
180            class.
181    
182    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/pMatrix.R: coercion pMatrix -> Tsparse
185    
186    2006-06-12  Douglas Bates  <bates@R-project.org>
187    
188            * DESCRIPTION (Version): 0.995-11 released to CRAN
189    
190            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
191            the output from mcmcsamp.
192    
193    2006-06-10  Douglas Bates  <bates@R-project.org>
194    
195            * R/lmer.R (simulestimate): added C code for calculating the trace
196            of the hat matrix.
197    
198    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
201            classes.
202            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
203    
204    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/dgTMatrix.R (colSums): etc. All four of
207            colSums(), rowSums(), colMeans(), rowMeans() now should work for
208            all "Matrices".
209    
210    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
211    
212            * R/lmer.R (panel.ci): Add a reference line at zero and a
213            background grid to the qqmath plot of ranef.lmer.
214    
215    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
216    
217            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
218            grouping factors to be specified in the formula as (1|foo/bar).
219    
220    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
221    
222            * R/lmer.R (findbars and others): Change check of is.numeric to
223            !is.language to resolve the bug reported by Jacob Wegelin.
224    
225            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
226            code to evaluate inbreeding coefficients without calculating T,
227            based on code in Sargolzaei and Iwaisaki's paper.
228    
229    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
230    
231            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
232            generic and mer methods for isNested and denomDF. This denomDF was
233            an attempt to emulate that in lme but I don't think that makes
234            sense.  Use the trace of the hat matrix instead.
235    
236    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
239            the C code depending on a slot structure that's no longer valid.
240            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
241    
242    
243    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
244    
245            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
246            of lowerTriMatrix generic and methods to tril (also upper to triu)
247            and added a general band extractor.
248    
249    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
250    
251            * R/pedigree.R (pedigree): Replace sire and dam values outside the
252            allowable range with NAs. Added a corresponding check in the
253            validity check for the pedigree class.
254    
255            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
256            crossprod methods now inherits from symmetricMatrix.
257    
258    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
259    
260            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
261            generics lowerTriMatrix and upperTriMatrix along with methods for
262            the Csparse virtual class.  Also added a C function Csparse_band
263            that implements these methods by calling cholmod_band.
264    
265    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
268            erased when it was NULL.  This led to invalid subselections!
269    
270    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
273            in method for "t" so as not to lose the unit diagonal property.
274    
275    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
276    
277            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
278            and methods.  This is now an option to the ranef method for the
279            mer class.
280    
281            * src/cs_utils.c: Ensure that the nz component is -1 for a
282            compressed column-oriented matrix.  Minor formatting cleanup.
283    
284            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
285            objects.
286    
287    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
290            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
291    
292    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
293    
294            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
295            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
296    
297            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
298            for the dtCMatrix class.
299    
300    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
301    
302            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
303            and methods for it.
304    
305    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
308            arguments, such that M %*% 1:6 now works
309            * Tests/matprod.R: test the above
310    
311    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
312    
313            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
314            the ranef.lmer class.
315    
316            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
317            methods to extract the posterior variances from the bVar slot.
318    
319    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
322            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
323    
324            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
325            * tests/simple: (extended)
326    
327            * R/sparseMatrix.R (isTriangular): now using much improved
328            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
329    
330    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
331    
332            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
333            (problem report from Franklin Parlamis).  This should be done
334            generally.
335    
336    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
337    
338            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
339            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
340            update the plot methods.
341    
342    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
343    
344            * R/lmer.R (resid and ranef methods):  Added methods for the
345            "residuals" and "resid" generic but only for linear mixed model
346            fits.  Changed the ranef method to return a list of data frames so
347            that the plot methods now work.
348    
349    2006-03-16  Douglas Bates  <bates@bates2>
350    
351            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
352            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
353    
354            * DESCRIPTION (Date): New release
355    
356    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
359    
360            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
361            * man/KNex.Rd: and other help files
362            * tests/*.R: several ones needed adaption
363            * inst/doc/Comparisons.Rnw: ditto
364    
365    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
368    
369            * tests/indexing.R: tests for new [<- methods for sparse matrices.
370    
371    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
374    
375            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
376    
377    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/dMatrix.R: enable things like  M [ M < 10 ]
380            * R/dgeMatrix.R: implement it
381    
382    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/AllClass.R: define "summary.mer" and "*.lmer"
385            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
386            * R/lmer.R (show): now works with summary()
387    
388    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
391            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
392                    support the above
393    
394  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
395    
396          * 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.
# Line 171  Line 564 
564  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
567          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
568          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
569    
570  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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