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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1373, Mon Aug 14 21:15:38 2006 UTC
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1    2006-08-14  Douglas Bates  <bates@R-project.org>
2    
3            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
4            Csparse_to_logical and Csparse_symmetric_to_general.
5            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
6            coercion methods between CsparseMatrix and TsparseMatrix.
7    
8    2006-08-14  Douglas Bates  <bates@R-project.org>
9    
10            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
11            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
12            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
13            possible.
14    
15    2006-08-12  Douglas Bates  <bates@R-project.org>
16    
17            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
18              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
19              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
20              generalize conversions between TsparseMatrix, CsparseMatrix,
21              denseMatrix and matrix.  Preserve triangularity property and
22              propagate Dimnames in the easy cases.
23    
24    2006-08-10  Douglas Bates  <bates@R-project.org>
25    
26            * src/lmer.c: adjust checks in glmer_init for S4SXP
27            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
28            before S4SXP but for the wrong reasons.
29    
30    2006-08-08  Douglas Bates  <bates@R-project.org>
31    
32            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
33            Later modified to return the upper triangle only.
34            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
35    
36    2006-08-07  Douglas Bates  <bates@R-project.org>
37    
38            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
39            R-level conversion to a sparse symmetric class.
40            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
41            Remove conversion to sparse symmetric classes (now done in C code).
42    
43    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
46            * man/band.Rd:  adapt the \dontshow{} unit test.
47    
48    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * DESCRIPTION (Version): 0.995-14  for CRAN
51    
52            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
53    
54            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
55            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
56    
57            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
58            * R/Tsparse.R (tril, triu, band): methods
59            * R/dgRMatrix.R (tril, ...):    ditto
60            * man/band.Rd:                  ditto
61    
62    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/Matrix.R (head, tail): directly use utils:::head.matrix
65                    to be up-to-date automatically.
66    
67    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
70    
71            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
72            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
73            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
74            such that the S4 objects are always created by the current version
75            of R and 'Matrix' class definitions.
76    
77    2006-08-01  Douglas Bates  <bates@R-project.org>
78    
79            * R/lmer.R (LMEoptimize method), tests/lmer.R,
80            inst/external/test3comp.rda: Added warnings for convergence on
81            boundary and test cases.
82    
83            * src/lmer.c (mer_postVar): Modified to return the variances that
84            are marginal to the fixed effects, not conditional on them (which
85            is what the bVar slot contents represent).
86    
87    2006-07-31  Douglas Bates  <bates@R-project.org>
88    
89            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
90            function which calls the C function mer_hat_trace2.
91    
92            * man/ranef.Rd: Include description of "postVar" argument and
93            producing a caterpillar plot.
94    
95    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * NAMESPACE:    change  "correlation" to "corMatrix"
98            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
99            * R/dpoMatrix.R: ditto
100            * R/lmer.R:      ditto
101    
102    2006-07-28  Douglas Bates  <bates@R-project.org>
103    
104            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
105            RZXinv slot's contents into a separate internal function that can
106            be used in mer_hat_trace.
107    
108    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
111            via new smart
112            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
113            utility functions.
114    
115    
116    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Csparse.R (tril, triu, band): do return *triangular* classed
119            matrices when appropriate; band() even symmetric ones.
120            (replCmat): extend to potentially all "CsparseMatrix"
121            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
122            allow subassignment for special sparse matrices.
123    
124            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
125    
126            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
127            argument; in glmer_*(): print only if(verbose).
128    
129            speed-optimize a few places by moving REAL(.) out of loops.
130    
131            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
132    
133    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
136                    since that wrongly triggers also for M[ logi , ]
137    
138            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
139            a symmetric matrix that results in a non-symmetric one.
140            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
141    
142            * R/dMatrix.R: make round(M) work as round(M, 0)
143    
144            * R/dgTMatrix.R (image): coordinate system and axis now use
145            1-based indices, not 0-based ones.
146    
147            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
148            * tests/indexing.R: test it.
149    
150            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
151            * man/isSymmetric-methods.Rd: and document it.
152    
153            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
154            * man/SparseM-conv.Rd: docu them
155    
156            * tests/other-pkgs.R: renamed from tests/graph.R and add example
157                    for 'SparseM' conversions
158    
159    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
160    
161            * R/Matrix.R (head): added head() and tail() methods.
162    
163    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * DESCRIPTION (Version): 0.995-12 released to CRAN
166    
167    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * tests/simple.R: add check for correct dsT -> dgT coercion;
170                    add check for correct printing of symmetric sparse matrices.
171    
172            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
173            for sparse symmetric matrices.
174    
175            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
176            diagonal twice.
177    
178    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
179    
180            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
181            being applied to the x slot (detected by Brian Ripley).
182    
183    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
186    
187            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
188    
189    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/lgCMatrix.c (lgCMatrix_diag): new function
192            * R/lgCMatrix.R (diag): for new method
193    
194            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
195                 ==> construction of illegal "*gTMatrix" via new() should
196                 now be much less easy:
197            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
198    
199            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
200                    directly.
201            * man/Matrix.Rd: documents it.
202    
203    2006-07-06  Douglas Bates  <bates@R-project.org>
204    
205            * src/pedigree.c (pedigree_inbreeding): Correction in
206            initialization.  This function is not currently being used and is
207            not fully tested.
208    
209            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
210            Introduced the glmer class.  Added code for mcmcmsamp on glmer
211            objects.  Modified validity check on pedigree objects to account
212            for nonparallel patterns of missingness of parents.
213    
214            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
215            class.
216    
217    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/pMatrix.R: coercion pMatrix -> Tsparse
220    
221    2006-06-12  Douglas Bates  <bates@R-project.org>
222    
223            * DESCRIPTION (Version): 0.995-11 released to CRAN
224    
225            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
226            the output from mcmcsamp.
227    
228    2006-06-10  Douglas Bates  <bates@R-project.org>
229    
230            * R/lmer.R (simulestimate): added C code for calculating the trace
231            of the hat matrix.
232    
233    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
236            classes.
237            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
238    
239    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgTMatrix.R (colSums): etc. All four of
242            colSums(), rowSums(), colMeans(), rowMeans() now should work for
243            all "Matrices".
244    
245    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
246    
247            * R/lmer.R (panel.ci): Add a reference line at zero and a
248            background grid to the qqmath plot of ranef.lmer.
249    
250    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
251    
252            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
253            grouping factors to be specified in the formula as (1|foo/bar).
254    
255    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
256    
257            * R/lmer.R (findbars and others): Change check of is.numeric to
258            !is.language to resolve the bug reported by Jacob Wegelin.
259    
260            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
261            code to evaluate inbreeding coefficients without calculating T,
262            based on code in Sargolzaei and Iwaisaki's paper.
263    
264    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
265    
266            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
267            generic and mer methods for isNested and denomDF. This denomDF was
268            an attempt to emulate that in lme but I don't think that makes
269            sense.  Use the trace of the hat matrix instead.
270    
271    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
274            the C code depending on a slot structure that's no longer valid.
275            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
276    
277    
278    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
279    
280            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
281            of lowerTriMatrix generic and methods to tril (also upper to triu)
282            and added a general band extractor.
283    
284    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * R/pedigree.R (pedigree): Replace sire and dam values outside the
287            allowable range with NAs. Added a corresponding check in the
288            validity check for the pedigree class.
289    
290            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
291            crossprod methods now inherits from symmetricMatrix.
292    
293    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
294    
295            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
296            generics lowerTriMatrix and upperTriMatrix along with methods for
297            the Csparse virtual class.  Also added a C function Csparse_band
298            that implements these methods by calling cholmod_band.
299    
300    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
303            erased when it was NULL.  This led to invalid subselections!
304    
305    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
306    
307            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
308            in method for "t" so as not to lose the unit diagonal property.
309    
310    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
311    
312            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
313            and methods.  This is now an option to the ranef method for the
314            mer class.
315    
316            * src/cs_utils.c: Ensure that the nz component is -1 for a
317            compressed column-oriented matrix.  Minor formatting cleanup.
318    
319            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
320            objects.
321    
322    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
325            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
326    
327    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
328    
329            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
330            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
331    
332            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
333            for the dtCMatrix class.
334    
335    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
338            and methods for it.
339    
340    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
343            arguments, such that M %*% 1:6 now works
344            * Tests/matprod.R: test the above
345    
346    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
347    
348            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
349            the ranef.lmer class.
350    
351            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
352            methods to extract the posterior variances from the bVar slot.
353    
354    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
357            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
358    
359            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
360            * tests/simple: (extended)
361    
362            * R/sparseMatrix.R (isTriangular): now using much improved
363            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
364    
365    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
366    
367            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
368            (problem report from Franklin Parlamis).  This should be done
369            generally.
370    
371    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
372    
373            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
374            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
375            update the plot methods.
376    
377    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
378    
379            * R/lmer.R (resid and ranef methods):  Added methods for the
380            "residuals" and "resid" generic but only for linear mixed model
381            fits.  Changed the ranef method to return a list of data frames so
382            that the plot methods now work.
383    
384    2006-03-16  Douglas Bates  <bates@bates2>
385    
386            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
387            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
388    
389            * DESCRIPTION (Date): New release
390    
391    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
394    
395            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
396            * man/KNex.Rd: and other help files
397            * tests/*.R: several ones needed adaption
398            * inst/doc/Comparisons.Rnw: ditto
399    
400    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
403    
404            * tests/indexing.R: tests for new [<- methods for sparse matrices.
405    
406    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
409    
410            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
411    
412    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/dMatrix.R: enable things like  M [ M < 10 ]
415            * R/dgeMatrix.R: implement it
416    
417    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/AllClass.R: define "summary.mer" and "*.lmer"
420            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
421            * R/lmer.R (show): now works with summary()
422    
423    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
426            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
427                    support the above
428    
429  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
430    
431          * 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 599 
599  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
602          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
603          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
604    
605  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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