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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1360, Tue Aug 8 17:29:03 2006 UTC
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1    2006-08-08  Douglas Bates  <bates@R-project.org>
2    
3            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
4            Later modified to return the upper triangle only.
5            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
6    
7    2006-08-07  Douglas Bates  <bates@R-project.org>
8    
9            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
10            R-level conversion to a sparse symmetric class.
11            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
12            Remove conversion to sparse symmetric classes (now done in C code).
13    
14    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
17            * man/band.Rd:  adapt the \dontshow{} unit test.
18    
19    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * DESCRIPTION (Version): 0.995-14  for CRAN
22    
23            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
24    
25            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
26            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
27    
28            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
29            * R/Tsparse.R (tril, triu, band): methods
30            * R/dgRMatrix.R (tril, ...):    ditto
31            * man/band.Rd:                  ditto
32    
33    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/Matrix.R (head, tail): directly use utils:::head.matrix
36                    to be up-to-date automatically.
37    
38    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
41    
42            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
43            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
44            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
45            such that the S4 objects are always created by the current version
46            of R and 'Matrix' class definitions.
47    
48    2006-08-01  Douglas Bates  <bates@R-project.org>
49    
50            * R/lmer.R (LMEoptimize method), tests/lmer.R,
51            inst/external/test3comp.rda: Added warnings for convergence on
52            boundary and test cases.
53    
54            * src/lmer.c (mer_postVar): Modified to return the variances that
55            are marginal to the fixed effects, not conditional on them (which
56            is what the bVar slot contents represent).
57    
58    2006-07-31  Douglas Bates  <bates@R-project.org>
59    
60            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
61            function which calls the C function mer_hat_trace2.
62    
63            * man/ranef.Rd: Include description of "postVar" argument and
64            producing a caterpillar plot.
65    
66    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * NAMESPACE:    change  "correlation" to "corMatrix"
69            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
70            * R/dpoMatrix.R: ditto
71            * R/lmer.R:      ditto
72    
73    2006-07-28  Douglas Bates  <bates@R-project.org>
74    
75            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
76            RZXinv slot's contents into a separate internal function that can
77            be used in mer_hat_trace.
78    
79    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
82            via new smart
83            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
84            utility functions.
85    
86    
87    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/Csparse.R (tril, triu, band): do return *triangular* classed
90            matrices when appropriate; band() even symmetric ones.
91            (replCmat): extend to potentially all "CsparseMatrix"
92            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
93            allow subassignment for special sparse matrices.
94    
95            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
96    
97            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
98            argument; in glmer_*(): print only if(verbose).
99    
100            speed-optimize a few places by moving REAL(.) out of loops.
101    
102            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
103    
104    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
107                    since that wrongly triggers also for M[ logi , ]
108    
109            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
110            a symmetric matrix that results in a non-symmetric one.
111            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
112    
113            * R/dMatrix.R: make round(M) work as round(M, 0)
114    
115            * R/dgTMatrix.R (image): coordinate system and axis now use
116            1-based indices, not 0-based ones.
117    
118            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
119            * tests/indexing.R: test it.
120    
121            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
122            * man/isSymmetric-methods.Rd: and document it.
123    
124            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
125            * man/SparseM-conv.Rd: docu them
126    
127            * tests/other-pkgs.R: renamed from tests/graph.R and add example
128                    for 'SparseM' conversions
129    
130    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
131    
132            * R/Matrix.R (head): added head() and tail() methods.
133    
134    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * DESCRIPTION (Version): 0.995-12 released to CRAN
137    
138    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * tests/simple.R: add check for correct dsT -> dgT coercion;
141                    add check for correct printing of symmetric sparse matrices.
142    
143            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
144            for sparse symmetric matrices.
145    
146            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
147            diagonal twice.
148    
149    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
150    
151            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
152            being applied to the x slot (detected by Brian Ripley).
153    
154    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
157    
158            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
159    
160    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * src/lgCMatrix.c (lgCMatrix_diag): new function
163            * R/lgCMatrix.R (diag): for new method
164    
165            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
166                 ==> construction of illegal "*gTMatrix" via new() should
167                 now be much less easy:
168            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
169    
170            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
171                    directly.
172            * man/Matrix.Rd: documents it.
173    
174    2006-07-06  Douglas Bates  <bates@R-project.org>
175    
176            * src/pedigree.c (pedigree_inbreeding): Correction in
177            initialization.  This function is not currently being used and is
178            not fully tested.
179    
180            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
181            Introduced the glmer class.  Added code for mcmcmsamp on glmer
182            objects.  Modified validity check on pedigree objects to account
183            for nonparallel patterns of missingness of parents.
184    
185            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
186            class.
187    
188    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/pMatrix.R: coercion pMatrix -> Tsparse
191    
192    2006-06-12  Douglas Bates  <bates@R-project.org>
193    
194            * DESCRIPTION (Version): 0.995-11 released to CRAN
195    
196            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
197            the output from mcmcsamp.
198    
199    2006-06-10  Douglas Bates  <bates@R-project.org>
200    
201            * R/lmer.R (simulestimate): added C code for calculating the trace
202            of the hat matrix.
203    
204    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
207            classes.
208            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
209    
210    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/dgTMatrix.R (colSums): etc. All four of
213            colSums(), rowSums(), colMeans(), rowMeans() now should work for
214            all "Matrices".
215    
216    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
217    
218            * R/lmer.R (panel.ci): Add a reference line at zero and a
219            background grid to the qqmath plot of ranef.lmer.
220    
221    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
222    
223            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
224            grouping factors to be specified in the formula as (1|foo/bar).
225    
226    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
227    
228            * R/lmer.R (findbars and others): Change check of is.numeric to
229            !is.language to resolve the bug reported by Jacob Wegelin.
230    
231            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
232            code to evaluate inbreeding coefficients without calculating T,
233            based on code in Sargolzaei and Iwaisaki's paper.
234    
235    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
236    
237            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
238            generic and mer methods for isNested and denomDF. This denomDF was
239            an attempt to emulate that in lme but I don't think that makes
240            sense.  Use the trace of the hat matrix instead.
241    
242    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
245            the C code depending on a slot structure that's no longer valid.
246            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
247    
248    
249    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
250    
251            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
252            of lowerTriMatrix generic and methods to tril (also upper to triu)
253            and added a general band extractor.
254    
255    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
256    
257            * R/pedigree.R (pedigree): Replace sire and dam values outside the
258            allowable range with NAs. Added a corresponding check in the
259            validity check for the pedigree class.
260    
261            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
262            crossprod methods now inherits from symmetricMatrix.
263    
264    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
265    
266            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
267            generics lowerTriMatrix and upperTriMatrix along with methods for
268            the Csparse virtual class.  Also added a C function Csparse_band
269            that implements these methods by calling cholmod_band.
270    
271    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
274            erased when it was NULL.  This led to invalid subselections!
275    
276    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
277    
278            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
279            in method for "t" so as not to lose the unit diagonal property.
280    
281    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
282    
283            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
284            and methods.  This is now an option to the ranef method for the
285            mer class.
286    
287            * src/cs_utils.c: Ensure that the nz component is -1 for a
288            compressed column-oriented matrix.  Minor formatting cleanup.
289    
290            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
291            objects.
292    
293    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
296            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
297    
298    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
299    
300            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
301            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
302    
303            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
304            for the dtCMatrix class.
305    
306    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
307    
308            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
309            and methods for it.
310    
311    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
314            arguments, such that M %*% 1:6 now works
315            * Tests/matprod.R: test the above
316    
317    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
318    
319            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
320            the ranef.lmer class.
321    
322            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
323            methods to extract the posterior variances from the bVar slot.
324    
325    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
328            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
329    
330            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
331            * tests/simple: (extended)
332    
333            * R/sparseMatrix.R (isTriangular): now using much improved
334            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
335    
336    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
337    
338            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
339            (problem report from Franklin Parlamis).  This should be done
340            generally.
341    
342    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
343    
344            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
345            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
346            update the plot methods.
347    
348    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
349    
350            * R/lmer.R (resid and ranef methods):  Added methods for the
351            "residuals" and "resid" generic but only for linear mixed model
352            fits.  Changed the ranef method to return a list of data frames so
353            that the plot methods now work.
354    
355    2006-03-16  Douglas Bates  <bates@bates2>
356    
357            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
358            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
359    
360            * DESCRIPTION (Date): New release
361    
362    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
365    
366            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
367            * man/KNex.Rd: and other help files
368            * tests/*.R: several ones needed adaption
369            * inst/doc/Comparisons.Rnw: ditto
370    
371    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
374    
375            * tests/indexing.R: tests for new [<- methods for sparse matrices.
376    
377    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
380    
381            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
382    
383    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/dMatrix.R: enable things like  M [ M < 10 ]
386            * R/dgeMatrix.R: implement it
387    
388    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/AllClass.R: define "summary.mer" and "*.lmer"
391            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
392            * R/lmer.R (show): now works with summary()
393    
394    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
397            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
398                    support the above
399    
400  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
401    
402          * 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 570 
570  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
573          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
574          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
575    
576  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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