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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1335, Mon Jul 31 12:11:35 2006 UTC
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1    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * NAMESPACE:    change  "correlation" to "corMatrix"
4            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
5            * R/dpoMatrix.R: dito
6            * R/lmer.R:      dito
7    
8    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
11            via new smart
12            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
13            utility functions.
14    
15    
16    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Csparse.R (tril, triu, band): do return *triangular* classed
19            matrices when appropriate; band() even symmetric ones.
20            (replCmat): extend to potentially all "CsparseMatrix"
21            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
22            allow subassignment for special sparse matrices.
23    
24            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
25    
26            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
27            argument; in glmer_*(): print only if(verbose).
28    
29            speed-optimize a few places by moving REAL(.) out of loops.
30    
31            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
32    
33    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
36                    since that wrongly triggers also for M[ logi , ]
37    
38            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
39            a symmetric matrix that results in a non-symmetric one.
40            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
41    
42            * R/dMatrix.R: make round(M) work as round(M, 0)
43    
44            * R/dgTMatrix.R (image): coordinate system and axis now use
45            1-based indices, not 0-based ones.
46    
47            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
48            * tests/indexing.R: test it.
49    
50            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
51            * man/isSymmetric-methods.Rd: and document it.
52    
53            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
54            * man/SparseM-conv.Rd: docu them
55    
56            * tests/other-pkgs.R: renamed from tests/graph.R and add example
57                    for 'SparseM' conversions
58    
59    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
60    
61            * R/Matrix.R (head): added head() and tail() methods.
62    
63    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * DESCRIPTION (Version): 0.995-12 released to CRAN
66    
67    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * tests/simple.R: add check for correct dsT -> dgT coercion;
70                    add check for correct printing of symmetric sparse matrices.
71    
72            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
73            for sparse symmetric matrices.
74    
75            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
76            diagonal twice.
77    
78    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
79    
80            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
81            being applied to the x slot (detected by Brian Ripley).
82    
83    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
86    
87            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
88    
89    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * src/lgCMatrix.c (lgCMatrix_diag): new function
92            * R/lgCMatrix.R (diag): for new method
93    
94            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
95                 ==> construction of illegal "*gTMatrix" via new() should
96                 now be much less easy:
97            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
98    
99            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
100                    directly.
101            * man/Matrix.Rd: documents it.
102    
103    2006-07-06  Douglas Bates  <bates@R-project.org>
104    
105            * src/pedigree.c (pedigree_inbreeding): Correction in
106            initialization.  This function is not currently being used and is
107            not fully tested.
108    
109            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
110            Introduced the glmer class.  Added code for mcmcmsamp on glmer
111            objects.  Modified validity check on pedigree objects to account
112            for nonparallel patterns of missingness of parents.
113    
114            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
115            class.
116    
117    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/pMatrix.R: coercion pMatrix -> Tsparse
120    
121    2006-06-12  Douglas Bates  <bates@R-project.org>
122    
123            * DESCRIPTION (Version): 0.995-11 released to CRAN
124    
125            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
126            the output from mcmcsamp.
127    
128    2006-06-10  Douglas Bates  <bates@R-project.org>
129    
130            * R/lmer.R (simulestimate): added C code for calculating the trace
131            of the hat matrix.
132    
133    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
136            classes.
137            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
138    
139    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/dgTMatrix.R (colSums): etc. All four of
142            colSums(), rowSums(), colMeans(), rowMeans() now should work for
143            all "Matrices".
144    
145    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
146    
147            * R/lmer.R (panel.ci): Add a reference line at zero and a
148            background grid to the qqmath plot of ranef.lmer.
149    
150    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
151    
152            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
153            grouping factors to be specified in the formula as (1|foo/bar).
154    
155    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
156    
157            * R/lmer.R (findbars and others): Change check of is.numeric to
158            !is.language to resolve the bug reported by Jacob Wegelin.
159    
160            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
161            code to evaluate inbreeding coefficients without calculating T,
162            based on code in Sargolzaei and Iwaisaki's paper.
163    
164    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
167            generic and mer methods for isNested and denomDF. This denomDF was
168            an attempt to emulate that in lme but I don't think that makes
169            sense.  Use the trace of the hat matrix instead.
170    
171    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
174            the C code depending on a slot structure that's no longer valid.
175            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
176    
177    
178    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
179    
180            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
181            of lowerTriMatrix generic and methods to tril (also upper to triu)
182            and added a general band extractor.
183    
184    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
185    
186            * R/pedigree.R (pedigree): Replace sire and dam values outside the
187            allowable range with NAs. Added a corresponding check in the
188            validity check for the pedigree class.
189    
190            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
191            crossprod methods now inherits from symmetricMatrix.
192    
193    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
196            generics lowerTriMatrix and upperTriMatrix along with methods for
197            the Csparse virtual class.  Also added a C function Csparse_band
198            that implements these methods by calling cholmod_band.
199    
200    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
203            erased when it was NULL.  This led to invalid subselections!
204    
205    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
206    
207            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
208            in method for "t" so as not to lose the unit diagonal property.
209    
210    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
211    
212            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
213            and methods.  This is now an option to the ranef method for the
214            mer class.
215    
216            * src/cs_utils.c: Ensure that the nz component is -1 for a
217            compressed column-oriented matrix.  Minor formatting cleanup.
218    
219            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
220            objects.
221    
222    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
225            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
226    
227    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
228    
229            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
230            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
231    
232            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
233            for the dtCMatrix class.
234    
235    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
236    
237            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
238            and methods for it.
239    
240    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
243            arguments, such that M %*% 1:6 now works
244            * Tests/matprod.R: test the above
245    
246    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
249            the ranef.lmer class.
250    
251            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
252            methods to extract the posterior variances from the bVar slot.
253    
254    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
257            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
258    
259            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
260            * tests/simple: (extended)
261    
262            * R/sparseMatrix.R (isTriangular): now using much improved
263            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
264    
265    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
266    
267            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
268            (problem report from Franklin Parlamis).  This should be done
269            generally.
270    
271    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
272    
273            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
274            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
275            update the plot methods.
276    
277    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
278    
279            * R/lmer.R (resid and ranef methods):  Added methods for the
280            "residuals" and "resid" generic but only for linear mixed model
281            fits.  Changed the ranef method to return a list of data frames so
282            that the plot methods now work.
283    
284    2006-03-16  Douglas Bates  <bates@bates2>
285    
286            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
287            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
288    
289            * DESCRIPTION (Date): New release
290    
291    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
294    
295            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
296            * man/KNex.Rd: and other help files
297            * tests/*.R: several ones needed adaption
298            * inst/doc/Comparisons.Rnw: dito
299    
300    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
303    
304            * tests/indexing.R: tests for new [<- methods for sparse matrices.
305    
306    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
309    
310            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
311    
312    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/dMatrix.R: enable things like  M [ M < 10 ]
315            * R/dgeMatrix.R: implement it
316    
317    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/AllClass.R: define "summary.mer" and "*.lmer"
320            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
321            * R/lmer.R (show): now works with summary()
322    
323    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
326            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
327                    support the above
328    
329  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
330    
331          * 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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