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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1329, Fri Jul 21 06:47:06 2006 UTC
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1    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
4                    since that wrongly triggers also for M[ logi , ]
5    
6            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
7            a symmetric matrix that results in a non-symmetric one.
8            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
9    
10            * R/dMatrix.R: make round(M) work as round(M, 0)
11    
12            * R/dgTMatrix.R (image): coordinate system and axis now use
13            1-based indices, not 0-based ones.
14    
15            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
16            * tests/indexing.R: test it.
17    
18            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
19            * man/isSymmetric-methods.Rd: and document it.
20    
21            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
22            * man/SparseM-conv.Rd: docu them
23    
24            * tests/other-pkgs.R: renamed from tests/graph.R and add example
25                    for 'SparseM' conversions
26    
27    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
28    
29            * R/Matrix.R (head): added head() and tail() methods.
30    
31    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * DESCRIPTION (Version): 0.995-12 released to CRAN
34    
35    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * tests/simple.R: add check for correct dsT -> dgT coercion;
38                    add check for correct printing of symmetric sparse matrices.
39    
40            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
41            for sparse symmetric matrices.
42    
43            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
44            diagonal twice.
45    
46    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
47    
48            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
49            being applied to the x slot (detected by Brian Ripley).
50    
51    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
54    
55            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
56    
57    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * src/lgCMatrix.c (lgCMatrix_diag): new function
60            * R/lgCMatrix.R (diag): for new method
61    
62            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
63                 ==> construction of illegal "*gTMatrix" via new() should
64                 now be much less easy:
65            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
66    
67            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
68                    directly.
69            * man/Matrix.Rd: documents it.
70    
71    2006-07-06  Douglas Bates  <bates@R-project.org>
72    
73            * src/pedigree.c (pedigree_inbreeding): Correction in
74            initialization.  This function is not currently being used and is
75            not fully tested.
76    
77            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
78            Introduced the glmer class.  Added code for mcmcmsamp on glmer
79            objects.  Modified validity check on pedigree objects to account
80            for nonparallel patterns of missingness of parents.
81    
82            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
83            class.
84    
85    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/pMatrix.R: coercion pMatrix -> Tsparse
88    
89    2006-06-12  Douglas Bates  <bates@R-project.org>
90    
91            * DESCRIPTION (Version): 0.995-11 released to CRAN
92    
93            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
94            the output from mcmcsamp.
95    
96    2006-06-10  Douglas Bates  <bates@R-project.org>
97    
98            * R/lmer.R (simulestimate): added C code for calculating the trace
99            of the hat matrix.
100    
101    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
104            classes.
105            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
106    
107    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/dgTMatrix.R (colSums): etc. All four of
110            colSums(), rowSums(), colMeans(), rowMeans() now should work for
111            all "Matrices".
112    
113    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/lmer.R (panel.ci): Add a reference line at zero and a
116            background grid to the qqmath plot of ranef.lmer.
117    
118    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
121            grouping factors to be specified in the formula as (1|foo/bar).
122    
123    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * R/lmer.R (findbars and others): Change check of is.numeric to
126            !is.language to resolve the bug reported by Jacob Wegelin.
127    
128            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
129            code to evaluate inbreeding coefficients without calculating T,
130            based on code in Sargolzaei and Iwaisaki's paper.
131    
132    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
135            generic and mer methods for isNested and denomDF. This denomDF was
136            an attempt to emulate that in lme but I don't think that makes
137            sense.  Use the trace of the hat matrix instead.
138    
139    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
142            the C code depending on a slot structure that's no longer valid.
143            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
144    
145    
146    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
147    
148            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
149            of lowerTriMatrix generic and methods to tril (also upper to triu)
150            and added a general band extractor.
151    
152    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
153    
154            * R/pedigree.R (pedigree): Replace sire and dam values outside the
155            allowable range with NAs. Added a corresponding check in the
156            validity check for the pedigree class.
157    
158            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
159            crossprod methods now inherits from symmetricMatrix.
160    
161    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
162    
163            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
164            generics lowerTriMatrix and upperTriMatrix along with methods for
165            the Csparse virtual class.  Also added a C function Csparse_band
166            that implements these methods by calling cholmod_band.
167    
168    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
171            erased when it was NULL.  This led to invalid subselections!
172    
173    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
174    
175            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
176            in method for "t" so as not to lose the unit diagonal property.
177    
178    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
179    
180            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
181            and methods.  This is now an option to the ranef method for the
182            mer class.
183    
184            * src/cs_utils.c: Ensure that the nz component is -1 for a
185            compressed column-oriented matrix.  Minor formatting cleanup.
186    
187            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
188            objects.
189    
190    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
193            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
194    
195    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
196    
197            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
198            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
199    
200            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
201            for the dtCMatrix class.
202    
203    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
204    
205            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
206            and methods for it.
207    
208    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
211            arguments, such that M %*% 1:6 now works
212            * Tests/matprod.R: test the above
213    
214    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
215    
216            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
217            the ranef.lmer class.
218    
219            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
220            methods to extract the posterior variances from the bVar slot.
221    
222    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
225            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
226    
227            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
228            * tests/simple: (extended)
229    
230            * R/sparseMatrix.R (isTriangular): now using much improved
231            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
232    
233    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
234    
235            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
236            (problem report from Franklin Parlamis).  This should be done
237            generally.
238    
239    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
240    
241            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
242            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
243            update the plot methods.
244    
245    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
246    
247            * R/lmer.R (resid and ranef methods):  Added methods for the
248            "residuals" and "resid" generic but only for linear mixed model
249            fits.  Changed the ranef method to return a list of data frames so
250            that the plot methods now work.
251    
252    2006-03-16  Douglas Bates  <bates@bates2>
253    
254            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
255            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
256    
257            * DESCRIPTION (Date): New release
258    
259    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
262    
263            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
264            * man/KNex.Rd: and other help files
265            * tests/*.R: several ones needed adaption
266            * inst/doc/Comparisons.Rnw: dito
267    
268    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
271    
272            * tests/indexing.R: tests for new [<- methods for sparse matrices.
273    
274    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
277    
278            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
279    
280    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/dMatrix.R: enable things like  M [ M < 10 ]
283            * R/dgeMatrix.R: implement it
284    
285    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/AllClass.R: define "summary.mer" and "*.lmer"
288            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
289            * R/lmer.R (show): now works with summary()
290    
291    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
294            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
295                    support the above
296    
297  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
298    
299          * 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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