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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1319, Mon Jul 17 13:08:04 2006 UTC
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1    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/simple.R: add check for correct dsT -> dgT coercion;
4                    add check for correct printing of symmetric sparse matrices.
5    
6            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
7            for sparse symmetric matrices.
8    
9            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
10            diagonal twice.
11    
12    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
13    
14            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
15            being applied to the x slot (detected by Brian Ripley).
16    
17    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
20    
21            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
22    
23    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * src/lgCMatrix.c (lgCMatrix_diag): new function
26            * R/lgCMatrix.R (diag): for new method
27    
28            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
29                 ==> construction of illegal "*gTMatrix" via new() should
30                 now be much less easy:
31            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
32    
33            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
34                    directly.
35            * man/Matrix.Rd: documents it.
36    
37    2006-07-06  Douglas Bates  <bates@R-project.org>
38    
39            * src/pedigree.c (pedigree_inbreeding): Correction in
40            initialization.  This function is not currently being used and is
41            not fully tested.
42    
43            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
44            Introduced the glmer class.  Added code for mcmcmsamp on glmer
45            objects.  Modified validity check on pedigree objects to account
46            for nonparallel patterns of missingness of parents.
47    
48            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
49            class.
50    
51    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/pMatrix.R: coercion pMatrix -> Tsparse
54    
55    2006-06-12  Douglas Bates  <bates@R-project.org>
56    
57            * DESCRIPTION (Version): 0.995-11 released to CRAN
58    
59            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
60            the output from mcmcsamp.
61    
62    2006-06-10  Douglas Bates  <bates@R-project.org>
63    
64            * R/lmer.R (simulestimate): added C code for calculating the trace
65            of the hat matrix.
66    
67    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
70            classes.
71            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
72    
73    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/dgTMatrix.R (colSums): etc. All four of
76            colSums(), rowSums(), colMeans(), rowMeans() now should work for
77            all "Matrices".
78    
79    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
80    
81            * R/lmer.R (panel.ci): Add a reference line at zero and a
82            background grid to the qqmath plot of ranef.lmer.
83    
84    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
85    
86            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
87            grouping factors to be specified in the formula as (1|foo/bar).
88    
89    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
90    
91            * R/lmer.R (findbars and others): Change check of is.numeric to
92            !is.language to resolve the bug reported by Jacob Wegelin.
93    
94            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
95            code to evaluate inbreeding coefficients without calculating T,
96            based on code in Sargolzaei and Iwaisaki's paper.
97    
98    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
101            generic and mer methods for isNested and denomDF. This denomDF was
102            an attempt to emulate that in lme but I don't think that makes
103            sense.  Use the trace of the hat matrix instead.
104    
105    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
108            the C code depending on a slot structure that's no longer valid.
109            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
110    
111    
112    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
113    
114            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
115            of lowerTriMatrix generic and methods to tril (also upper to triu)
116            and added a general band extractor.
117    
118    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * R/pedigree.R (pedigree): Replace sire and dam values outside the
121            allowable range with NAs. Added a corresponding check in the
122            validity check for the pedigree class.
123    
124            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
125            crossprod methods now inherits from symmetricMatrix.
126    
127    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
130            generics lowerTriMatrix and upperTriMatrix along with methods for
131            the Csparse virtual class.  Also added a C function Csparse_band
132            that implements these methods by calling cholmod_band.
133    
134    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
137            erased when it was NULL.  This led to invalid subselections!
138    
139    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
140    
141            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
142            in method for "t" so as not to lose the unit diagonal property.
143    
144    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
145    
146            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
147            and methods.  This is now an option to the ranef method for the
148            mer class.
149    
150            * src/cs_utils.c: Ensure that the nz component is -1 for a
151            compressed column-oriented matrix.  Minor formatting cleanup.
152    
153            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
154            objects.
155    
156    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
159            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
160    
161    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
162    
163            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
164            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
165    
166            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
167            for the dtCMatrix class.
168    
169    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
170    
171            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
172            and methods for it.
173    
174    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
177            arguments, such that M %*% 1:6 now works
178            * Tests/matprod.R: test the above
179    
180    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
181    
182            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
183            the ranef.lmer class.
184    
185            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
186            methods to extract the posterior variances from the bVar slot.
187    
188    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
191            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
192    
193            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
194            * tests/simple: (extended)
195    
196            * R/sparseMatrix.R (isTriangular): now using much improved
197            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
198    
199    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
200    
201            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
202            (problem report from Franklin Parlamis).  This should be done
203            generally.
204    
205    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
206    
207            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
208            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
209            update the plot methods.
210    
211    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
212    
213            * R/lmer.R (resid and ranef methods):  Added methods for the
214            "residuals" and "resid" generic but only for linear mixed model
215            fits.  Changed the ranef method to return a list of data frames so
216            that the plot methods now work.
217    
218    2006-03-16  Douglas Bates  <bates@bates2>
219    
220            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
221            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
222    
223            * DESCRIPTION (Date): New release
224    
225    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
228    
229            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
230            * man/KNex.Rd: and other help files
231            * tests/*.R: several ones needed adaption
232            * inst/doc/Comparisons.Rnw: dito
233    
234    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
237    
238            * tests/indexing.R: tests for new [<- methods for sparse matrices.
239    
240    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
243    
244            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
245    
246    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dMatrix.R: enable things like  M [ M < 10 ]
249            * R/dgeMatrix.R: implement it
250    
251    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/AllClass.R: define "summary.mer" and "*.lmer"
254            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
255            * R/lmer.R (show): now works with summary()
256    
257    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
260            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
261                    support the above
262    
263  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
264    
265          * 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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