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revision 1123, Tue Jan 10 17:04:29 2006 UTC revision 1298, Sat Jun 10 19:56:18 2006 UTC
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1    2006-06-10  Douglas Bates  <bates@R-project.org>
2    
3            * R/lmer.R (simulestimate): added
4    
5    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
8            classes.
9    
10    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/dgTMatrix.R (colSums): etc. All four of
13            colSums(), rowSums(), colMeans(), rowMeans() now should work for
14            all "Matrices".
15    
16    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
17    
18            * R/lmer.R (panel.ci): Add a reference line at zero and a
19            background grid to the qqmath plot of ranef.lmer.
20    
21    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
22    
23            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
24            grouping factors to be specified in the formula as (1|foo/bar).
25    
26    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * R/lmer.R (findbars and others): Change check of is.numeric to
29            !is.language to resolve the bug reported by Jacob Wegelin.
30    
31            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
32            code to evaluate inbreeding coefficients without calculating T,
33            based on code in Sargolzaei and Iwaisaki's paper.
34    
35    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
38            generic and mer methods for isNested and denomDF. This denomDF was
39            an attempt to emulate that in lme but I don't think that makes
40            sense.  Use the trace of the hat matrix instead.
41    
42    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
45            the C code depending on a slot structure that's no longer valid.
46            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
47    
48    
49    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
50    
51            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
52            of lowerTriMatrix generic and methods to tril (also upper to triu)
53            and added a general band extractor.
54    
55    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
56    
57            * R/pedigree.R (pedigree): Replace sire and dam values outside the
58            allowable range with NAs. Added a corresponding check in the
59            validity check for the pedigree class.
60    
61            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
62            crossprod methods now inherits from symmetricMatrix.
63    
64    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
67            generics lowerTriMatrix and upperTriMatrix along with methods for
68            the Csparse virtual class.  Also added a C function Csparse_band
69            that implements these methods by calling cholmod_band.
70    
71    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
74            erased when it was NULL.  This led to invalid subselections!
75    
76    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
77    
78            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
79            in method for "t" so as not to lose the unit diagonal property.
80    
81    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
84            and methods.  This is now an option to the ranef method for the
85            mer class.
86    
87            * src/cs_utils.c: Ensure that the nz component is -1 for a
88            compressed column-oriented matrix.  Minor formatting cleanup.
89    
90            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
91            objects.
92    
93    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
96            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
97    
98    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
101            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
102    
103            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
104            for the dtCMatrix class.
105    
106    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
107    
108            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
109            and methods for it.
110    
111    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
114            arguments, such that M %*% 1:6 now works
115            * Tests/matprod.R: test the above
116    
117    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
120            the ranef.lmer class.
121    
122            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
123            methods to extract the posterior variances from the bVar slot.
124    
125    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
128            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
129    
130            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
131            * tests/simple: (extended)
132    
133            * R/sparseMatrix.R (isTriangular): now using much improved
134            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
135    
136    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
139            (problem report from Franklin Parlamis).  This should be done
140            generally.
141    
142    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
143    
144            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
145            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
146            update the plot methods.
147    
148    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
149    
150            * R/lmer.R (resid and ranef methods):  Added methods for the
151            "residuals" and "resid" generic but only for linear mixed model
152            fits.  Changed the ranef method to return a list of data frames so
153            that the plot methods now work.
154    
155    2006-03-16  Douglas Bates  <bates@bates2>
156    
157            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
158            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
159    
160            * DESCRIPTION (Date): New release
161    
162    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
165    
166            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
167            * man/KNex.Rd: and other help files
168            * tests/*.R: several ones needed adaption
169            * inst/doc/Comparisons.Rnw: dito
170    
171    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
174    
175            * tests/indexing.R: tests for new [<- methods for sparse matrices.
176    
177    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
180    
181            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
182    
183    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/dMatrix.R: enable things like  M [ M < 10 ]
186            * R/dgeMatrix.R: implement it
187    
188    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/AllClass.R: define "summary.mer" and "*.lmer"
191            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
192            * R/lmer.R (show): now works with summary()
193    
194    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
197            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
198                    support the above
199    
200    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
201    
202            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
203            Use glmFit$prior.weights for weights in a glmm.
204            Allow an option usePQL = FALSE to skip the PQL steps for the
205            Laplace method (and, in time, the AGQ method).
206    
207            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
208            into a separate function internal_mer_Xfactor to be able to call
209            it from internal_bhat.
210    
211    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * tests/Class+Meth.R (tstMatrixClass): function for much better
214            testing; now again of all actual classes.
215    
216            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
217                    use macros and define make_d_matrix_* and make_i_matrix_*
218                    where _i_ is for the ldense routines:
219    
220            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
221            * src/ldense.c (lsyMatrix_as_lgeMatrix):
222    
223            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
224    
225    
226    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
229                    many different kinds of matrices.
230            * R/*.R: quite a few new methods were needed for R CMD check with
231                    new Matrix().  Very good for users playing around.
232    
233    
234    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/dgeMatrix.c (dMatrix_validate): new
237            * src/Mutils.c (dense_nonpacked_validate): new
238    
239            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
240    
241    
242    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
245    
246  2006-01-07  Douglas Bates  <bates@stat.wisc.edu>  2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * DESCRIPTION (Version): 0.99-6 released to CRAN
249    
250          * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for          * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
251          segfault in cases with multiple non-nested grouping factors.          segfault in cases with multiple non-nested grouping factors.
252    

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