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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1295, Fri Jun 9 21:47:22 2006 UTC
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1    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
4            classes.
5    
6    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/dgTMatrix.R (colSums): etc. All four of
9            colSums(), rowSums(), colMeans(), rowMeans() now should work for
10            all "Matrices".
11    
12    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
13    
14            * R/lmer.R (panel.ci): Add a reference line at zero and a
15            background grid to the qqmath plot of ranef.lmer.
16    
17    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
20            grouping factors to be specified in the formula as (1|foo/bar).
21    
22    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
23    
24            * R/lmer.R (findbars and others): Change check of is.numeric to
25            !is.language to resolve the bug reported by Jacob Wegelin.
26    
27            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
28            code to evaluate inbreeding coefficients without calculating T,
29            based on code in Sargolzaei and Iwaisaki's paper.
30    
31    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
32    
33            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
34            generic and mer methods for isNested and denomDF. This denomDF was
35            an attempt to emulate that in lme but I don't think that makes
36            sense.  Use the trace of the hat matrix instead.
37    
38    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
41            the C code depending on a slot structure that's no longer valid.
42            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
43    
44    
45    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
46    
47            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
48            of lowerTriMatrix generic and methods to tril (also upper to triu)
49            and added a general band extractor.
50    
51    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
52    
53            * R/pedigree.R (pedigree): Replace sire and dam values outside the
54            allowable range with NAs. Added a corresponding check in the
55            validity check for the pedigree class.
56    
57            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
58            crossprod methods now inherits from symmetricMatrix.
59    
60    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
61    
62            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
63            generics lowerTriMatrix and upperTriMatrix along with methods for
64            the Csparse virtual class.  Also added a C function Csparse_band
65            that implements these methods by calling cholmod_band.
66    
67    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
70            erased when it was NULL.  This led to invalid subselections!
71    
72    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
75            in method for "t" so as not to lose the unit diagonal property.
76    
77    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
78    
79            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
80            and methods.  This is now an option to the ranef method for the
81            mer class.
82    
83            * src/cs_utils.c: Ensure that the nz component is -1 for a
84            compressed column-oriented matrix.  Minor formatting cleanup.
85    
86            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
87            objects.
88    
89    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
92            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
93    
94    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
97            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
98    
99            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
100            for the dtCMatrix class.
101    
102    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
105            and methods for it.
106    
107    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
110            arguments, such that M %*% 1:6 now works
111            * Tests/matprod.R: test the above
112    
113    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
116            the ranef.lmer class.
117    
118            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
119            methods to extract the posterior variances from the bVar slot.
120    
121    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
124            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
125    
126            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
127            * tests/simple: (extended)
128    
129            * R/sparseMatrix.R (isTriangular): now using much improved
130            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
131    
132    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
135            (problem report from Franklin Parlamis).  This should be done
136            generally.
137    
138    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
139    
140            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
141            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
142            update the plot methods.
143    
144    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
145    
146            * R/lmer.R (resid and ranef methods):  Added methods for the
147            "residuals" and "resid" generic but only for linear mixed model
148            fits.  Changed the ranef method to return a list of data frames so
149            that the plot methods now work.
150    
151    2006-03-16  Douglas Bates  <bates@bates2>
152    
153            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
154            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
155    
156            * DESCRIPTION (Date): New release
157    
158    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
161    
162            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
163            * man/KNex.Rd: and other help files
164            * tests/*.R: several ones needed adaption
165            * inst/doc/Comparisons.Rnw: dito
166    
167    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
170    
171            * tests/indexing.R: tests for new [<- methods for sparse matrices.
172    
173    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
176    
177            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
178    
179    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/dMatrix.R: enable things like  M [ M < 10 ]
182            * R/dgeMatrix.R: implement it
183    
184    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/AllClass.R: define "summary.mer" and "*.lmer"
187            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
188            * R/lmer.R (show): now works with summary()
189    
190    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
193            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
194                    support the above
195    
196  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
197    
198          * 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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