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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1283, Sat May 27 19:51:01 2006 UTC
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1    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
4            generic and mer methods for isNested and denomDF. This denomDF was
5            an attempt to emulate that in lme but I don't think that makes
6            sense.  Use the trace of the hat matrix instead.
7    
8    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
11            the C code depending on a slot structure that's no longer valid.
12            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
13    
14    
15    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
16    
17            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
18            of lowerTriMatrix generic and methods to tril (also upper to triu)
19            and added a general band extractor.
20    
21    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
22    
23            * R/pedigree.R (pedigree): Replace sire and dam values outside the
24            allowable range with NAs. Added a corresponding check in the
25            validity check for the pedigree class.
26    
27            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
28            crossprod methods now inherits from symmetricMatrix.
29    
30    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
33            generics lowerTriMatrix and upperTriMatrix along with methods for
34            the Csparse virtual class.  Also added a C function Csparse_band
35            that implements these methods by calling cholmod_band.
36    
37    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
40            erased when it was NULL.  This led to invalid subselections!
41    
42    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
43    
44            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
45            in method for "t" so as not to lose the unit diagonal property.
46    
47    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
48    
49            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
50            and methods.  This is now an option to the ranef method for the
51            mer class.
52    
53            * src/cs_utils.c: Ensure that the nz component is -1 for a
54            compressed column-oriented matrix.  Minor formatting cleanup.
55    
56            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
57            objects.
58    
59    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
62            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
63    
64    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
67            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
68    
69            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
70            for the dtCMatrix class.
71    
72    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
75            and methods for it.
76    
77    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
80            arguments, such that M %*% 1:6 now works
81            * Tests/matprod.R: test the above
82    
83    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
84    
85            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
86            the ranef.lmer class.
87    
88            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
89            methods to extract the posterior variances from the bVar slot.
90    
91    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
94            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
95    
96            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
97            * tests/simple: (extended)
98    
99            * R/sparseMatrix.R (isTriangular): now using much improved
100            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
101    
102    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
105            (problem report from Franklin Parlamis).  This should be done
106            generally.
107    
108    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
109    
110            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
111            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
112            update the plot methods.
113    
114    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
115    
116            * R/lmer.R (resid and ranef methods):  Added methods for the
117            "residuals" and "resid" generic but only for linear mixed model
118            fits.  Changed the ranef method to return a list of data frames so
119            that the plot methods now work.
120    
121    2006-03-16  Douglas Bates  <bates@bates2>
122    
123            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
124            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
125    
126            * DESCRIPTION (Date): New release
127    
128    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
131    
132            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
133            * man/KNex.Rd: and other help files
134            * tests/*.R: several ones needed adaption
135            * inst/doc/Comparisons.Rnw: dito
136    
137    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
140    
141            * tests/indexing.R: tests for new [<- methods for sparse matrices.
142    
143    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
146    
147            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
148    
149    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/dMatrix.R: enable things like  M [ M < 10 ]
152            * R/dgeMatrix.R: implement it
153    
154    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/AllClass.R: define "summary.mer" and "*.lmer"
157            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
158            * R/lmer.R (show): now works with summary()
159    
160    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
163            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
164                    support the above
165    
166  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
167    
168          * 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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