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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1267, Tue May 16 19:12:13 2006 UTC
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1    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/pedigree.R (pedigree): Replace sire and dam values outside the
4            allowable range with NAs. Added a corresponding check in the
5            validity check for the pedigree class.
6    
7            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
8            crossprod methods now inherits from symmetricMatrix.
9    
10    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
11    
12            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
13            generics lowerTriMatrix and upperTriMatrix along with methods for
14            the Csparse virtual class.  Also added a C function Csparse_band
15            that implements these methods by calling cholmod_band.
16    
17    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
20            erased when it was NULL.  This led to invalid subselections!
21    
22    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
23    
24            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
25            in method for "t" so as not to lose the unit diagonal property.
26    
27    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
28    
29            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
30            and methods.  This is now an option to the ranef method for the
31            mer class.
32    
33            * src/cs_utils.c: Ensure that the nz component is -1 for a
34            compressed column-oriented matrix.  Minor formatting cleanup.
35    
36            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
37            objects.
38    
39    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
42            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
43    
44    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
45    
46            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
47            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
48    
49            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
50            for the dtCMatrix class.
51    
52    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
55            and methods for it.
56    
57    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
60            arguments, such that M %*% 1:6 now works
61            * Tests/matprod.R: test the above
62    
63    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
64    
65            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
66            the ranef.lmer class.
67    
68            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
69            methods to extract the posterior variances from the bVar slot.
70    
71    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
74            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
75    
76            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
77            * tests/simple: (extended)
78    
79            * R/sparseMatrix.R (isTriangular): now using much improved
80            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
81    
82    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
83    
84            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
85            (problem report from Franklin Parlamis).  This should be done
86            generally.
87    
88    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
89    
90            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
91            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
92            update the plot methods.
93    
94    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * R/lmer.R (resid and ranef methods):  Added methods for the
97            "residuals" and "resid" generic but only for linear mixed model
98            fits.  Changed the ranef method to return a list of data frames so
99            that the plot methods now work.
100    
101    2006-03-16  Douglas Bates  <bates@bates2>
102    
103            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
104            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
105    
106            * DESCRIPTION (Date): New release
107    
108    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
111    
112            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
113            * man/KNex.Rd: and other help files
114            * tests/*.R: several ones needed adaption
115            * inst/doc/Comparisons.Rnw: dito
116    
117    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
120    
121            * tests/indexing.R: tests for new [<- methods for sparse matrices.
122    
123    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
126    
127            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
128    
129    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/dMatrix.R: enable things like  M [ M < 10 ]
132            * R/dgeMatrix.R: implement it
133    
134    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/AllClass.R: define "summary.mer" and "*.lmer"
137            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
138            * R/lmer.R (show): now works with summary()
139    
140    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
143            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
144                    support the above
145    
146  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
147    
148          * 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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