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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1265, Mon May 15 22:36:59 2006 UTC
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1    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
4            generics lowerTriMatrix and upperTriMatrix along with methods for
5            the Csparse virtual class.  Also added a C function Csparse_band
6            that implements these methods by calling cholmod_band.
7    
8    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
11            erased when it was NULL.  This led to invalid subselections!
12    
13    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
16            in method for "t" so as not to lose the unit diagonal property.
17    
18    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
21            and methods.  This is now an option to the ranef method for the
22            mer class.
23    
24            * src/cs_utils.c: Ensure that the nz component is -1 for a
25            compressed column-oriented matrix.  Minor formatting cleanup.
26    
27            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
28            objects.
29    
30    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
33            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
34    
35    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
38            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
39    
40            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
41            for the dtCMatrix class.
42    
43    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
44    
45            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
46            and methods for it.
47    
48    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
51            arguments, such that M %*% 1:6 now works
52            * Tests/matprod.R: test the above
53    
54    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
55    
56            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
57            the ranef.lmer class.
58    
59            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
60            methods to extract the posterior variances from the bVar slot.
61    
62    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
65            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
66    
67            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
68            * tests/simple: (extended)
69    
70            * R/sparseMatrix.R (isTriangular): now using much improved
71            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
72    
73    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
74    
75            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
76            (problem report from Franklin Parlamis).  This should be done
77            generally.
78    
79    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
80    
81            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
82            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
83            update the plot methods.
84    
85    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * R/lmer.R (resid and ranef methods):  Added methods for the
88            "residuals" and "resid" generic but only for linear mixed model
89            fits.  Changed the ranef method to return a list of data frames so
90            that the plot methods now work.
91    
92    2006-03-16  Douglas Bates  <bates@bates2>
93    
94            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
95            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
96    
97            * DESCRIPTION (Date): New release
98    
99    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
102    
103            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
104            * man/KNex.Rd: and other help files
105            * tests/*.R: several ones needed adaption
106            * inst/doc/Comparisons.Rnw: dito
107    
108    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
111    
112            * tests/indexing.R: tests for new [<- methods for sparse matrices.
113    
114    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
117    
118            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
119    
120    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/dMatrix.R: enable things like  M [ M < 10 ]
123            * R/dgeMatrix.R: implement it
124    
125    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/AllClass.R: define "summary.mer" and "*.lmer"
128            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
129            * R/lmer.R (show): now works with summary()
130    
131    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
134            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
135                    support the above
136    
137  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
138    
139          * 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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