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Diff of /pkg/ChangeLog

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revision 1245, Wed Apr 12 20:31:18 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45            the C code depending on a slot structure that's no longer valid.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>  2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113          * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"          * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"

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