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revision 1226, Mon Mar 13 14:07:58 2006 UTC revision 1288, Thu Jun 1 20:41:20 2006 UTC
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1    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/lmer.R (panel.ci): Add a reference line at zero and a
4            background grid to the qqmath plot of ranef.lmer.
5    
6    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
9            grouping factors to be specified in the formula as (1|foo/bar).
10    
11    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
12    
13            * R/lmer.R (findbars and others): Change check of is.numeric to
14            !is.language to resolve the bug reported by Jacob Wegelin.
15    
16            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
17            code to evaluate inbreeding coefficients without calculating T,
18            based on code in Sargolzaei and Iwaisaki's paper.
19    
20    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
21    
22            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
23            generic and mer methods for isNested and denomDF. This denomDF was
24            an attempt to emulate that in lme but I don't think that makes
25            sense.  Use the trace of the hat matrix instead.
26    
27    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
30            the C code depending on a slot structure that's no longer valid.
31            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
32    
33    
34    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
35    
36            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
37            of lowerTriMatrix generic and methods to tril (also upper to triu)
38            and added a general band extractor.
39    
40    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * R/pedigree.R (pedigree): Replace sire and dam values outside the
43            allowable range with NAs. Added a corresponding check in the
44            validity check for the pedigree class.
45    
46            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
47            crossprod methods now inherits from symmetricMatrix.
48    
49    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
50    
51            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
52            generics lowerTriMatrix and upperTriMatrix along with methods for
53            the Csparse virtual class.  Also added a C function Csparse_band
54            that implements these methods by calling cholmod_band.
55    
56    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
59            erased when it was NULL.  This led to invalid subselections!
60    
61    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
64            in method for "t" so as not to lose the unit diagonal property.
65    
66    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
69            and methods.  This is now an option to the ranef method for the
70            mer class.
71    
72            * src/cs_utils.c: Ensure that the nz component is -1 for a
73            compressed column-oriented matrix.  Minor formatting cleanup.
74    
75            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
76            objects.
77    
78    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
81            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
82    
83    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
84    
85            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
86            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
87    
88            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
89            for the dtCMatrix class.
90    
91    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
92    
93            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
94            and methods for it.
95    
96    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
99            arguments, such that M %*% 1:6 now works
100            * Tests/matprod.R: test the above
101    
102    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
105            the ranef.lmer class.
106    
107            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
108            methods to extract the posterior variances from the bVar slot.
109    
110    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
113            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
114    
115            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
116            * tests/simple: (extended)
117    
118            * R/sparseMatrix.R (isTriangular): now using much improved
119            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
120    
121    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
124            (problem report from Franklin Parlamis).  This should be done
125            generally.
126    
127    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
130            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
131            update the plot methods.
132    
133    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
134    
135            * R/lmer.R (resid and ranef methods):  Added methods for the
136            "residuals" and "resid" generic but only for linear mixed model
137            fits.  Changed the ranef method to return a list of data frames so
138            that the plot methods now work.
139    
140    2006-03-16  Douglas Bates  <bates@bates2>
141    
142            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
143            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
144    
145            * DESCRIPTION (Date): New release
146    
147    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
150    
151            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
152            * man/KNex.Rd: and other help files
153            * tests/*.R: several ones needed adaption
154            * inst/doc/Comparisons.Rnw: dito
155    
156  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158          * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix          * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix

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