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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1287, Tue May 30 23:23:24 2006 UTC
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1    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
4            grouping factors to be specified in the formula as (1|foo/bar).
5    
6    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/lmer.R (findbars and others): Change check of is.numeric to
9            !is.language to resolve the bug reported by Jacob Wegelin.
10    
11            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
12            code to evaluate inbreeding coefficients without calculating T,
13            based on code in Sargolzaei and Iwaisaki's paper.
14    
15    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
16    
17            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
18            generic and mer methods for isNested and denomDF. This denomDF was
19            an attempt to emulate that in lme but I don't think that makes
20            sense.  Use the trace of the hat matrix instead.
21    
22    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
25            the C code depending on a slot structure that's no longer valid.
26            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
27    
28    
29    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
30    
31            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
32            of lowerTriMatrix generic and methods to tril (also upper to triu)
33            and added a general band extractor.
34    
35    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * R/pedigree.R (pedigree): Replace sire and dam values outside the
38            allowable range with NAs. Added a corresponding check in the
39            validity check for the pedigree class.
40    
41            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
42            crossprod methods now inherits from symmetricMatrix.
43    
44    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
45    
46            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
47            generics lowerTriMatrix and upperTriMatrix along with methods for
48            the Csparse virtual class.  Also added a C function Csparse_band
49            that implements these methods by calling cholmod_band.
50    
51    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
54            erased when it was NULL.  This led to invalid subselections!
55    
56    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
57    
58            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
59            in method for "t" so as not to lose the unit diagonal property.
60    
61    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
62    
63            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
64            and methods.  This is now an option to the ranef method for the
65            mer class.
66    
67            * src/cs_utils.c: Ensure that the nz component is -1 for a
68            compressed column-oriented matrix.  Minor formatting cleanup.
69    
70            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
71            objects.
72    
73    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
76            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
77    
78    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
79    
80            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
81            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
82    
83            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
84            for the dtCMatrix class.
85    
86    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
87    
88            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
89            and methods for it.
90    
91    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
94            arguments, such that M %*% 1:6 now works
95            * Tests/matprod.R: test the above
96    
97    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
98    
99            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
100            the ranef.lmer class.
101    
102            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
103            methods to extract the posterior variances from the bVar slot.
104    
105    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
108            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
109    
110            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
111            * tests/simple: (extended)
112    
113            * R/sparseMatrix.R (isTriangular): now using much improved
114            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
115    
116    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
117    
118            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
119            (problem report from Franklin Parlamis).  This should be done
120            generally.
121    
122    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
123    
124            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
125            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
126            update the plot methods.
127    
128    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
129    
130            * R/lmer.R (resid and ranef methods):  Added methods for the
131            "residuals" and "resid" generic but only for linear mixed model
132            fits.  Changed the ranef method to return a list of data frames so
133            that the plot methods now work.
134    
135    2006-03-16  Douglas Bates  <bates@bates2>
136    
137            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
138            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
139    
140            * DESCRIPTION (Date): New release
141    
142    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
145    
146            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
147            * man/KNex.Rd: and other help files
148            * tests/*.R: several ones needed adaption
149            * inst/doc/Comparisons.Rnw: dito
150    
151    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
154    
155            * tests/indexing.R: tests for new [<- methods for sparse matrices.
156    
157    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
160    
161            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
162    
163    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/dMatrix.R: enable things like  M [ M < 10 ]
166            * R/dgeMatrix.R: implement it
167    
168    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/AllClass.R: define "summary.mer" and "*.lmer"
171            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
172            * R/lmer.R (show): now works with summary()
173    
174    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
177            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
178                    support the above
179    
180  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
181    
182          * 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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