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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1284, Sat May 27 20:01:11 2006 UTC
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1    2006-05-27  Douglas Bates  <bates@.stat.wisc.edu>
2    
3            * R/lmer.R (findbars and others): Change check of is.numeric to
4            !is.language to resolve the bug reported by Jacob Wegelin.
5    
6            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
7            code to evaluate inbreeding coefficients without calculating T,
8            based on code in Sargolzaei and Iwaisaki's paper.
9    
10    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
11    
12            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
13            generic and mer methods for isNested and denomDF. This denomDF was
14            an attempt to emulate that in lme but I don't think that makes
15            sense.  Use the trace of the hat matrix instead.
16    
17    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
20            the C code depending on a slot structure that's no longer valid.
21            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
22    
23    
24    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
25    
26            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
27            of lowerTriMatrix generic and methods to tril (also upper to triu)
28            and added a general band extractor.
29    
30    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * R/pedigree.R (pedigree): Replace sire and dam values outside the
33            allowable range with NAs. Added a corresponding check in the
34            validity check for the pedigree class.
35    
36            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
37            crossprod methods now inherits from symmetricMatrix.
38    
39    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
40    
41            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
42            generics lowerTriMatrix and upperTriMatrix along with methods for
43            the Csparse virtual class.  Also added a C function Csparse_band
44            that implements these methods by calling cholmod_band.
45    
46    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
49            erased when it was NULL.  This led to invalid subselections!
50    
51    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
52    
53            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
54            in method for "t" so as not to lose the unit diagonal property.
55    
56    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
57    
58            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
59            and methods.  This is now an option to the ranef method for the
60            mer class.
61    
62            * src/cs_utils.c: Ensure that the nz component is -1 for a
63            compressed column-oriented matrix.  Minor formatting cleanup.
64    
65            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
66            objects.
67    
68    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
71            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
72    
73    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
74    
75            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
76            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
77    
78            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
79            for the dtCMatrix class.
80    
81    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
84            and methods for it.
85    
86    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
89            arguments, such that M %*% 1:6 now works
90            * Tests/matprod.R: test the above
91    
92    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
93    
94            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
95            the ranef.lmer class.
96    
97            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
98            methods to extract the posterior variances from the bVar slot.
99    
100    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
103            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
104    
105            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
106            * tests/simple: (extended)
107    
108            * R/sparseMatrix.R (isTriangular): now using much improved
109            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
110    
111    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
112    
113            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
114            (problem report from Franklin Parlamis).  This should be done
115            generally.
116    
117    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
120            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
121            update the plot methods.
122    
123    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * R/lmer.R (resid and ranef methods):  Added methods for the
126            "residuals" and "resid" generic but only for linear mixed model
127            fits.  Changed the ranef method to return a list of data frames so
128            that the plot methods now work.
129    
130    2006-03-16  Douglas Bates  <bates@bates2>
131    
132            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
133            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
134    
135            * DESCRIPTION (Date): New release
136    
137    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
140    
141            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
142            * man/KNex.Rd: and other help files
143            * tests/*.R: several ones needed adaption
144            * inst/doc/Comparisons.Rnw: dito
145    
146    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
149    
150            * tests/indexing.R: tests for new [<- methods for sparse matrices.
151    
152    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
155    
156            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
157    
158    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/dMatrix.R: enable things like  M [ M < 10 ]
161            * R/dgeMatrix.R: implement it
162    
163    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/AllClass.R: define "summary.mer" and "*.lmer"
166            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
167            * R/lmer.R (show): now works with summary()
168    
169    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
172            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
173                    support the above
174    
175  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
176    
177          * 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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