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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1290, Thu Jun 8 09:30:21 2006 UTC
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1    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgTMatrix.R (colSums): etc. All four of
4            colSums(), rowSums(), colMeans(), rowMeans() now should work for
5            all "Matrices".
6    
7    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
8    
9            * R/lmer.R (panel.ci): Add a reference line at zero and a
10            background grid to the qqmath plot of ranef.lmer.
11    
12    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
13    
14            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
15            grouping factors to be specified in the formula as (1|foo/bar).
16    
17    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * R/lmer.R (findbars and others): Change check of is.numeric to
20            !is.language to resolve the bug reported by Jacob Wegelin.
21    
22            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
23            code to evaluate inbreeding coefficients without calculating T,
24            based on code in Sargolzaei and Iwaisaki's paper.
25    
26    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
27    
28            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
29            generic and mer methods for isNested and denomDF. This denomDF was
30            an attempt to emulate that in lme but I don't think that makes
31            sense.  Use the trace of the hat matrix instead.
32    
33    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
36            the C code depending on a slot structure that's no longer valid.
37            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
38    
39    
40    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
41    
42            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
43            of lowerTriMatrix generic and methods to tril (also upper to triu)
44            and added a general band extractor.
45    
46    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
47    
48            * R/pedigree.R (pedigree): Replace sire and dam values outside the
49            allowable range with NAs. Added a corresponding check in the
50            validity check for the pedigree class.
51    
52            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
53            crossprod methods now inherits from symmetricMatrix.
54    
55    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
56    
57            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
58            generics lowerTriMatrix and upperTriMatrix along with methods for
59            the Csparse virtual class.  Also added a C function Csparse_band
60            that implements these methods by calling cholmod_band.
61    
62    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
65            erased when it was NULL.  This led to invalid subselections!
66    
67    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
68    
69            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
70            in method for "t" so as not to lose the unit diagonal property.
71    
72    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
75            and methods.  This is now an option to the ranef method for the
76            mer class.
77    
78            * src/cs_utils.c: Ensure that the nz component is -1 for a
79            compressed column-oriented matrix.  Minor formatting cleanup.
80    
81            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
82            objects.
83    
84    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
87            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
88    
89    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
90    
91            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
92            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
93    
94            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
95            for the dtCMatrix class.
96    
97    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
98    
99            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
100            and methods for it.
101    
102    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
105            arguments, such that M %*% 1:6 now works
106            * Tests/matprod.R: test the above
107    
108    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
109    
110            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
111            the ranef.lmer class.
112    
113            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
114            methods to extract the posterior variances from the bVar slot.
115    
116    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
119            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
120    
121            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
122            * tests/simple: (extended)
123    
124            * R/sparseMatrix.R (isTriangular): now using much improved
125            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
126    
127    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
130            (problem report from Franklin Parlamis).  This should be done
131            generally.
132    
133    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
134    
135            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
136            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
137            update the plot methods.
138    
139    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
140    
141            * R/lmer.R (resid and ranef methods):  Added methods for the
142            "residuals" and "resid" generic but only for linear mixed model
143            fits.  Changed the ranef method to return a list of data frames so
144            that the plot methods now work.
145    
146    2006-03-16  Douglas Bates  <bates@bates2>
147    
148            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
149            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
150    
151            * DESCRIPTION (Date): New release
152    
153    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
156    
157            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
158            * man/KNex.Rd: and other help files
159            * tests/*.R: several ones needed adaption
160            * inst/doc/Comparisons.Rnw: dito
161    
162    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
165    
166            * tests/indexing.R: tests for new [<- methods for sparse matrices.
167    
168    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
171    
172            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
173    
174    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/dMatrix.R: enable things like  M [ M < 10 ]
177            * R/dgeMatrix.R: implement it
178    
179    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/AllClass.R: define "summary.mer" and "*.lmer"
182            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
183            * R/lmer.R (show): now works with summary()
184    
185    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
188            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
189                    support the above
190    
191  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
192    
193          * 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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