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revision 1222, Tue Mar 7 11:05:08 2006 UTC revision 1312, Thu Jul 6 15:29:56 2006 UTC
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1    2006-07-06  Douglas Bates  <bates@R-project.org>
2    
3            * src/pedigree.c (pedigree_inbreeding): Correction in
4            initialization.  This function is not currently being used and is
5            not fully tested.
6    
7            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
8            Introduced the glmer class.  Added code for mcmcmsamp on glmer
9            objects.  Modified validity check on pedigree objects to account
10            for nonparallel patterns of missingness of parents.
11    
12    2006-06-12  Douglas Bates  <bates@R-project.org>
13    
14            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
15            the output from mcmcsamp.
16    
17    2006-06-10  Douglas Bates  <bates@R-project.org>
18    
19            * R/lmer.R (simulestimate): added C code for calculating the trace
20            of the hat matrix.
21    
22    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
25            classes.
26    
27    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/dgTMatrix.R (colSums): etc. All four of
30            colSums(), rowSums(), colMeans(), rowMeans() now should work for
31            all "Matrices".
32    
33    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
34    
35            * R/lmer.R (panel.ci): Add a reference line at zero and a
36            background grid to the qqmath plot of ranef.lmer.
37    
38    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
41            grouping factors to be specified in the formula as (1|foo/bar).
42    
43    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
44    
45            * R/lmer.R (findbars and others): Change check of is.numeric to
46            !is.language to resolve the bug reported by Jacob Wegelin.
47    
48            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
49            code to evaluate inbreeding coefficients without calculating T,
50            based on code in Sargolzaei and Iwaisaki's paper.
51    
52    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
55            generic and mer methods for isNested and denomDF. This denomDF was
56            an attempt to emulate that in lme but I don't think that makes
57            sense.  Use the trace of the hat matrix instead.
58    
59    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
62            the C code depending on a slot structure that's no longer valid.
63            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
64    
65    
66    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
67    
68            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
69            of lowerTriMatrix generic and methods to tril (also upper to triu)
70            and added a general band extractor.
71    
72    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/pedigree.R (pedigree): Replace sire and dam values outside the
75            allowable range with NAs. Added a corresponding check in the
76            validity check for the pedigree class.
77    
78            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
79            crossprod methods now inherits from symmetricMatrix.
80    
81    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
84            generics lowerTriMatrix and upperTriMatrix along with methods for
85            the Csparse virtual class.  Also added a C function Csparse_band
86            that implements these methods by calling cholmod_band.
87    
88    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
91            erased when it was NULL.  This led to invalid subselections!
92    
93    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
94    
95            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
96            in method for "t" so as not to lose the unit diagonal property.
97    
98    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
101            and methods.  This is now an option to the ranef method for the
102            mer class.
103    
104            * src/cs_utils.c: Ensure that the nz component is -1 for a
105            compressed column-oriented matrix.  Minor formatting cleanup.
106    
107            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
108            objects.
109    
110    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
113            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
114    
115    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
118            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
119    
120            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
121            for the dtCMatrix class.
122    
123    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
124    
125            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
126            and methods for it.
127    
128    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
131            arguments, such that M %*% 1:6 now works
132            * Tests/matprod.R: test the above
133    
134    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
135    
136            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
137            the ranef.lmer class.
138    
139            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
140            methods to extract the posterior variances from the bVar slot.
141    
142    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
145            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
146    
147            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
148            * tests/simple: (extended)
149    
150            * R/sparseMatrix.R (isTriangular): now using much improved
151            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
152    
153    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
154    
155            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
156            (problem report from Franklin Parlamis).  This should be done
157            generally.
158    
159    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
160    
161            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
162            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
163            update the plot methods.
164    
165    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
166    
167            * R/lmer.R (resid and ranef methods):  Added methods for the
168            "residuals" and "resid" generic but only for linear mixed model
169            fits.  Changed the ranef method to return a list of data frames so
170            that the plot methods now work.
171    
172    2006-03-16  Douglas Bates  <bates@bates2>
173    
174            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
175            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
176    
177            * DESCRIPTION (Date): New release
178    
179    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
182    
183            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
184            * man/KNex.Rd: and other help files
185            * tests/*.R: several ones needed adaption
186            * inst/doc/Comparisons.Rnw: dito
187    
188    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
191    
192            * tests/indexing.R: tests for new [<- methods for sparse matrices.
193    
194    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
197    
198            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
199    
200    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/dMatrix.R: enable things like  M [ M < 10 ]
203            * R/dgeMatrix.R: implement it
204    
205  2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207          * R/AllClass.R: define "summary.mer" and "*.lmer"          * R/AllClass.R: define "summary.mer" and "*.lmer"

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