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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1342, Tue Aug 1 20:26:45 2006 UTC
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1    2006-08-01  Douglas Bates  <bates@R-project.org>
2    
3            * R/lmer.R (LMEoptimize method), tests/lmer.R,
4            inst/external/test3comp.rda: Added warnings for convergence on
5            boundary and test cases.
6    
7            * src/lmer.c (mer_postVar): Modified to return the variances that
8            are marginal to the fixed effects, not conditional on them (which
9            is what the bVar slot contents represent).
10    
11    2006-07-31  Douglas Bates  <bates@R-project.org>
12    
13            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
14            function which calls the C function mer_hat_trace2.
15    
16            * man/ranef.Rd: Include description of "postVar" argument and
17            producing a caterpillar plot.
18    
19    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * NAMESPACE:    change  "correlation" to "corMatrix"
22            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
23            * R/dpoMatrix.R: dito
24            * R/lmer.R:      dito
25    
26    2006-07-28  Douglas Bates  <bates@R-project.org>
27    
28            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
29            RZXinv slot's contents into a separate internal function that can
30            be used in mer_hat_trace.
31    
32    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
35            via new smart
36            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
37            utility functions.
38    
39    
40    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/Csparse.R (tril, triu, band): do return *triangular* classed
43            matrices when appropriate; band() even symmetric ones.
44            (replCmat): extend to potentially all "CsparseMatrix"
45            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
46            allow subassignment for special sparse matrices.
47    
48            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
49    
50            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
51            argument; in glmer_*(): print only if(verbose).
52    
53            speed-optimize a few places by moving REAL(.) out of loops.
54    
55            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
56    
57    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
60                    since that wrongly triggers also for M[ logi , ]
61    
62            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
63            a symmetric matrix that results in a non-symmetric one.
64            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
65    
66            * R/dMatrix.R: make round(M) work as round(M, 0)
67    
68            * R/dgTMatrix.R (image): coordinate system and axis now use
69            1-based indices, not 0-based ones.
70    
71            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
72            * tests/indexing.R: test it.
73    
74            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
75            * man/isSymmetric-methods.Rd: and document it.
76    
77            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
78            * man/SparseM-conv.Rd: docu them
79    
80            * tests/other-pkgs.R: renamed from tests/graph.R and add example
81                    for 'SparseM' conversions
82    
83    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
84    
85            * R/Matrix.R (head): added head() and tail() methods.
86    
87    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * DESCRIPTION (Version): 0.995-12 released to CRAN
90    
91    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * tests/simple.R: add check for correct dsT -> dgT coercion;
94                    add check for correct printing of symmetric sparse matrices.
95    
96            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
97            for sparse symmetric matrices.
98    
99            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
100            diagonal twice.
101    
102    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
103    
104            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
105            being applied to the x slot (detected by Brian Ripley).
106    
107    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
110    
111            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
112    
113    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * src/lgCMatrix.c (lgCMatrix_diag): new function
116            * R/lgCMatrix.R (diag): for new method
117    
118            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
119                 ==> construction of illegal "*gTMatrix" via new() should
120                 now be much less easy:
121            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
122    
123            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
124                    directly.
125            * man/Matrix.Rd: documents it.
126    
127    2006-07-06  Douglas Bates  <bates@R-project.org>
128    
129            * src/pedigree.c (pedigree_inbreeding): Correction in
130            initialization.  This function is not currently being used and is
131            not fully tested.
132    
133            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
134            Introduced the glmer class.  Added code for mcmcmsamp on glmer
135            objects.  Modified validity check on pedigree objects to account
136            for nonparallel patterns of missingness of parents.
137    
138            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
139            class.
140    
141    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/pMatrix.R: coercion pMatrix -> Tsparse
144    
145    2006-06-12  Douglas Bates  <bates@R-project.org>
146    
147            * DESCRIPTION (Version): 0.995-11 released to CRAN
148    
149            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
150            the output from mcmcsamp.
151    
152    2006-06-10  Douglas Bates  <bates@R-project.org>
153    
154            * R/lmer.R (simulestimate): added C code for calculating the trace
155            of the hat matrix.
156    
157    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
160            classes.
161            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
162    
163    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/dgTMatrix.R (colSums): etc. All four of
166            colSums(), rowSums(), colMeans(), rowMeans() now should work for
167            all "Matrices".
168    
169    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
170    
171            * R/lmer.R (panel.ci): Add a reference line at zero and a
172            background grid to the qqmath plot of ranef.lmer.
173    
174    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
175    
176            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
177            grouping factors to be specified in the formula as (1|foo/bar).
178    
179    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
180    
181            * R/lmer.R (findbars and others): Change check of is.numeric to
182            !is.language to resolve the bug reported by Jacob Wegelin.
183    
184            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
185            code to evaluate inbreeding coefficients without calculating T,
186            based on code in Sargolzaei and Iwaisaki's paper.
187    
188    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
189    
190            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
191            generic and mer methods for isNested and denomDF. This denomDF was
192            an attempt to emulate that in lme but I don't think that makes
193            sense.  Use the trace of the hat matrix instead.
194    
195    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
198            the C code depending on a slot structure that's no longer valid.
199            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
200    
201    
202    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
203    
204            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
205            of lowerTriMatrix generic and methods to tril (also upper to triu)
206            and added a general band extractor.
207    
208    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * R/pedigree.R (pedigree): Replace sire and dam values outside the
211            allowable range with NAs. Added a corresponding check in the
212            validity check for the pedigree class.
213    
214            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
215            crossprod methods now inherits from symmetricMatrix.
216    
217    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
218    
219            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
220            generics lowerTriMatrix and upperTriMatrix along with methods for
221            the Csparse virtual class.  Also added a C function Csparse_band
222            that implements these methods by calling cholmod_band.
223    
224    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
227            erased when it was NULL.  This led to invalid subselections!
228    
229    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
230    
231            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
232            in method for "t" so as not to lose the unit diagonal property.
233    
234    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
235    
236            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
237            and methods.  This is now an option to the ranef method for the
238            mer class.
239    
240            * src/cs_utils.c: Ensure that the nz component is -1 for a
241            compressed column-oriented matrix.  Minor formatting cleanup.
242    
243            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
244            objects.
245    
246    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
249            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
250    
251    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
254            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
255    
256            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
257            for the dtCMatrix class.
258    
259    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
262            and methods for it.
263    
264    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
267            arguments, such that M %*% 1:6 now works
268            * Tests/matprod.R: test the above
269    
270    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
273            the ranef.lmer class.
274    
275            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
276            methods to extract the posterior variances from the bVar slot.
277    
278    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
281            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
282    
283            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
284            * tests/simple: (extended)
285    
286            * R/sparseMatrix.R (isTriangular): now using much improved
287            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
288    
289    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
290    
291            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
292            (problem report from Franklin Parlamis).  This should be done
293            generally.
294    
295    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
298            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
299            update the plot methods.
300    
301    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
302    
303            * R/lmer.R (resid and ranef methods):  Added methods for the
304            "residuals" and "resid" generic but only for linear mixed model
305            fits.  Changed the ranef method to return a list of data frames so
306            that the plot methods now work.
307    
308    2006-03-16  Douglas Bates  <bates@bates2>
309    
310            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
311            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
312    
313            * DESCRIPTION (Date): New release
314    
315    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
318    
319            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
320            * man/KNex.Rd: and other help files
321            * tests/*.R: several ones needed adaption
322            * inst/doc/Comparisons.Rnw: dito
323    
324    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
327    
328            * tests/indexing.R: tests for new [<- methods for sparse matrices.
329    
330    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
333    
334            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
335    
336    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/dMatrix.R: enable things like  M [ M < 10 ]
339            * R/dgeMatrix.R: implement it
340    
341    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/AllClass.R: define "summary.mer" and "*.lmer"
344            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
345            * R/lmer.R (show): now works with summary()
346    
347    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
350            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
351                    support the above
352    
353  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
354    
355          * 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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