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revision 876, Sat Aug 27 22:50:57 2005 UTC revision 1316, Tue Jul 11 22:00:41 2006 UTC
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1    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
2    
3            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
4            being applied to the x slot (detected by Brian Ripley).  Possible
5            problem with copying the diagonal elements twice?
6    
7    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
10    
11            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
12    
13    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * src/lgCMatrix.c (lgCMatrix_diag): new function
16            * R/lgCMatrix.R (diag): for new method
17    
18            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
19                 ==> construction of illegal "*gTMatrix" via new() should
20                 now be much less easy:
21            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
22    
23            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
24                    directly.
25            * man/Matrix.Rd: documents it.
26    
27    2006-07-06  Douglas Bates  <bates@R-project.org>
28    
29            * src/pedigree.c (pedigree_inbreeding): Correction in
30            initialization.  This function is not currently being used and is
31            not fully tested.
32    
33            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
34            Introduced the glmer class.  Added code for mcmcmsamp on glmer
35            objects.  Modified validity check on pedigree objects to account
36            for nonparallel patterns of missingness of parents.
37    
38            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
39            class.
40    
41    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * R/pMatrix.R: coercion pMatrix -> Tsparse
44    
45    2006-06-12  Douglas Bates  <bates@R-project.org>
46    
47            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
48            the output from mcmcsamp.
49    
50    2006-06-10  Douglas Bates  <bates@R-project.org>
51    
52            * R/lmer.R (simulestimate): added C code for calculating the trace
53            of the hat matrix.
54    
55    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
58            classes.
59            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
60    
61    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/dgTMatrix.R (colSums): etc. All four of
64            colSums(), rowSums(), colMeans(), rowMeans() now should work for
65            all "Matrices".
66    
67    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
68    
69            * R/lmer.R (panel.ci): Add a reference line at zero and a
70            background grid to the qqmath plot of ranef.lmer.
71    
72    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
73    
74            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
75            grouping factors to be specified in the formula as (1|foo/bar).
76    
77    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
78    
79            * R/lmer.R (findbars and others): Change check of is.numeric to
80            !is.language to resolve the bug reported by Jacob Wegelin.
81    
82            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
83            code to evaluate inbreeding coefficients without calculating T,
84            based on code in Sargolzaei and Iwaisaki's paper.
85    
86    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
87    
88            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
89            generic and mer methods for isNested and denomDF. This denomDF was
90            an attempt to emulate that in lme but I don't think that makes
91            sense.  Use the trace of the hat matrix instead.
92    
93    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
96            the C code depending on a slot structure that's no longer valid.
97            * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)
98    
99    
100    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
101    
102            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
103            of lowerTriMatrix generic and methods to tril (also upper to triu)
104            and added a general band extractor.
105    
106    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
107    
108            * R/pedigree.R (pedigree): Replace sire and dam values outside the
109            allowable range with NAs. Added a corresponding check in the
110            validity check for the pedigree class.
111    
112            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
113            crossprod methods now inherits from symmetricMatrix.
114    
115    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
118            generics lowerTriMatrix and upperTriMatrix along with methods for
119            the Csparse virtual class.  Also added a C function Csparse_band
120            that implements these methods by calling cholmod_band.
121    
122    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
125            erased when it was NULL.  This led to invalid subselections!
126    
127    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
130            in method for "t" so as not to lose the unit diagonal property.
131    
132    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
135            and methods.  This is now an option to the ranef method for the
136            mer class.
137    
138            * src/cs_utils.c: Ensure that the nz component is -1 for a
139            compressed column-oriented matrix.  Minor formatting cleanup.
140    
141            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
142            objects.
143    
144    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
147            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
148    
149    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
150    
151            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
152            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
153    
154            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
155            for the dtCMatrix class.
156    
157    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
158    
159            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
160            and methods for it.
161    
162    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
165            arguments, such that M %*% 1:6 now works
166            * Tests/matprod.R: test the above
167    
168    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
169    
170            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
171            the ranef.lmer class.
172    
173            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
174            methods to extract the posterior variances from the bVar slot.
175    
176    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
179            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
180    
181            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
182            * tests/simple: (extended)
183    
184            * R/sparseMatrix.R (isTriangular): now using much improved
185            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
186    
187    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
188    
189            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
190            (problem report from Franklin Parlamis).  This should be done
191            generally.
192    
193    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
196            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
197            update the plot methods.
198    
199    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
200    
201            * R/lmer.R (resid and ranef methods):  Added methods for the
202            "residuals" and "resid" generic but only for linear mixed model
203            fits.  Changed the ranef method to return a list of data frames so
204            that the plot methods now work.
205    
206    2006-03-16  Douglas Bates  <bates@bates2>
207    
208            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
209            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
210    
211            * DESCRIPTION (Date): New release
212    
213    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
216    
217            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
218            * man/KNex.Rd: and other help files
219            * tests/*.R: several ones needed adaption
220            * inst/doc/Comparisons.Rnw: dito
221    
222    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
225    
226            * tests/indexing.R: tests for new [<- methods for sparse matrices.
227    
228    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
231    
232            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
233    
234    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/dMatrix.R: enable things like  M [ M < 10 ]
237            * R/dgeMatrix.R: implement it
238    
239    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/AllClass.R: define "summary.mer" and "*.lmer"
242            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
243            * R/lmer.R (show): now works with summary()
244    
245    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
248            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
249                    support the above
250    
251    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
254            Use glmFit$prior.weights for weights in a glmm.
255            Allow an option usePQL = FALSE to skip the PQL steps for the
256            Laplace method (and, in time, the AGQ method).
257    
258            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
259            into a separate function internal_mer_Xfactor to be able to call
260            it from internal_bhat.
261    
262    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * tests/Class+Meth.R (tstMatrixClass): function for much better
265            testing; now again of all actual classes.
266    
267            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
268                    use macros and define make_d_matrix_* and make_i_matrix_*
269                    where _i_ is for the ldense routines:
270    
271            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
272            * src/ldense.c (lsyMatrix_as_lgeMatrix):
273    
274            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
275    
276    
277    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
280                    many different kinds of matrices.
281            * R/*.R: quite a few new methods were needed for R CMD check with
282                    new Matrix().  Very good for users playing around.
283    
284    
285    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * src/dgeMatrix.c (dMatrix_validate): new
288            * src/Mutils.c (dense_nonpacked_validate): new
289    
290            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
291    
292    
293    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
294    
295            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
296    
297    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
298    
299            * DESCRIPTION (Version): 0.99-6 released to CRAN
300    
301            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
302            segfault in cases with multiple non-nested grouping factors.
303    
304    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
307                    (Depends): also on 'utils'
308    
309            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
310            * R/diagMatrix.R (Diagonal): constructor and methods for
311            diagonal matrices
312    
313            * R/ltTMatrix.R: new "minimal methods"
314    
315    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
318            all methods (and help files).
319    
320    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
323                    for case (dimn.  op  no_dimn.)
324    
325    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
326    
327            * DESCRIPTION (Version): 0.99-2  released to CRAN
328    
329    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
332            by Julian Faraway.
333    
334    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Auxiliaries.R (try_as): new utility
337            * R/sparseMatrix.R: use try_as() in coercion to original class
338    
339    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
342    
343    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/Auxiliaries.R (dimNamesCheck): added
346    
347            * R/Matrix.R (as.array), (as.vector): new
348    
349    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
352                    default.
353            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
354                    "pMatrix" now contains "sparseMatrix"
355    
356    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * tests/Class+Meth.R: new tests; t(t(m)) == m
359    
360            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
361    
362            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
363            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
364    
365            * R/dspMatrix.R: typo in "t" method
366    
367    2005-09-18  Douglas Bates  <bates@wisc.edu>
368    
369            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
370            * R/Tsparse.R: instead of R/gTMatrix.R
371            * R/Csparse.R: new
372            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
373            * src/Tsparse.c: new; many trivial methods calling cholmod_()
374            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
375                            via cholmod
376    
377    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/Auxiliaries.R (non0ind): new function using new C code
380            * src/dgCMatrix.c (compressed_non_0_ij): new utility
381    
382    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
383    
384            * src/chm_common.h: header file required by all C sources that
385            call CHOLMOD functions.  It defines a cholmod_common structure
386            called 'c' whose address is passed as the last argument to
387            (virtually) every CHOLMOD function.
388    
389            * src/Pattern.c: Simple example of the use of CHOLMOD.
390    
391            * src/init.c: initialize and finalize the cholmod_common structure.
392    
393            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
394            LDL and CCOLAMD from the U. of Florida sparse matrix library.
395    
396    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * inst/test-tools.R: new file collecting the utility functions used
399                    in ./tests/*.R
400    
401            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
402            * R/Matrix.R (cbind2): methods for NULL and missing
403    
404    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/AllClass.R: new "index" class for "[" and "[<-":
407                    First cut at "symmetricMatrix" and "triangularMatrix"
408            * R/gTMatrix.R (.ind.prep): new function;
409                    Logical and character indexing now work too.
410            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
411            * tests/indexing.R: new, including *.Rout.save
412            * tests/dgTMatrix.R: new
413    
414  2005-08-29  Douglas Bates  <bates@wisc.edu>  2005-08-29  Douglas Bates  <bates@wisc.edu>
415    
416          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position          * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position

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