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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1546, Mon Sep 11 14:49:05 2006 UTC
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1    2006-09-11  Douglas Bates  <bates@R-project.org>
2    
3            * src/Mutils.[ch],init.c inst/include/*.h: Move the
4            alloc_d**Matrix functions to the lme4 package.
5    
6    2006-09-09  Douglas Bates  <bates@R-project.org>
7    
8            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
9            fixed
10    
11    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
14    
15            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
16            * man/tcrossprod.Rd: dito
17    
18    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
19    
20            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
21            for exported functions
22            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
23            Remove partitioning algorithms for sparse matrix reordering.  The
24            copyright on the Metis code was problematic and the methods were
25            rarely used.
26            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
27            operations are now done entirely in CHOLMOD code.
28    
29    2006-09-06  Douglas Bates  <bates@R-project.org>
30    
31            * src/Mutils.h: Remove functions that are no longer used.
32    
33    2006-09-04  Douglas Bates  <bates@R-project.org>
34    
35            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
36            * src/DEPS.mkf: update
37    
38    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * created branches/Matrix-for-R-2.3.x;  on trunk: do
41            * DESCRIPTION (Version): 0.9975-0
42            (Depends): R (>= 2.4.0)
43    
44    2006-09-01  Douglas Bates  <bates@R-project.org>
45    
46            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
47    
48    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
51            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
52    
53            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
54    
55    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
58            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
59            * R/dsparseMatrix.R: dito
60            * R/Csparse.R: dito
61    
62    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dMatrix.R (Compare): improve availability of "<", etc
65            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
66    
67    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
70            of a 0-index which was used as 1-index (..hmm)
71    
72            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
73    
74            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
75            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
76            (.is.diagonal): dito
77    
78            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
79    
80            * R/Matrix.R (Matrix): also work for NA data
81    
82    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
85            in all cases.
86    
87    2006-08-27  Douglas Bates  <bates@R-project.org>
88    
89            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
90            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
91    
92    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
95            subclasses of "ddenseMatrix"
96            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
97            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
98            instead of half dozen specialized ones.
99    
100    2006-08-25  Douglas Bates  <bates@R-project.org>
101    
102            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
103            <tillard@cirad.fr> - ordering standard errors to match effects.
104    
105    2006-08-24  Douglas Bates  <bates@R-project.org>
106    
107            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
108            on R_ldl.
109            * R/lCholCMatrix.R,
110            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
111            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
112            * many files in ./R and ./src: Use more general version of
113            dup_mMatrix_as_dgeMatrix to simplify method definitions.
114            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
115            dtpMatrix, dspMatrix and dppMatrix conversions.
116    
117    
118    2006-08-23  Douglas Bates  <bates@R-project.org>
119    
120            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
121            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
122            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
123            dgeMatrix_crossprod (may need to do this in other places).
124            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
125            generic and method for dsCMatrix.  Use CHOLMOD for chol().
126    
127    2006-08-22  Douglas Bates  <bates@R-project.org>
128    
129            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
130            types of classed Matrices, matrices or numeric or logical vectors.
131            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
132            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
133            to Mutils.h (as an inline) and change name to Matrix_check_class;
134            fixes in as_cholmod_factor and chm_factor_to_SEXP.
135            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
136            dsCMatrix_matrix_solve.  Comment out vestigial functions.
137            * src/Csparse.c: use diag_P and uplo_P macros.
138    
139    2006-08-21  Douglas Bates  <bates@R-project.org>
140    
141            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
142            valgrind.
143            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
144            inverses.
145            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
146            -Wall warnings.
147            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
148            Use dup_mMatrix_as_dgeMatrix.
149    
150    2006-08-20  Douglas Bates  <bates@R-project.org>
151    
152            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
153            * tests/sparseQR.R: Added
154            * man/sparseQR-class.Rd: Document methods for qr.* generics
155            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
156    
157    2006-08-19  Douglas Bates  <bates@R-project.org>
158    
159            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
160            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
161            and qr.fitted.
162            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
163            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
164    
165    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
168            the base version has no "..." argument.
169    
170            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
171    
172            * R/Matrix.R: define and
173            * NAMESPACE: export as.numeric() and as.logical() methods.
174                    Let's hope these do not badly slow down something...
175            Finally export the zapsmall() method.
176    
177    2006-08-17  Douglas Bates  <bates@R-project.org>
178    
179            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
180            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
181            * src/dtCMatrix.c :Remove code that is no longer used
182            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
183    
184    2006-08-14  Douglas Bates  <bates@R-project.org>
185    
186            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
187            Csparse_to_logical and Csparse_symmetric_to_general.
188            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
189            coercion methods between CsparseMatrix and TsparseMatrix.
190    
191    2006-08-14  Douglas Bates  <bates@R-project.org>
192    
193            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
194            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
195            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
196            possible.
197    
198    2006-08-12  Douglas Bates  <bates@R-project.org>
199    
200            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
201              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
202              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
203              generalize conversions between TsparseMatrix, CsparseMatrix,
204              denseMatrix and matrix.  Preserve triangularity property and
205              propagate Dimnames in the easy cases.
206    
207    2006-08-10  Douglas Bates  <bates@R-project.org>
208    
209            * src/lmer.c: adjust checks in glmer_init for S4SXP
210            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
211            before S4SXP but for the wrong reasons.
212    
213    2006-08-08  Douglas Bates  <bates@R-project.org>
214    
215            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
216            Later modified to return the upper triangle only.
217            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
218    
219    2006-08-07  Douglas Bates  <bates@R-project.org>
220    
221            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
222            R-level conversion to a sparse symmetric class.
223            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
224            Remove conversion to sparse symmetric classes (now done in C code).
225    
226    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
229            * man/band.Rd:  adapt the \dontshow{} unit test.
230    
231    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * DESCRIPTION (Version): 0.995-14  for CRAN
234    
235            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
236    
237            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
238            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
239    
240            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
241            * R/Tsparse.R (tril, triu, band): methods
242            * R/dgRMatrix.R (tril, ...):    ditto
243            * man/band.Rd:                  ditto
244    
245    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Matrix.R (head, tail): directly use utils:::head.matrix
248                    to be up-to-date automatically.
249    
250    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
253    
254            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
255            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
256            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
257            such that the S4 objects are always created by the current version
258            of R and 'Matrix' class definitions.
259    
260    2006-08-01  Douglas Bates  <bates@R-project.org>
261    
262            * R/lmer.R (LMEoptimize method), tests/lmer.R,
263            inst/external/test3comp.rda: Added warnings for convergence on
264            boundary and test cases.
265    
266            * src/lmer.c (mer_postVar): Modified to return the variances that
267            are marginal to the fixed effects, not conditional on them (which
268            is what the bVar slot contents represent).
269    
270    2006-07-31  Douglas Bates  <bates@R-project.org>
271    
272            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
273            function which calls the C function mer_hat_trace2.
274    
275            * man/ranef.Rd: Include description of "postVar" argument and
276            producing a caterpillar plot.
277    
278    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * NAMESPACE:    change  "correlation" to "corMatrix"
281            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
282            * R/dpoMatrix.R: ditto
283            * R/lmer.R:      ditto
284    
285    2006-07-28  Douglas Bates  <bates@R-project.org>
286    
287            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
288            RZXinv slot's contents into a separate internal function that can
289            be used in mer_hat_trace.
290    
291    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
294            via new smart
295            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
296            utility functions.
297    
298    
299    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/Csparse.R (tril, triu, band): do return *triangular* classed
302            matrices when appropriate; band() even symmetric ones.
303            (replCmat): extend to potentially all "CsparseMatrix"
304            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
305            allow subassignment for special sparse matrices.
306    
307            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
308    
309            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
310            argument; in glmer_*(): print only if(verbose).
311    
312            speed-optimize a few places by moving REAL(.) out of loops.
313    
314            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
315    
316    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
319                    since that wrongly triggers also for M[ logi , ]
320    
321            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
322            a symmetric matrix that results in a non-symmetric one.
323            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
324    
325            * R/dMatrix.R: make round(M) work as round(M, 0)
326    
327            * R/dgTMatrix.R (image): coordinate system and axis now use
328            1-based indices, not 0-based ones.
329    
330            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
331            * tests/indexing.R: test it.
332    
333            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
334            * man/isSymmetric-methods.Rd: and document it.
335    
336            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
337            * man/SparseM-conv.Rd: docu them
338    
339            * tests/other-pkgs.R: renamed from tests/graph.R and add example
340                    for 'SparseM' conversions
341    
342    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
343    
344            * R/Matrix.R (head): added head() and tail() methods.
345    
346    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * DESCRIPTION (Version): 0.995-12 released to CRAN
349    
350    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * tests/simple.R: add check for correct dsT -> dgT coercion;
353                    add check for correct printing of symmetric sparse matrices.
354    
355            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
356            for sparse symmetric matrices.
357    
358            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
359            diagonal twice.
360    
361    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
362    
363            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
364            being applied to the x slot (detected by Brian Ripley).
365    
366    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
369    
370            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
371    
372    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * src/lgCMatrix.c (lgCMatrix_diag): new function
375            * R/lgCMatrix.R (diag): for new method
376    
377            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
378                 ==> construction of illegal "*gTMatrix" via new() should
379                 now be much less easy:
380            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
381    
382            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
383                    directly.
384            * man/Matrix.Rd: documents it.
385    
386    2006-07-06  Douglas Bates  <bates@R-project.org>
387    
388            * src/pedigree.c (pedigree_inbreeding): Correction in
389            initialization.  This function is not currently being used and is
390            not fully tested.
391    
392            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
393            Introduced the glmer class.  Added code for mcmcmsamp on glmer
394            objects.  Modified validity check on pedigree objects to account
395            for nonparallel patterns of missingness of parents.
396    
397            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
398            class.
399    
400    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/pMatrix.R: coercion pMatrix -> Tsparse
403    
404    2006-06-12  Douglas Bates  <bates@R-project.org>
405    
406            * DESCRIPTION (Version): 0.995-11 released to CRAN
407    
408            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
409            the output from mcmcsamp.
410    
411    2006-06-10  Douglas Bates  <bates@R-project.org>
412    
413            * R/lmer.R (simulestimate): added C code for calculating the trace
414            of the hat matrix.
415    
416    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
419            classes.
420            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
421    
422    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * R/dgTMatrix.R (colSums): etc. All four of
425            colSums(), rowSums(), colMeans(), rowMeans() now should work for
426            all "Matrices".
427    
428    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
429    
430            * R/lmer.R (panel.ci): Add a reference line at zero and a
431            background grid to the qqmath plot of ranef.lmer.
432    
433    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
434    
435            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
436            grouping factors to be specified in the formula as (1|foo/bar).
437    
438    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
439    
440            * R/lmer.R (findbars and others): Change check of is.numeric to
441            !is.language to resolve the bug reported by Jacob Wegelin.
442    
443            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
444            code to evaluate inbreeding coefficients without calculating T,
445            based on code in Sargolzaei and Iwaisaki's paper.
446    
447    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
448    
449            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
450            generic and mer methods for isNested and denomDF. This denomDF was
451            an attempt to emulate that in lme but I don't think that makes
452            sense.  Use the trace of the hat matrix instead.
453    
454    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
457            the C code depending on a slot structure that's no longer valid.
458            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
459    
460    
461    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
462    
463            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
464            of lowerTriMatrix generic and methods to tril (also upper to triu)
465            and added a general band extractor.
466    
467    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
468    
469            * R/pedigree.R (pedigree): Replace sire and dam values outside the
470            allowable range with NAs. Added a corresponding check in the
471            validity check for the pedigree class.
472    
473            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
474            crossprod methods now inherits from symmetricMatrix.
475    
476    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
477    
478            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
479            generics lowerTriMatrix and upperTriMatrix along with methods for
480            the Csparse virtual class.  Also added a C function Csparse_band
481            that implements these methods by calling cholmod_band.
482    
483    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
486            erased when it was NULL.  This led to invalid subselections!
487    
488    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
489    
490            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
491            in method for "t" so as not to lose the unit diagonal property.
492    
493    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
494    
495            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
496            and methods.  This is now an option to the ranef method for the
497            mer class.
498    
499            * src/cs_utils.c: Ensure that the nz component is -1 for a
500            compressed column-oriented matrix.  Minor formatting cleanup.
501    
502            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
503            objects.
504    
505    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
508            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
509    
510    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
511    
512            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
513            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
514    
515            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
516            for the dtCMatrix class.
517    
518    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
519    
520            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
521            and methods for it.
522    
523    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
526            arguments, such that M %*% 1:6 now works
527            * Tests/matprod.R: test the above
528    
529    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
530    
531            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
532            the ranef.lmer class.
533    
534            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
535            methods to extract the posterior variances from the bVar slot.
536    
537    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
540            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
541    
542            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
543            * tests/simple: (extended)
544    
545            * R/sparseMatrix.R (isTriangular): now using much improved
546            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
547    
548    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
549    
550            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
551            (problem report from Franklin Parlamis).  This should be done
552            generally.
553    
554    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
555    
556            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
557            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
558            update the plot methods.
559    
560    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
561    
562            * R/lmer.R (resid and ranef methods):  Added methods for the
563            "residuals" and "resid" generic but only for linear mixed model
564            fits.  Changed the ranef method to return a list of data frames so
565            that the plot methods now work.
566    
567    2006-03-16  Douglas Bates  <bates@bates2>
568    
569            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
570            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
571    
572            * DESCRIPTION (Date): New release
573    
574    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
577    
578            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
579            * man/KNex.Rd: and other help files
580            * tests/*.R: several ones needed adaption
581            * inst/doc/Comparisons.Rnw: ditto
582    
583    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
586    
587            * tests/indexing.R: tests for new [<- methods for sparse matrices.
588    
589    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
592    
593            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
594    
595    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * R/dMatrix.R: enable things like  M [ M < 10 ]
598            * R/dgeMatrix.R: implement it
599    
600    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/AllClass.R: define "summary.mer" and "*.lmer"
603            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
604            * R/lmer.R (show): now works with summary()
605    
606    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
609            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
610                    support the above
611    
612  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
613    
614          * 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.
# Line 171  Line 782 
782  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
785          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
786          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
787    
788  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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