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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1600, Fri Sep 29 13:37:25 2006 UTC
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1    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
4    
5            * R/lsTMatrix.R: new files w/ missing methods
6            * R/nsTMatrix.R:  "  'for completeness'
7    
8            * tests/Class+Meth.R: a bit less 'not.ok.classes'
9    
10            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
11    
12    
13    2006-09-28  Douglas Bates  <bates@R-project.org>
14    
15            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
16            included.
17    
18            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
19            Export C-callable functions used in Zt_create in lme4.
20    
21    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * DESCRIPTION (Version): 0.9975-1
24    
25            * tests/simple.R: less checks fail; using NA, found that our
26                    kronecker() is not base-compatible with NA's.
27    
28            * R/dMatrix.R: "Compare" method now implemented for all cases
29    
30            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
31    
32            * man/dtpMatrix-class.Rd: mention length of 'x' slot
33    
34            * src/dtpMatrix.c (dtpMatrix_validate): fix check
35            * src/dspMatrix.c (dspMatrix_validate): ditto
36    
37            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
38              including coercion to [nl]tTMatrix.
39    
40            * R/diagMatrix.R (show): print a header line as for other classes.
41    
42    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/Makefile.win (SUBDIRS): fix typo
45    
46    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
49    
50    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
51    
52            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
53            symmetric and y missing in R code using %*% (cholmod_aat doesn't
54            accept a symmetric matrix).
55            * tests/group-methods.R: Uncomment test of crossprod applied to
56            lsCMatrix objects.
57    
58    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/AllClass.R (symmetricMatrix): add validity method (available
61            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
62    
63            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
64    
65            * tests/indexing.Rout.save:
66            * tests/indexing.R: additions, mainly for 'lsparse'
67    
68            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
69            case.
70    
71            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
72    
73    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
76                    as 'N' (1-letter - Ok?)
77    
78            * tests/group-methods.R: add test for logical + NAs
79    
80            * R/dMatrix.R ("Compare"): fix to work with NA's
81    
82            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
83    
84            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
85                    which is implemented.
86    
87    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * src/chm_common.c: coerce logical <-> double instead of
90            typecasting;  needed for "l" matrix handling in cholmod.
91    
92            * tests/other-pkgs.R (graph): small extension in "graph" checks.
93    
94            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
95            (Tsp2grNEL): other fixes needed
96    
97    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
100                    Matrices, since "lMatrix", also "lsparseM" can have NA
101            * R/ndenseMatrix.R, etc: new source files
102            * man/nsparseMatrix-classes.Rd, etc: new help files
103            * tests/: adaptions
104            * src/chm_common.c (chm_dense_to_SEXP): and others:
105                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
106            * src/Csparse.c, etc: ditto
107    
108    2006-09-11  Douglas Bates  <bates@R-project.org>
109    
110            * src/Mutils.[ch],init.c inst/include/*.h: Move the
111            alloc_d**Matrix functions to the lme4 package.
112    
113    2006-09-09  Douglas Bates  <bates@R-project.org>
114    
115            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
116            fixed
117    
118    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/lMatrix.R: new
121    
122            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
123    
124            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
125            * man/tcrossprod.Rd: ditto
126    
127    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
128    
129            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
130            for exported functions
131            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
132            Remove partitioning algorithms for sparse matrix reordering.  The
133            copyright on the Metis code was problematic and the methods were
134            rarely used.
135            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
136            operations are now done entirely in CHOLMOD code.
137    
138    2006-09-06  Douglas Bates  <bates@R-project.org>
139    
140            * src/Mutils.h: Remove functions that are no longer used.
141    
142    2006-09-04  Douglas Bates  <bates@R-project.org>
143    
144            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
145            * src/DEPS.mkf: update
146    
147    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * created branches/Matrix-for-R-2.3.x;  on trunk: do
150            * DESCRIPTION (Version): 0.9975-0
151            (Depends): R (>= 2.4.0)
152    
153    2006-09-01  Douglas Bates  <bates@R-project.org>
154    
155            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
156    
157    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
160            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
161    
162            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
163    
164    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
167            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
168            * R/dsparseMatrix.R: ditto
169            * R/Csparse.R: ditto
170    
171    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/dMatrix.R (Compare): improve availability of "<", etc
174            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
175    
176    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
179            of a 0-index which was used as 1-index (..hmm)
180    
181            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
182    
183            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
184            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
185            (.is.diagonal): ditto
186    
187            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
188    
189            * R/Matrix.R (Matrix): also work for NA data
190    
191    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
194            in all cases.
195    
196    2006-08-27  Douglas Bates  <bates@R-project.org>
197    
198            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
199            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
200    
201    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
204            subclasses of "ddenseMatrix"
205            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
206            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
207            instead of half dozen specialized ones.
208    
209    2006-08-25  Douglas Bates  <bates@R-project.org>
210    
211            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
212            <tillard@cirad.fr> - ordering standard errors to match effects.
213    
214    2006-08-24  Douglas Bates  <bates@R-project.org>
215    
216            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
217            on R_ldl.
218            * R/lCholCMatrix.R,
219            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
220            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
221            * many files in ./R and ./src: Use more general version of
222            dup_mMatrix_as_dgeMatrix to simplify method definitions.
223            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
224            dtpMatrix, dspMatrix and dppMatrix conversions.
225    
226    
227    2006-08-23  Douglas Bates  <bates@R-project.org>
228    
229            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
230            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
231            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
232            dgeMatrix_crossprod (may need to do this in other places).
233            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
234            generic and method for dsCMatrix.  Use CHOLMOD for chol().
235    
236    2006-08-22  Douglas Bates  <bates@R-project.org>
237    
238            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
239            types of classed Matrices, matrices or numeric or logical vectors.
240            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
241            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
242            to Mutils.h (as an inline) and change name to Matrix_check_class;
243            fixes in as_cholmod_factor and chm_factor_to_SEXP.
244            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
245            dsCMatrix_matrix_solve.  Comment out vestigial functions.
246            * src/Csparse.c: use diag_P and uplo_P macros.
247    
248    2006-08-21  Douglas Bates  <bates@R-project.org>
249    
250            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
251            valgrind.
252            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
253            inverses.
254            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
255            -Wall warnings.
256            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
257            Use dup_mMatrix_as_dgeMatrix.
258    
259    2006-08-20  Douglas Bates  <bates@R-project.org>
260    
261            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
262            * tests/sparseQR.R: Added
263            * man/sparseQR-class.Rd: Document methods for qr.* generics
264            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
265    
266    2006-08-19  Douglas Bates  <bates@R-project.org>
267    
268            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
269            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
270            and qr.fitted.
271            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
272            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
273    
274    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
277            the base version has no "..." argument.
278    
279            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
280    
281            * R/Matrix.R: define and
282            * NAMESPACE: export as.numeric() and as.logical() methods.
283                    Let's hope these do not badly slow down something...
284            Finally export the zapsmall() method.
285    
286    2006-08-17  Douglas Bates  <bates@R-project.org>
287    
288            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
289            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
290            * src/dtCMatrix.c :Remove code that is no longer used
291            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
292    
293    2006-08-14  Douglas Bates  <bates@R-project.org>
294    
295            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
296            Csparse_to_logical and Csparse_symmetric_to_general.
297            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
298            coercion methods between CsparseMatrix and TsparseMatrix.
299    
300    2006-08-14  Douglas Bates  <bates@R-project.org>
301    
302            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
303            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
304            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
305            possible.
306    
307    2006-08-12  Douglas Bates  <bates@R-project.org>
308    
309            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
310              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
311              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
312              generalize conversions between TsparseMatrix, CsparseMatrix,
313              denseMatrix and matrix.  Preserve triangularity property and
314              propagate Dimnames in the easy cases.
315    
316    2006-08-10  Douglas Bates  <bates@R-project.org>
317    
318            * src/lmer.c: adjust checks in glmer_init for S4SXP
319            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
320            before S4SXP but for the wrong reasons.
321    
322    2006-08-08  Douglas Bates  <bates@R-project.org>
323    
324            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
325            Later modified to return the upper triangle only.
326            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
327    
328    2006-08-07  Douglas Bates  <bates@R-project.org>
329    
330            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
331            R-level conversion to a sparse symmetric class.
332            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
333            Remove conversion to sparse symmetric classes (now done in C code).
334    
335    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
338            * man/band.Rd:  adapt the \dontshow{} unit test.
339    
340    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * DESCRIPTION (Version): 0.995-14  for CRAN
343    
344            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
345    
346            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
347            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
348    
349            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
350            * R/Tsparse.R (tril, triu, band): methods
351            * R/dgRMatrix.R (tril, ...):    ditto
352            * man/band.Rd:                  ditto
353    
354    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Matrix.R (head, tail): directly use utils:::head.matrix
357                    to be up-to-date automatically.
358    
359    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
362    
363            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
364            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
365            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
366            such that the S4 objects are always created by the current version
367            of R and 'Matrix' class definitions.
368    
369    2006-08-01  Douglas Bates  <bates@R-project.org>
370    
371            * R/lmer.R (LMEoptimize method), tests/lmer.R,
372            inst/external/test3comp.rda: Added warnings for convergence on
373            boundary and test cases.
374    
375            * src/lmer.c (mer_postVar): Modified to return the variances that
376            are marginal to the fixed effects, not conditional on them (which
377            is what the bVar slot contents represent).
378    
379    2006-07-31  Douglas Bates  <bates@R-project.org>
380    
381            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
382            function which calls the C function mer_hat_trace2.
383    
384            * man/ranef.Rd: Include description of "postVar" argument and
385            producing a caterpillar plot.
386    
387    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * NAMESPACE:    change  "correlation" to "corMatrix"
390            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
391            * R/dpoMatrix.R: ditto
392            * R/lmer.R:      ditto
393    
394    2006-07-28  Douglas Bates  <bates@R-project.org>
395    
396            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
397            RZXinv slot's contents into a separate internal function that can
398            be used in mer_hat_trace.
399    
400    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
403            via new smart
404            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
405            utility functions.
406    
407    
408    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/Csparse.R (tril, triu, band): do return *triangular* classed
411            matrices when appropriate; band() even symmetric ones.
412            (replCmat): extend to potentially all "CsparseMatrix"
413            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
414            allow subassignment for special sparse matrices.
415    
416            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
417    
418            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
419            argument; in glmer_*(): print only if(verbose).
420    
421            speed-optimize a few places by moving REAL(.) out of loops.
422    
423            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
424    
425    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
428                    since that wrongly triggers also for M[ logi , ]
429    
430            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
431            a symmetric matrix that results in a non-symmetric one.
432            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
433    
434            * R/dMatrix.R: make round(M) work as round(M, 0)
435    
436            * R/dgTMatrix.R (image): coordinate system and axis now use
437            1-based indices, not 0-based ones.
438    
439            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
440            * tests/indexing.R: test it.
441    
442            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
443            * man/isSymmetric-methods.Rd: and document it.
444    
445            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
446            * man/SparseM-conv.Rd: docu them
447    
448            * tests/other-pkgs.R: renamed from tests/graph.R and add example
449                    for 'SparseM' conversions
450    
451    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
452    
453            * R/Matrix.R (head): added head() and tail() methods.
454    
455    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * DESCRIPTION (Version): 0.995-12 released to CRAN
458    
459    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * tests/simple.R: add check for correct dsT -> dgT coercion;
462                    add check for correct printing of symmetric sparse matrices.
463    
464            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
465            for sparse symmetric matrices.
466    
467            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
468            diagonal twice.
469    
470    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
471    
472            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
473            being applied to the x slot (detected by Brian Ripley).
474    
475    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
478    
479            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
480    
481    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * src/lgCMatrix.c (lgCMatrix_diag): new function
484            * R/lgCMatrix.R (diag): for new method
485    
486            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
487                 ==> construction of illegal "*gTMatrix" via new() should
488                 now be much less easy:
489            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
490    
491            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
492                    directly.
493            * man/Matrix.Rd: documents it.
494    
495    2006-07-06  Douglas Bates  <bates@R-project.org>
496    
497            * src/pedigree.c (pedigree_inbreeding): Correction in
498            initialization.  This function is not currently being used and is
499            not fully tested.
500    
501            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
502            Introduced the glmer class.  Added code for mcmcmsamp on glmer
503            objects.  Modified validity check on pedigree objects to account
504            for nonparallel patterns of missingness of parents.
505    
506            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
507            class.
508    
509    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/pMatrix.R: coercion pMatrix -> Tsparse
512    
513    2006-06-12  Douglas Bates  <bates@R-project.org>
514    
515            * DESCRIPTION (Version): 0.995-11 released to CRAN
516    
517            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
518            the output from mcmcsamp.
519    
520    2006-06-10  Douglas Bates  <bates@R-project.org>
521    
522            * R/lmer.R (simulestimate): added C code for calculating the trace
523            of the hat matrix.
524    
525    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
528            classes.
529            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
530    
531    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/dgTMatrix.R (colSums): etc. All four of
534            colSums(), rowSums(), colMeans(), rowMeans() now should work for
535            all "Matrices".
536    
537    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
538    
539            * R/lmer.R (panel.ci): Add a reference line at zero and a
540            background grid to the qqmath plot of ranef.lmer.
541    
542    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
543    
544            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
545            grouping factors to be specified in the formula as (1|foo/bar).
546    
547    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
548    
549            * R/lmer.R (findbars and others): Change check of is.numeric to
550            !is.language to resolve the bug reported by Jacob Wegelin.
551    
552            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
553            code to evaluate inbreeding coefficients without calculating T,
554            based on code in Sargolzaei and Iwaisaki's paper.
555    
556    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
557    
558            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
559            generic and mer methods for isNested and denomDF. This denomDF was
560            an attempt to emulate that in lme but I don't think that makes
561            sense.  Use the trace of the hat matrix instead.
562    
563  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
566          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
567          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
568    
569    
570  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 687 
687          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
688          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
689          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
690          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
691    
692  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
# Line 329  Line 891 
891  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
894          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
895          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
896    
897  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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