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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1657, Wed Nov 1 16:29:53 2006 UTC
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1    2006-11-01  Douglas Bates  <bates@r-project.org>
2    
3            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
4            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
5            <CsparseMatrix>) added
6    
7    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * tests/matprod.R: add a variation of Harri's example
10    
11            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
12            recursive infinitely.
13    
14            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
15    
16            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
17    
18    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
21            matrix if possible; test m+m == 2*m; now test dgRMatrix.
22            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
23            satisfy the above test.
24    
25    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
28    
29            * R/dgCMatrix.R: solve(a, b="missing") based on
30            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
31            RHS = NULL.
32    
33            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
34            add more (needed) [t]crossprod() methods.
35    
36            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
37    
38            * R/Auxiliaries.R (as_CspClass): cleanup
39            (drop0): internal utility for "Csparse_drop(*, 0)"
40            (.bail.out.2): encourage active feedback
41    
42    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dMatrix.R(Compare): new(), then slots [no validity check]
45    
46            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
47            non-valid or 'sorted' case).
48    
49            * R/dsparseMatrix.R: add "chol" method.
50            * R/ddenseMatrix.R: ditto
51    
52            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
53            * NAMESPACE (Ops)
54            * R/diagMatrix.R (diag2T): simple utility used "higher level"
55            coercion; deprecating direct lower level coercions.
56    
57            * R/*.R (seq): use seq_len() and seq_along() where possible.
58    
59    
60    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * DESCRIPTION (Version): 0.9975-5 ready for release
63    
64    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
67    
68    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/AllClass.R (corMatrix): add 'validity' check;
71                    comment out unused "LDL" class definition
72            * NAMESPACE: mention, but do not export "LDL" class
73            * R/corMatrix.R: new (simple), needed for R-devel with
74            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
75              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
76    
77    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
78    
79            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
80            use Rprintf and R's error handling.
81    
82    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
85            * tests/matprod.R: add tests for the bug fixed.
86    
87    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
88    
89            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
90            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
91    
92    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
93    
94            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
95    
96    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * DESCRIPTION (Version): 0.9975-3
99    
100            * R/diagMatrix.R (bdiag): new function constructing block diagonal
101            (sparse) matrices.
102            * man/bdiag.Rd: docu + examples
103    
104            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
105    
106            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
107            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
108    
109            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
110            that result is sparse or diagonal (and not dense).
111    
112            * man/Subassign-methods.Rd: fix examples
113    
114            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
115            should always return a sparse (and not sometimes a diagonal) matrix.
116    
117    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
120    
121    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
122    
123            * DESCRIPTION (Version): 0.9975-2
124    
125            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
126    
127    2006-10-02  Douglas Bates  <bates@R-project.org>
128    
129            * tests/dg_Matrix.R: Simplify test taking into account new code.
130    
131    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
134    
135            * R/lsTMatrix.R: new files w/ missing methods
136            * R/nsTMatrix.R:  "  'for completeness'
137    
138            * tests/Class+Meth.R: a bit less 'not.ok.classes'
139    
140            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
141    
142    
143    2006-09-28  Douglas Bates  <bates@R-project.org>
144    
145            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
146            included.
147    
148            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
149            Export C-callable functions used in Zt_create in lme4.
150    
151    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * DESCRIPTION (Version): 0.9975-1
154    
155            * tests/simple.R: less checks fail; using NA, found that our
156                    kronecker() is not base-compatible with NA's.
157    
158            * R/dMatrix.R: "Compare" method now implemented for all cases
159    
160            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
161    
162            * man/dtpMatrix-class.Rd: mention length of 'x' slot
163    
164            * src/dtpMatrix.c (dtpMatrix_validate): fix check
165            * src/dspMatrix.c (dspMatrix_validate): ditto
166    
167            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
168              including coercion to [nl]tTMatrix.
169    
170            * R/diagMatrix.R (show): print a header line as for other classes.
171    
172    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * src/Makefile.win (SUBDIRS): fix typo
175    
176    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
179    
180    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
181    
182            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
183            symmetric and y missing in R code using %*% (cholmod_aat doesn't
184            accept a symmetric matrix).
185            * tests/group-methods.R: Uncomment test of crossprod applied to
186            lsCMatrix objects.
187    
188    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/AllClass.R (symmetricMatrix): add validity method (available
191            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
192    
193            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
194    
195            * tests/indexing.Rout.save:
196            * tests/indexing.R: additions, mainly for 'lsparse'
197    
198            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
199            case.
200    
201            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
202    
203    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
206                    as 'N' (1-letter - Ok?)
207    
208            * tests/group-methods.R: add test for logical + NAs
209    
210            * R/dMatrix.R ("Compare"): fix to work with NA's
211    
212            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
213    
214            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
215                    which is implemented.
216    
217    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * src/chm_common.c: coerce logical <-> double instead of
220            typecasting;  needed for "l" matrix handling in cholmod.
221    
222            * tests/other-pkgs.R (graph): small extension in "graph" checks.
223    
224            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
225            (Tsp2grNEL): other fixes needed
226    
227    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
230                    Matrices, since "lMatrix", also "lsparseM" can have NA
231            * R/ndenseMatrix.R, etc: new source files
232            * man/nsparseMatrix-classes.Rd, etc: new help files
233            * tests/: adaptions
234            * src/chm_common.c (chm_dense_to_SEXP): and others:
235                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
236            * src/Csparse.c, etc: ditto
237    
238    2006-09-11  Douglas Bates  <bates@R-project.org>
239    
240            * src/Mutils.[ch],init.c inst/include/*.h: Move the
241            alloc_d**Matrix functions to the lme4 package.
242    
243    2006-09-09  Douglas Bates  <bates@R-project.org>
244    
245            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
246            fixed
247    
248    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/lMatrix.R: new
251    
252            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
253    
254            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
255            * man/tcrossprod.Rd: ditto
256    
257    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
258    
259            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
260            for exported functions
261            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
262            Remove partitioning algorithms for sparse matrix reordering.  The
263            copyright on the Metis code was problematic and the methods were
264            rarely used.
265            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
266            operations are now done entirely in CHOLMOD code.
267    
268    2006-09-06  Douglas Bates  <bates@R-project.org>
269    
270            * src/Mutils.h: Remove functions that are no longer used.
271    
272    2006-09-04  Douglas Bates  <bates@R-project.org>
273    
274            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
275            * src/DEPS.mkf: update
276    
277    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * created branches/Matrix-for-R-2.3.x;  on trunk: do
280            * DESCRIPTION (Version): 0.9975-0
281            (Depends): R (>= 2.4.0)
282    
283    2006-09-01  Douglas Bates  <bates@R-project.org>
284    
285            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
286    
287    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
290            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
291    
292            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
293    
294    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
297            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
298            * R/dsparseMatrix.R: ditto
299            * R/Csparse.R: ditto
300    
301    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/dMatrix.R (Compare): improve availability of "<", etc
304            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
305    
306    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
309            of a 0-index which was used as 1-index (..hmm)
310    
311            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
312    
313            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
314            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
315            (.is.diagonal): ditto
316    
317            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
318    
319            * R/Matrix.R (Matrix): also work for NA data
320    
321    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
324            in all cases.
325    
326    2006-08-27  Douglas Bates  <bates@R-project.org>
327    
328            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
329            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
330    
331    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
334            subclasses of "ddenseMatrix"
335            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
336            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
337            instead of half dozen specialized ones.
338    
339    2006-08-25  Douglas Bates  <bates@R-project.org>
340    
341            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
342            <tillard@cirad.fr> - ordering standard errors to match effects.
343    
344    2006-08-24  Douglas Bates  <bates@R-project.org>
345    
346            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
347            on R_ldl.
348            * R/lCholCMatrix.R,
349            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
350            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
351            * many files in ./R and ./src: Use more general version of
352            dup_mMatrix_as_dgeMatrix to simplify method definitions.
353            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
354            dtpMatrix, dspMatrix and dppMatrix conversions.
355    
356    
357    2006-08-23  Douglas Bates  <bates@R-project.org>
358    
359            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
360            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
361            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
362            dgeMatrix_crossprod (may need to do this in other places).
363            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
364            generic and method for dsCMatrix.  Use CHOLMOD for chol().
365    
366    2006-08-22  Douglas Bates  <bates@R-project.org>
367    
368            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
369            types of classed Matrices, matrices or numeric or logical vectors.
370            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
371            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
372            to Mutils.h (as an inline) and change name to Matrix_check_class;
373            fixes in as_cholmod_factor and chm_factor_to_SEXP.
374            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
375            dsCMatrix_matrix_solve.  Comment out vestigial functions.
376            * src/Csparse.c: use diag_P and uplo_P macros.
377    
378    2006-08-21  Douglas Bates  <bates@R-project.org>
379    
380            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
381            valgrind.
382            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
383            inverses.
384            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
385            -Wall warnings.
386            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
387            Use dup_mMatrix_as_dgeMatrix.
388    
389    2006-08-20  Douglas Bates  <bates@R-project.org>
390    
391            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
392            * tests/sparseQR.R: Added
393            * man/sparseQR-class.Rd: Document methods for qr.* generics
394            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
395    
396    2006-08-19  Douglas Bates  <bates@R-project.org>
397    
398            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
399            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
400            and qr.fitted.
401            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
402            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
403    
404    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
407            the base version has no "..." argument.
408    
409            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
410    
411            * R/Matrix.R: define and
412            * NAMESPACE: export as.numeric() and as.logical() methods.
413                    Let's hope these do not badly slow down something...
414            Finally export the zapsmall() method.
415    
416    2006-08-17  Douglas Bates  <bates@R-project.org>
417    
418            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
419            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
420            * src/dtCMatrix.c :Remove code that is no longer used
421            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
422    
423    2006-08-14  Douglas Bates  <bates@R-project.org>
424    
425            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
426            Csparse_to_logical and Csparse_symmetric_to_general.
427            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
428            coercion methods between CsparseMatrix and TsparseMatrix.
429    
430    2006-08-14  Douglas Bates  <bates@R-project.org>
431    
432            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
433            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
434            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
435            possible.
436    
437    2006-08-12  Douglas Bates  <bates@R-project.org>
438    
439            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
440              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
441              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
442              generalize conversions between TsparseMatrix, CsparseMatrix,
443              denseMatrix and matrix.  Preserve triangularity property and
444              propagate Dimnames in the easy cases.
445    
446    2006-08-10  Douglas Bates  <bates@R-project.org>
447    
448            * src/lmer.c: adjust checks in glmer_init for S4SXP
449            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
450            before S4SXP but for the wrong reasons.
451    
452    2006-08-08  Douglas Bates  <bates@R-project.org>
453    
454            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
455            Later modified to return the upper triangle only.
456            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
457    
458    2006-08-07  Douglas Bates  <bates@R-project.org>
459    
460            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
461            R-level conversion to a sparse symmetric class.
462            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
463            Remove conversion to sparse symmetric classes (now done in C code).
464    
465    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
468            * man/band.Rd:  adapt the \dontshow{} unit test.
469    
470    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * DESCRIPTION (Version): 0.995-14  for CRAN
473    
474            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
475    
476            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
477            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
478    
479            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
480            * R/Tsparse.R (tril, triu, band): methods
481            * R/dgRMatrix.R (tril, ...):    ditto
482            * man/band.Rd:                  ditto
483    
484    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/Matrix.R (head, tail): directly use utils:::head.matrix
487                    to be up-to-date automatically.
488    
489    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
492    
493            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
494            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
495            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
496            such that the S4 objects are always created by the current version
497            of R and 'Matrix' class definitions.
498    
499    2006-08-01  Douglas Bates  <bates@R-project.org>
500    
501            * R/lmer.R (LMEoptimize method), tests/lmer.R,
502            inst/external/test3comp.rda: Added warnings for convergence on
503            boundary and test cases.
504    
505            * src/lmer.c (mer_postVar): Modified to return the variances that
506            are marginal to the fixed effects, not conditional on them (which
507            is what the bVar slot contents represent).
508    
509    2006-07-31  Douglas Bates  <bates@R-project.org>
510    
511            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
512            function which calls the C function mer_hat_trace2.
513    
514            * man/ranef.Rd: Include description of "postVar" argument and
515            producing a caterpillar plot.
516    
517    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * NAMESPACE:    change  "correlation" to "corMatrix"
520            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
521            * R/dpoMatrix.R: ditto
522            * R/lmer.R:      ditto
523    
524    2006-07-28  Douglas Bates  <bates@R-project.org>
525    
526            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
527            RZXinv slot's contents into a separate internal function that can
528            be used in mer_hat_trace.
529    
530    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
533            via new smart
534            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
535            utility functions.
536    
537    
538    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/Csparse.R (tril, triu, band): do return *triangular* classed
541            matrices when appropriate; band() even symmetric ones.
542            (replCmat): extend to potentially all "CsparseMatrix"
543            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
544            allow subassignment for special sparse matrices.
545    
546            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
547    
548            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
549            argument; in glmer_*(): print only if(verbose).
550    
551            speed-optimize a few places by moving REAL(.) out of loops.
552    
553            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
554    
555    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
558                    since that wrongly triggers also for M[ logi , ]
559    
560            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
561            a symmetric matrix that results in a non-symmetric one.
562            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
563    
564            * R/dMatrix.R: make round(M) work as round(M, 0)
565    
566            * R/dgTMatrix.R (image): coordinate system and axis now use
567            1-based indices, not 0-based ones.
568    
569            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
570            * tests/indexing.R: test it.
571    
572            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
573            * man/isSymmetric-methods.Rd: and document it.
574    
575            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
576            * man/SparseM-conv.Rd: docu them
577    
578            * tests/other-pkgs.R: renamed from tests/graph.R and add example
579                    for 'SparseM' conversions
580    
581    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
582    
583            * R/Matrix.R (head): added head() and tail() methods.
584    
585    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * DESCRIPTION (Version): 0.995-12 released to CRAN
588    
589    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * tests/simple.R: add check for correct dsT -> dgT coercion;
592                    add check for correct printing of symmetric sparse matrices.
593    
594            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
595            for sparse symmetric matrices.
596    
597            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
598            diagonal twice.
599    
600    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
601    
602            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
603            being applied to the x slot (detected by Brian Ripley).
604    
605    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
608    
609            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
610    
611    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * src/lgCMatrix.c (lgCMatrix_diag): new function
614            * R/lgCMatrix.R (diag): for new method
615    
616            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
617                 ==> construction of illegal "*gTMatrix" via new() should
618                 now be much less easy:
619            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
620    
621            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
622                    directly.
623            * man/Matrix.Rd: documents it.
624    
625    2006-07-06  Douglas Bates  <bates@R-project.org>
626    
627            * src/pedigree.c (pedigree_inbreeding): Correction in
628            initialization.  This function is not currently being used and is
629            not fully tested.
630    
631            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
632            Introduced the glmer class.  Added code for mcmcmsamp on glmer
633            objects.  Modified validity check on pedigree objects to account
634            for nonparallel patterns of missingness of parents.
635    
636            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
637            class.
638    
639    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * R/pMatrix.R: coercion pMatrix -> Tsparse
642    
643    2006-06-12  Douglas Bates  <bates@R-project.org>
644    
645            * DESCRIPTION (Version): 0.995-11 released to CRAN
646    
647            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
648            the output from mcmcsamp.
649    
650    2006-06-10  Douglas Bates  <bates@R-project.org>
651    
652            * R/lmer.R (simulestimate): added C code for calculating the trace
653            of the hat matrix.
654    
655    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
658            classes.
659            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
660    
661    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * R/dgTMatrix.R (colSums): etc. All four of
664            colSums(), rowSums(), colMeans(), rowMeans() now should work for
665            all "Matrices".
666    
667    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
668    
669            * R/lmer.R (panel.ci): Add a reference line at zero and a
670            background grid to the qqmath plot of ranef.lmer.
671    
672    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
673    
674            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
675            grouping factors to be specified in the formula as (1|foo/bar).
676    
677    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
678    
679            * R/lmer.R (findbars and others): Change check of is.numeric to
680            !is.language to resolve the bug reported by Jacob Wegelin.
681    
682            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
683            code to evaluate inbreeding coefficients without calculating T,
684            based on code in Sargolzaei and Iwaisaki's paper.
685    
686    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
687    
688            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
689            generic and mer methods for isNested and denomDF. This denomDF was
690            an attempt to emulate that in lme but I don't think that makes
691            sense.  Use the trace of the hat matrix instead.
692    
693  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
696          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.
697          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
698    
699    
700  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 817 
817          * 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)
818          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
819          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
820          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
821    
822  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
# Line 329  Line 1021 
1021  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
1024          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
1025          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
1026    
1027  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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