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revision 687, Fri Apr 1 07:36:09 2005 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>
694    
695            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
696            the C code depending on a slot structure that's no longer valid.
697            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
698    
699    
700    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
701    
702            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
703            of lowerTriMatrix generic and methods to tril (also upper to triu)
704            and added a general band extractor.
705    
706    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
707    
708            * R/pedigree.R (pedigree): Replace sire and dam values outside the
709            allowable range with NAs. Added a corresponding check in the
710            validity check for the pedigree class.
711    
712            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
713            crossprod methods now inherits from symmetricMatrix.
714    
715    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
716    
717            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
718            generics lowerTriMatrix and upperTriMatrix along with methods for
719            the Csparse virtual class.  Also added a C function Csparse_band
720            that implements these methods by calling cholmod_band.
721    
722    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
725            erased when it was NULL.  This led to invalid subselections!
726    
727    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
728    
729            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
730            in method for "t" so as not to lose the unit diagonal property.
731    
732    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
733    
734            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
735            and methods.  This is now an option to the ranef method for the
736            mer class.
737    
738            * src/cs_utils.c: Ensure that the nz component is -1 for a
739            compressed column-oriented matrix.  Minor formatting cleanup.
740    
741            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
742            objects.
743    
744    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
747            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
748    
749    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
750    
751            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
752            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
753    
754            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
755            for the dtCMatrix class.
756    
757    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
758    
759            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
760            and methods for it.
761    
762    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
765            arguments, such that M %*% 1:6 now works
766            * Tests/matprod.R: test the above
767    
768    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
769    
770            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
771            the ranef.lmer class.
772    
773            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
774            methods to extract the posterior variances from the bVar slot.
775    
776    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
779            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
780    
781            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
782            * tests/simple: (extended)
783    
784            * R/sparseMatrix.R (isTriangular): now using much improved
785            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
786    
787    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
788    
789            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
790            (problem report from Franklin Parlamis).  This should be done
791            generally.
792    
793    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
794    
795            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
796            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
797            update the plot methods.
798    
799    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
800    
801            * R/lmer.R (resid and ranef methods):  Added methods for the
802            "residuals" and "resid" generic but only for linear mixed model
803            fits.  Changed the ranef method to return a list of data frames so
804            that the plot methods now work.
805    
806    2006-03-16  Douglas Bates  <bates@bates2>
807    
808            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
809            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
810    
811            * DESCRIPTION (Date): New release
812    
813    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
814    
815            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
816    
817            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
818            * man/KNex.Rd: and other help files
819            * tests/*.R: several ones needed adaption
820            * inst/doc/Comparisons.Rnw: ditto
821    
822    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
825    
826            * tests/indexing.R: tests for new [<- methods for sparse matrices.
827    
828    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
831    
832            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
833    
834    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/dMatrix.R: enable things like  M [ M < 10 ]
837            * R/dgeMatrix.R: implement it
838    
839    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
840    
841            * R/AllClass.R: define "summary.mer" and "*.lmer"
842            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
843            * R/lmer.R (show): now works with summary()
844    
845    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
848            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
849                    support the above
850    
851    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
852    
853            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
854            Use glmFit$prior.weights for weights in a glmm.
855            Allow an option usePQL = FALSE to skip the PQL steps for the
856            Laplace method (and, in time, the AGQ method).
857    
858            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
859            into a separate function internal_mer_Xfactor to be able to call
860            it from internal_bhat.
861    
862    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * tests/Class+Meth.R (tstMatrixClass): function for much better
865            testing; now again of all actual classes.
866    
867            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
868                    use macros and define make_d_matrix_* and make_i_matrix_*
869                    where _i_ is for the ldense routines:
870    
871            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
872            * src/ldense.c (lsyMatrix_as_lgeMatrix):
873    
874            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
875    
876    
877    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
878    
879            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
880                    many different kinds of matrices.
881            * R/*.R: quite a few new methods were needed for R CMD check with
882                    new Matrix().  Very good for users playing around.
883    
884    
885    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * src/dgeMatrix.c (dMatrix_validate): new
888            * src/Mutils.c (dense_nonpacked_validate): new
889    
890            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
891    
892    
893    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
894    
895            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
896    
897    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
898    
899            * DESCRIPTION (Version): 0.99-6 released to CRAN
900    
901            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
902            segfault in cases with multiple non-nested grouping factors.
903    
904    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
905    
906            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
907                    (Depends): also on 'utils'
908    
909            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
910            * R/diagMatrix.R (Diagonal): constructor and methods for
911            diagonal matrices
912    
913            * R/ltTMatrix.R: new "minimal methods"
914    
915    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
918            all methods (and help files).
919    
920    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
921    
922            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
923                    for case (dimn.  op  no_dimn.)
924    
925    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
926    
927            * DESCRIPTION (Version): 0.99-2  released to CRAN
928    
929    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
930    
931            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
932            by Julian Faraway.
933    
934    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
935    
936            * R/Auxiliaries.R (try_as): new utility
937            * R/sparseMatrix.R: use try_as() in coercion to original class
938    
939    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
942    
943    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
944    
945            * R/Auxiliaries.R (dimNamesCheck): added
946    
947            * R/Matrix.R (as.array), (as.vector): new
948    
949    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
952                    default.
953            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
954                    "pMatrix" now contains "sparseMatrix"
955    
956    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
957    
958            * tests/Class+Meth.R: new tests; t(t(m)) == m
959    
960            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
961    
962            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
963            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
964    
965            * R/dspMatrix.R: typo in "t" method
966    
967    2005-09-18  Douglas Bates  <bates@wisc.edu>
968    
969            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
970            * R/Tsparse.R: instead of R/gTMatrix.R
971            * R/Csparse.R: new
972            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
973            * src/Tsparse.c: new; many trivial methods calling cholmod_()
974            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
975                            via cholmod
976    
977    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
978    
979            * R/Auxiliaries.R (non0ind): new function using new C code
980            * src/dgCMatrix.c (compressed_non_0_ij): new utility
981    
982    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
983    
984            * src/chm_common.h: header file required by all C sources that
985            call CHOLMOD functions.  It defines a cholmod_common structure
986            called 'c' whose address is passed as the last argument to
987            (virtually) every CHOLMOD function.
988    
989            * src/Pattern.c: Simple example of the use of CHOLMOD.
990    
991            * src/init.c: initialize and finalize the cholmod_common structure.
992    
993            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
994            LDL and CCOLAMD from the U. of Florida sparse matrix library.
995    
996    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
997    
998            * inst/test-tools.R: new file collecting the utility functions used
999                    in ./tests/*.R
1000    
1001            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1002            * R/Matrix.R (cbind2): methods for NULL and missing
1003    
1004    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * R/AllClass.R: new "index" class for "[" and "[<-":
1007                    First cut at "symmetricMatrix" and "triangularMatrix"
1008            * R/gTMatrix.R (.ind.prep): new function;
1009                    Logical and character indexing now work too.
1010            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1011            * tests/indexing.R: new, including *.Rout.save
1012            * tests/dgTMatrix.R: new
1013    
1014    2005-08-29  Douglas Bates  <bates@wisc.edu>
1015    
1016            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1017            indicator pos not being updated.  Also enforced upper triangular
1018            for symmetric case.  Need to coerce edges component of elements of
1019            edge list - grr! (Why don't they define their classes cleanly?)
1020    
1021    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * R/Matrix.R:  added first "[<-" methods; not yet functional
1024            * R/denseMatrix.R: ditto
1025            * man/Subassign-methods.Rd: new help file for these
1026    
1027    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1028    
1029            * DESCRIPTION (Version): 0.98-6
1030    
1031            * R/denseMatrix.R: new file for "[" fallback methods for all dense
1032            matrices.
1033    
1034    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1035    
1036            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1037                    as( <logical>, "matrix")
1038    
1039            * R/pMatrix.R: coercion to "lgTMatrix"
1040    
1041            * R/gTMatrix.R: new virtual class to define "[" methods for.
1042            * man/gTMatrix-class.Rd:
1043            * General slight re-organization of where "[" methods are defined.
1044              more to come.
1045    
1046    2005-08-18  Douglas Bates  <bates@wisc.edu>
1047    
1048            * DESCRIPTION (Version): 0.98-5  released to CRAN
1049    
1050            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1051            * .....
1052    
1053    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
1054    
1055            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1056            or glmer objects.
1057    
1058    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1059    
1060            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1061    
1062    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
1063    
1064            * R/HBMM.R: finish re-writing R-only code.
1065    
1066    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
1067    
1068            * man/externalFormats.Rd: move documentation for writeHB and
1069            writeMM here.
1070    
1071            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1072            (suggested by Paul Roecker).
1073    
1074            * tests/validObj.R (assertError): Comment out test that is failing
1075            after recent changes in r-devel.
1076    
1077    
1078    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1079    
1080            * R/AllClass.R: intermediate virtual class "denseMatrix"
1081            * man/denseMatrix-class.Rd
1082            * NAMESPACE: export it, and also export
1083            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1084    
1085    2005-08-10  Douglas Bates  <bates@wisc.edu>
1086    
1087            * DESCRIPTION (Version): 0.98-3 to CRAN
1088    
1089            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1090            matrix_solve code (which was really, really wrong).
1091    
1092    2005-08-07  Douglas Bates  <bates@wisc.edu>
1093    
1094            * DESCRIPTION (Version): 0.98-2
1095    
1096            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1097    
1098            * R/lmer.R (abbrvNms): new
1099            * R/lmer.R (mcmcsamp): allow transformed parameters
1100            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1101            for the Harwell-Boeing and the MatrixMarket formats.
1102    
1103    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1104    
1105            * man/dtrMatrix-class.Rd: add examples
1106            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1107    
1108            * TODO: note the dtpMatrix (docu) bug
1109    
1110            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1111            in order to ensure that new as.matrix() is used by old functions,
1112            e.g., svd(), qr(), eigen(), dist(),..;
1113                  apply(), also matplot() or pairs().
1114    
1115    
1116    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1119              add comments about 'control' / lmerControl() arguments
1120    
1121    2005-07-27  Douglas Bates  <bates@wisc.edu>
1122    
1123            * man/sleepstudy.Rd: Added the sleep data set.
1124            * DESCRIPTION (Version): 0.98-1  released to CRAN
1125    
1126    2005-07-12  Douglas Bates  <bates@wisc.edu>
1127            * man/sleepstudy.Rd: Added the sleep data set.
1128    
1129            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1130            .Call calls that were producing spurious output.
1131    
1132    2005-07-05  Douglas Bates  <bates@wisc.edu>
1133    
1134            * R/lmer.R (lmer): stored updated variance component estimates in
1135            mer object for the generalized model.  (Bug reported by Renaud
1136            Lancelot).
1137    
1138    2005-07-03  Douglas Bates  <bates@wisc.edu>
1139    
1140            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1141            unidimensional case.
1142    
1143    2005-06-08  Douglas Bates  <bates@wisc.edu>
1144    
1145            * DESCRIPTION (Version): 0.96-1
1146    
1147            * moved  lmer-class' R and C code moved from lme4 to here
1148    
1149    2005-06-04  Douglas Bates  <bates@wisc.edu>
1150    
1151            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1152            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1153    
1154    2005-06-02  Douglas Bates  <bates@wisc.edu>
1155    
1156            * src/Makefile.win: Forgot to update this when Makefile changed.
1157    
1158    2005-05-11  Douglas Bates  <bates@wisc.edu>
1159    
1160            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1161            bug reported by Kurt Hornik and Michael Hahsler.
1162    
1163    2005-05-10  Douglas Bates  <bates@wisc.edu>
1164    
1165            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1166            logical sparse matrices.  These will also be used in the symbolic
1167            analysis for lmer objects.
1168    
1169            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1170            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
1171    
1172    2005-05-06  Douglas Bates  <bates@wisc.edu>
1173    
1174            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1175            colMeans, colSums, rowMeans and rowSums.
1176    
1177    2005-04-18  Douglas Bates  <bates@wisc.edu>
1178    
1179            * src/lgCMatrix.[ch]: code for _validate method and stub for
1180            multiplication operation.
1181    
1182            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1183            to dgetrs.
1184    
1185            * src/init.c: Fix cut-and-paste error in definition of
1186            dgeMatrix_matrix_solve
1187    
1188            * src/{many files}: Tighten code by using ALLOC_SLOT.
1189    
1190    2005-04-15  Douglas Bates  <bates@wisc.edu>
1191    
1192            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1193    
1194            * DESCRIPTION: Eliminate import of stats.
1195    
1196    
1197    2005-04-06  Douglas Bates  <bates@wisc.edu>
1198    
1199            * R/AllClass.R : add logical sparse matrix classes
1200    
1201  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1202    
1203          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
1204          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1205    
1206  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
1207    
1208          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
1209    
# Line 29  Line 1229 
1229          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
1230            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
1231    
1232  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
1233    
1234          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
1235          * ....          * ....
1236    
1237  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
1238    
1239          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
1240    
# Line 49  Line 1249 
1249            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1250          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1251    
1252  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1253    
1254          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1255    
1256  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1257    
1258          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1259    
1260  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1261    
1262          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1263          the package.          the package.
# Line 105  Line 1305 
1305    
1306          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1307    
1308  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1309    
1310          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1311          for the geMatrix class.          for the geMatrix class.
1312    
1313  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1314    
1315          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1316    
1317          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1318    
1319  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1320    
1321          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1322          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1323    
1324  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1325    
1326          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1327    
1328  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1329    
1330          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1331          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1332    
1333  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1334    
1335          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1336    
1337          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1338          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1339    
1340  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1341    
1342          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1343          no longer used.          no longer used.
# Line 149  Line 1349 
1349          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1350          Fixes part but not all of #15.          Fixes part but not all of #15.
1351    
1352  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1353    
1354          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1355          scalar grouping factors corrected.          scalar grouping factors corrected.
1356    
1357  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1358    
1359          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1360    
1361  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1362    
1363          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
1364          .h file can be included.          .h file can be included.
1365    
1366  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1367    
1368          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1369          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1370    
1371          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1372    
1373  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1374    
1375          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1376    
1377  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1378    
1379          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1380    
1381  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1382    
1383          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1384    
1385  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1386    
1387          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1388    
1389  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1390    
1391          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1392          routines.          routines.
1393    
1394  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1395    
1396          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1397    
1398  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1399    
1400          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1401    

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