SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 388, Mon Dec 13 16:00:22 2004 UTC revision 1543, Sat Sep 9 13:44:15 2006 UTC
# Line 1  Line 1 
1  2004-12-13  Douglas Bates  <bates@bates1-home>  2006-09-09  Douglas Bates  <bates@R-project.org>
2    
3            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
4            fixed
5    
6    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
9            for exported functions
10            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
11            Remove partitioning algorithms for sparse matrix reordering.  The
12            copyright on the Metis code was problematic and the methods were
13            rarely used.
14            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
15            operations are now done entirely in CHOLMOD code.
16    
17    2006-09-06  Douglas Bates  <bates@R-project.org>
18    
19            * src/Mutils.h: Remove functions that are no longer used.
20    
21    2006-09-04  Douglas Bates  <bates@R-project.org>
22    
23            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
24            * src/DEPS.mkf: update
25    
26    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * created branches/Matrix-for-R-2.3.x;  on trunk: do
29            * DESCRIPTION (Version): 0.9975-0
30            (Depends): R (>= 2.4.0)
31    
32    2006-09-01  Douglas Bates  <bates@R-project.org>
33    
34            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
35    
36    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
39            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
40    
41            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
42    
43    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
46            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
47            * R/dsparseMatrix.R: dito
48            * R/Csparse.R: dito
49    
50    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/dMatrix.R (Compare): improve availability of "<", etc
53            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
54    
55    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
58            of a 0-index which was used as 1-index (..hmm)
59    
60            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
61    
62            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
63            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
64            (.is.diagonal): dito
65    
66            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
67    
68            * R/Matrix.R (Matrix): also work for NA data
69    
70    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
73            in all cases.
74    
75    2006-08-27  Douglas Bates  <bates@R-project.org>
76    
77            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
78            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
79    
80    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
83            subclasses of "ddenseMatrix"
84            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
85            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
86            instead of half dozen specialized ones.
87    
88    2006-08-25  Douglas Bates  <bates@R-project.org>
89    
90            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
91            <tillard@cirad.fr> - ordering standard errors to match effects.
92    
93    2006-08-24  Douglas Bates  <bates@R-project.org>
94    
95            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
96            on R_ldl.
97            * R/lCholCMatrix.R,
98            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
99            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
100            * many files in ./R and ./src: Use more general version of
101            dup_mMatrix_as_dgeMatrix to simplify method definitions.
102            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
103            dtpMatrix, dspMatrix and dppMatrix conversions.
104    
105    
106    2006-08-23  Douglas Bates  <bates@R-project.org>
107    
108            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
109            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
110            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
111            dgeMatrix_crossprod (may need to do this in other places).
112            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
113            generic and method for dsCMatrix.  Use CHOLMOD for chol().
114    
115    2006-08-22  Douglas Bates  <bates@R-project.org>
116    
117            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
118            types of classed Matrices, matrices or numeric or logical vectors.
119            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
120            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
121            to Mutils.h (as an inline) and change name to Matrix_check_class;
122            fixes in as_cholmod_factor and chm_factor_to_SEXP.
123            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
124            dsCMatrix_matrix_solve.  Comment out vestigial functions.
125            * src/Csparse.c: use diag_P and uplo_P macros.
126    
127    2006-08-21  Douglas Bates  <bates@R-project.org>
128    
129            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
130            valgrind.
131            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
132            inverses.
133            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
134            -Wall warnings.
135            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
136            Use dup_mMatrix_as_dgeMatrix.
137    
138    2006-08-20  Douglas Bates  <bates@R-project.org>
139    
140            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
141            * tests/sparseQR.R: Added
142            * man/sparseQR-class.Rd: Document methods for qr.* generics
143            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
144    
145    2006-08-19  Douglas Bates  <bates@R-project.org>
146    
147            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
148            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
149            and qr.fitted.
150            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
151            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
152    
153    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
156            the base version has no "..." argument.
157    
158            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
159    
160            * R/Matrix.R: define and
161            * NAMESPACE: export as.numeric() and as.logical() methods.
162                    Let's hope these do not badly slow down something...
163            Finally export the zapsmall() method.
164    
165    2006-08-17  Douglas Bates  <bates@R-project.org>
166    
167            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
168            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
169            * src/dtCMatrix.c :Remove code that is no longer used
170            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
171    
172    2006-08-14  Douglas Bates  <bates@R-project.org>
173    
174            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
175            Csparse_to_logical and Csparse_symmetric_to_general.
176            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
177            coercion methods between CsparseMatrix and TsparseMatrix.
178    
179    2006-08-14  Douglas Bates  <bates@R-project.org>
180    
181            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
182            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
183            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
184            possible.
185    
186    2006-08-12  Douglas Bates  <bates@R-project.org>
187    
188            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
189              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
190              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
191              generalize conversions between TsparseMatrix, CsparseMatrix,
192              denseMatrix and matrix.  Preserve triangularity property and
193              propagate Dimnames in the easy cases.
194    
195    2006-08-10  Douglas Bates  <bates@R-project.org>
196    
197            * src/lmer.c: adjust checks in glmer_init for S4SXP
198            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
199            before S4SXP but for the wrong reasons.
200    
201    2006-08-08  Douglas Bates  <bates@R-project.org>
202    
203            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
204            Later modified to return the upper triangle only.
205            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
206    
207    2006-08-07  Douglas Bates  <bates@R-project.org>
208    
209            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
210            R-level conversion to a sparse symmetric class.
211            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
212            Remove conversion to sparse symmetric classes (now done in C code).
213    
214    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
217            * man/band.Rd:  adapt the \dontshow{} unit test.
218    
219    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * DESCRIPTION (Version): 0.995-14  for CRAN
222    
223            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
224    
225            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
226            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
227    
228            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
229            * R/Tsparse.R (tril, triu, band): methods
230            * R/dgRMatrix.R (tril, ...):    ditto
231            * man/band.Rd:                  ditto
232    
233    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/Matrix.R (head, tail): directly use utils:::head.matrix
236                    to be up-to-date automatically.
237    
238    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
241    
242            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
243            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
244            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
245            such that the S4 objects are always created by the current version
246            of R and 'Matrix' class definitions.
247    
248    2006-08-01  Douglas Bates  <bates@R-project.org>
249    
250            * R/lmer.R (LMEoptimize method), tests/lmer.R,
251            inst/external/test3comp.rda: Added warnings for convergence on
252            boundary and test cases.
253    
254            * src/lmer.c (mer_postVar): Modified to return the variances that
255            are marginal to the fixed effects, not conditional on them (which
256            is what the bVar slot contents represent).
257    
258    2006-07-31  Douglas Bates  <bates@R-project.org>
259    
260            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
261            function which calls the C function mer_hat_trace2.
262    
263            * man/ranef.Rd: Include description of "postVar" argument and
264            producing a caterpillar plot.
265    
266    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * NAMESPACE:    change  "correlation" to "corMatrix"
269            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
270            * R/dpoMatrix.R: ditto
271            * R/lmer.R:      ditto
272    
273    2006-07-28  Douglas Bates  <bates@R-project.org>
274    
275            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
276            RZXinv slot's contents into a separate internal function that can
277            be used in mer_hat_trace.
278    
279    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
282            via new smart
283            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
284            utility functions.
285    
286    
287    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/Csparse.R (tril, triu, band): do return *triangular* classed
290            matrices when appropriate; band() even symmetric ones.
291            (replCmat): extend to potentially all "CsparseMatrix"
292            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
293            allow subassignment for special sparse matrices.
294    
295            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
296    
297            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
298            argument; in glmer_*(): print only if(verbose).
299    
300            speed-optimize a few places by moving REAL(.) out of loops.
301    
302            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
303    
304    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
307                    since that wrongly triggers also for M[ logi , ]
308    
309            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
310            a symmetric matrix that results in a non-symmetric one.
311            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
312    
313            * R/dMatrix.R: make round(M) work as round(M, 0)
314    
315            * R/dgTMatrix.R (image): coordinate system and axis now use
316            1-based indices, not 0-based ones.
317    
318            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
319            * tests/indexing.R: test it.
320    
321            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
322            * man/isSymmetric-methods.Rd: and document it.
323    
324            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
325            * man/SparseM-conv.Rd: docu them
326    
327            * tests/other-pkgs.R: renamed from tests/graph.R and add example
328                    for 'SparseM' conversions
329    
330    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
331    
332            * R/Matrix.R (head): added head() and tail() methods.
333    
334    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * DESCRIPTION (Version): 0.995-12 released to CRAN
337    
338    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * tests/simple.R: add check for correct dsT -> dgT coercion;
341                    add check for correct printing of symmetric sparse matrices.
342    
343            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
344            for sparse symmetric matrices.
345    
346            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
347            diagonal twice.
348    
349    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
350    
351            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
352            being applied to the x slot (detected by Brian Ripley).
353    
354    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
357    
358            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
359    
360    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * src/lgCMatrix.c (lgCMatrix_diag): new function
363            * R/lgCMatrix.R (diag): for new method
364    
365            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
366                 ==> construction of illegal "*gTMatrix" via new() should
367                 now be much less easy:
368            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
369    
370            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
371                    directly.
372            * man/Matrix.Rd: documents it.
373    
374    2006-07-06  Douglas Bates  <bates@R-project.org>
375    
376            * src/pedigree.c (pedigree_inbreeding): Correction in
377            initialization.  This function is not currently being used and is
378            not fully tested.
379    
380            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
381            Introduced the glmer class.  Added code for mcmcmsamp on glmer
382            objects.  Modified validity check on pedigree objects to account
383            for nonparallel patterns of missingness of parents.
384    
385            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
386            class.
387    
388    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/pMatrix.R: coercion pMatrix -> Tsparse
391    
392    2006-06-12  Douglas Bates  <bates@R-project.org>
393    
394            * DESCRIPTION (Version): 0.995-11 released to CRAN
395    
396            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
397            the output from mcmcsamp.
398    
399    2006-06-10  Douglas Bates  <bates@R-project.org>
400    
401            * R/lmer.R (simulestimate): added C code for calculating the trace
402            of the hat matrix.
403    
404    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
407            classes.
408            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
409    
410    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/dgTMatrix.R (colSums): etc. All four of
413            colSums(), rowSums(), colMeans(), rowMeans() now should work for
414            all "Matrices".
415    
416    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
417    
418            * R/lmer.R (panel.ci): Add a reference line at zero and a
419            background grid to the qqmath plot of ranef.lmer.
420    
421    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
422    
423            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
424            grouping factors to be specified in the formula as (1|foo/bar).
425    
426    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
427    
428            * R/lmer.R (findbars and others): Change check of is.numeric to
429            !is.language to resolve the bug reported by Jacob Wegelin.
430    
431            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
432            code to evaluate inbreeding coefficients without calculating T,
433            based on code in Sargolzaei and Iwaisaki's paper.
434    
435    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
436    
437            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
438            generic and mer methods for isNested and denomDF. This denomDF was
439            an attempt to emulate that in lme but I don't think that makes
440            sense.  Use the trace of the hat matrix instead.
441    
442    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
445            the C code depending on a slot structure that's no longer valid.
446            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
447    
448    
449    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
450    
451            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
452            of lowerTriMatrix generic and methods to tril (also upper to triu)
453            and added a general band extractor.
454    
455    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
456    
457            * R/pedigree.R (pedigree): Replace sire and dam values outside the
458            allowable range with NAs. Added a corresponding check in the
459            validity check for the pedigree class.
460    
461            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
462            crossprod methods now inherits from symmetricMatrix.
463    
464    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
465    
466            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
467            generics lowerTriMatrix and upperTriMatrix along with methods for
468            the Csparse virtual class.  Also added a C function Csparse_band
469            that implements these methods by calling cholmod_band.
470    
471    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
472    
473            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
474            erased when it was NULL.  This led to invalid subselections!
475    
476    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
477    
478            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
479            in method for "t" so as not to lose the unit diagonal property.
480    
481    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
482    
483            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
484            and methods.  This is now an option to the ranef method for the
485            mer class.
486    
487            * src/cs_utils.c: Ensure that the nz component is -1 for a
488            compressed column-oriented matrix.  Minor formatting cleanup.
489    
490            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
491            objects.
492    
493    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
494    
495            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
496            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
497    
498    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
499    
500            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
501            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
502    
503            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
504            for the dtCMatrix class.
505    
506    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
507    
508            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
509            and methods for it.
510    
511    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
514            arguments, such that M %*% 1:6 now works
515            * Tests/matprod.R: test the above
516    
517    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
518    
519            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
520            the ranef.lmer class.
521    
522            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
523            methods to extract the posterior variances from the bVar slot.
524    
525    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
528            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
529    
530            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
531            * tests/simple: (extended)
532    
533            * R/sparseMatrix.R (isTriangular): now using much improved
534            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
535    
536    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
537    
538            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
539            (problem report from Franklin Parlamis).  This should be done
540            generally.
541    
542    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
543    
544            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
545            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
546            update the plot methods.
547    
548    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
549    
550            * R/lmer.R (resid and ranef methods):  Added methods for the
551            "residuals" and "resid" generic but only for linear mixed model
552            fits.  Changed the ranef method to return a list of data frames so
553            that the plot methods now work.
554    
555    2006-03-16  Douglas Bates  <bates@bates2>
556    
557            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
558            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
559    
560            * DESCRIPTION (Date): New release
561    
562    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
565    
566            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
567            * man/KNex.Rd: and other help files
568            * tests/*.R: several ones needed adaption
569            * inst/doc/Comparisons.Rnw: ditto
570    
571    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
574    
575            * tests/indexing.R: tests for new [<- methods for sparse matrices.
576    
577    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
580    
581            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
582    
583    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/dMatrix.R: enable things like  M [ M < 10 ]
586            * R/dgeMatrix.R: implement it
587    
588    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/AllClass.R: define "summary.mer" and "*.lmer"
591            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
592            * R/lmer.R (show): now works with summary()
593    
594    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
597            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
598                    support the above
599    
600    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
601    
602            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
603            Use glmFit$prior.weights for weights in a glmm.
604            Allow an option usePQL = FALSE to skip the PQL steps for the
605            Laplace method (and, in time, the AGQ method).
606    
607            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
608            into a separate function internal_mer_Xfactor to be able to call
609            it from internal_bhat.
610    
611    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * tests/Class+Meth.R (tstMatrixClass): function for much better
614            testing; now again of all actual classes.
615    
616            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
617                    use macros and define make_d_matrix_* and make_i_matrix_*
618                    where _i_ is for the ldense routines:
619    
620            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
621            * src/ldense.c (lsyMatrix_as_lgeMatrix):
622    
623            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
624    
625    
626    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
629                    many different kinds of matrices.
630            * R/*.R: quite a few new methods were needed for R CMD check with
631                    new Matrix().  Very good for users playing around.
632    
633    
634    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * src/dgeMatrix.c (dMatrix_validate): new
637            * src/Mutils.c (dense_nonpacked_validate): new
638    
639            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
640    
641    
642    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
643    
644            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
645    
646    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
647    
648            * DESCRIPTION (Version): 0.99-6 released to CRAN
649    
650            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
651            segfault in cases with multiple non-nested grouping factors.
652    
653    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
654    
655            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
656                    (Depends): also on 'utils'
657    
658            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
659            * R/diagMatrix.R (Diagonal): constructor and methods for
660            diagonal matrices
661    
662            * R/ltTMatrix.R: new "minimal methods"
663    
664    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
667            all methods (and help files).
668    
669    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
670    
671            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
672                    for case (dimn.  op  no_dimn.)
673    
674    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
675    
676            * DESCRIPTION (Version): 0.99-2  released to CRAN
677    
678    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
679    
680            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
681            by Julian Faraway.
682    
683    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/Auxiliaries.R (try_as): new utility
686            * R/sparseMatrix.R: use try_as() in coercion to original class
687    
688    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
689    
690            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
691    
692    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * R/Auxiliaries.R (dimNamesCheck): added
695    
696            * R/Matrix.R (as.array), (as.vector): new
697    
698    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
701                    default.
702            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
703                    "pMatrix" now contains "sparseMatrix"
704    
705    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * tests/Class+Meth.R: new tests; t(t(m)) == m
708    
709            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
710    
711            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
712            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
713    
714            * R/dspMatrix.R: typo in "t" method
715    
716    2005-09-18  Douglas Bates  <bates@wisc.edu>
717    
718            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
719            * R/Tsparse.R: instead of R/gTMatrix.R
720            * R/Csparse.R: new
721            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
722            * src/Tsparse.c: new; many trivial methods calling cholmod_()
723            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
724                            via cholmod
725    
726    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
727    
728            * R/Auxiliaries.R (non0ind): new function using new C code
729            * src/dgCMatrix.c (compressed_non_0_ij): new utility
730    
731    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
732    
733            * src/chm_common.h: header file required by all C sources that
734            call CHOLMOD functions.  It defines a cholmod_common structure
735            called 'c' whose address is passed as the last argument to
736            (virtually) every CHOLMOD function.
737    
738            * src/Pattern.c: Simple example of the use of CHOLMOD.
739    
740            * src/init.c: initialize and finalize the cholmod_common structure.
741    
742            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
743            LDL and CCOLAMD from the U. of Florida sparse matrix library.
744    
745    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * inst/test-tools.R: new file collecting the utility functions used
748                    in ./tests/*.R
749    
750            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
751            * R/Matrix.R (cbind2): methods for NULL and missing
752    
753    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/AllClass.R: new "index" class for "[" and "[<-":
756                    First cut at "symmetricMatrix" and "triangularMatrix"
757            * R/gTMatrix.R (.ind.prep): new function;
758                    Logical and character indexing now work too.
759            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
760            * tests/indexing.R: new, including *.Rout.save
761            * tests/dgTMatrix.R: new
762    
763    2005-08-29  Douglas Bates  <bates@wisc.edu>
764    
765            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
766            indicator pos not being updated.  Also enforced upper triangular
767            for symmetric case.  Need to coerce edges component of elements of
768            edge list - grr! (Why don't they define their classes cleanly?)
769    
770    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * R/Matrix.R:  added first "[<-" methods; not yet functional
773            * R/denseMatrix.R: ditto
774            * man/Subassign-methods.Rd: new help file for these
775    
776    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * DESCRIPTION (Version): 0.98-6
779    
780            * R/denseMatrix.R: new file for "[" fallback methods for all dense
781            matrices.
782    
783    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
786                    as( <logical>, "matrix")
787    
788            * R/pMatrix.R: coercion to "lgTMatrix"
789    
790            * R/gTMatrix.R: new virtual class to define "[" methods for.
791            * man/gTMatrix-class.Rd:
792            * General slight re-organization of where "[" methods are defined.
793              more to come.
794    
795    2005-08-18  Douglas Bates  <bates@wisc.edu>
796    
797            * DESCRIPTION (Version): 0.98-5  released to CRAN
798    
799            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
800            * .....
801    
802    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
803    
804            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
805            or glmer objects.
806    
807    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
810    
811    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
812    
813            * R/HBMM.R: finish re-writing R-only code.
814    
815    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
816    
817            * man/externalFormats.Rd: move documentation for writeHB and
818            writeMM here.
819    
820            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
821            (suggested by Paul Roecker).
822    
823            * tests/validObj.R (assertError): Comment out test that is failing
824            after recent changes in r-devel.
825    
826    
827    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/AllClass.R: intermediate virtual class "denseMatrix"
830            * man/denseMatrix-class.Rd
831            * NAMESPACE: export it, and also export
832            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
833    
834    2005-08-10  Douglas Bates  <bates@wisc.edu>
835    
836            * DESCRIPTION (Version): 0.98-3 to CRAN
837    
838            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
839            matrix_solve code (which was really, really wrong).
840    
841    2005-08-07  Douglas Bates  <bates@wisc.edu>
842    
843            * DESCRIPTION (Version): 0.98-2
844    
845            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
846    
847            * R/lmer.R (abbrvNms): new
848            * R/lmer.R (mcmcsamp): allow transformed parameters
849            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
850            for the Harwell-Boeing and the MatrixMarket formats.
851    
852    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * man/dtrMatrix-class.Rd: add examples
855            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
856    
857            * TODO: note the dtpMatrix (docu) bug
858    
859            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
860            in order to ensure that new as.matrix() is used by old functions,
861            e.g., svd(), qr(), eigen(), dist(),..;
862                  apply(), also matplot() or pairs().
863    
864    
865    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
866    
867            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
868              add comments about 'control' / lmerControl() arguments
869    
870    2005-07-27  Douglas Bates  <bates@wisc.edu>
871    
872            * man/sleepstudy.Rd: Added the sleep data set.
873            * DESCRIPTION (Version): 0.98-1  released to CRAN
874    
875    2005-07-12  Douglas Bates  <bates@wisc.edu>
876            * man/sleepstudy.Rd: Added the sleep data set.
877    
878            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
879            .Call calls that were producing spurious output.
880    
881    2005-07-05  Douglas Bates  <bates@wisc.edu>
882    
883            * R/lmer.R (lmer): stored updated variance component estimates in
884            mer object for the generalized model.  (Bug reported by Renaud
885            Lancelot).
886    
887    2005-07-03  Douglas Bates  <bates@wisc.edu>
888    
889            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
890            unidimensional case.
891    
892    2005-06-08  Douglas Bates  <bates@wisc.edu>
893    
894            * DESCRIPTION (Version): 0.96-1
895    
896            * moved  lmer-class' R and C code moved from lme4 to here
897    
898    2005-06-04  Douglas Bates  <bates@wisc.edu>
899    
900            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
901            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
902    
903    2005-06-02  Douglas Bates  <bates@wisc.edu>
904    
905            * src/Makefile.win: Forgot to update this when Makefile changed.
906    
907    2005-05-11  Douglas Bates  <bates@wisc.edu>
908    
909            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
910            bug reported by Kurt Hornik and Michael Hahsler.
911    
912    2005-05-10  Douglas Bates  <bates@wisc.edu>
913    
914            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
915            logical sparse matrices.  These will also be used in the symbolic
916            analysis for lmer objects.
917    
918            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
919            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
920    
921    2005-05-06  Douglas Bates  <bates@wisc.edu>
922    
923            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
924            colMeans, colSums, rowMeans and rowSums.
925    
926    2005-04-18  Douglas Bates  <bates@wisc.edu>
927    
928            * src/lgCMatrix.[ch]: code for _validate method and stub for
929            multiplication operation.
930    
931            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
932            to dgetrs.
933    
934            * src/init.c: Fix cut-and-paste error in definition of
935            dgeMatrix_matrix_solve
936    
937            * src/{many files}: Tighten code by using ALLOC_SLOT.
938    
939    2005-04-15  Douglas Bates  <bates@wisc.edu>
940    
941            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
942    
943            * DESCRIPTION: Eliminate import of stats.
944    
945    
946    2005-04-06  Douglas Bates  <bates@wisc.edu>
947    
948            * R/AllClass.R : add logical sparse matrix classes
949    
950    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * R/dgTMatrix.R: add "[" method for triplet matrices
953            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
954    
955    2005-03-31  Douglas Bates  <bates@wisc.edu>
956    
957            * DESCRIPTION (Version): release 0.95-5 to CRAN
958    
959            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
960            * R/sparseMatrix.R: %*%, crossprod()
961            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
962            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
963            * src/lmer.c (lmer_fitted): fix thinko
964    
965    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
966    
967            * R/AllClass.R: add two virtual sparse classes ``on top''
968    
969    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
972                    correspondingly fix examples and tests/ since new()
973                    doesn't work for virtual classes.
974    
975    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
976    
977            * R/Matrix.R (as.matrix): method and one for unname()
978            * tests/dpoMatrix.R: tests should now be less platform dependent;
979              also run for R 2.1.0; using as.matrix()
980    
981    2005-03-15  Douglas Bates  <bates@wisc.edu>
982    
983            * R/pMatrix.R: "pMatrix" class added
984            * ....
985    
986    2005-03-14  Douglas Bates  <bates@wisc.edu>
987    
988            * R/dtpMatrix.R: Add unpack method and an example.
989    
990            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
991            of general symmetric matrices and associated S4 methods.
992    
993    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
994            +
995    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/dgeMatrix.R (setAs): and many other files: more coercion,
998              crossprod() and "%*%" methods added; tests, too.
999            * tests/matprod.R: new, for testing these
1000    
1001    2005-03-03  Douglas Bates  <bates@wisc.edu>
1002    
1003            * src/lmer.c (lmer_fitted): Added.
1004    
1005    2005-03-02  Douglas Bates  <bates@wisc.edu>
1006    
1007            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1008    
1009    2005-02-28  Douglas Bates  <bates@wisc.edu>
1010    
1011            * src/*.c,po/,inst/po: Internationalization and localization of
1012            the package.
1013    
1014            * src/ldl.[ch]: Removed these as their contents are referenced in the
1015            R_ldl.c file.
1016    
1017            * src/flame.[ch]: Removed these source files.
1018    
1019            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1020    
1021            * src/LU.[ch],src/init.c: absorb in factorizations
1022    
1023            * src/Mutils.h: prepare for internationalization
1024    
1025            * src/cblas.h: move the enum definitions to Mutils.h and remove
1026            this file
1027    
1028    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1029    
1030            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1031    
1032            * R/dtrMatrix.R: fix t() method
1033    
1034            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1035            * NAMESPACE: export them (and import generics from "methods")
1036            * tests/group-methods.R : and test them.
1037    
1038            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1039            border case
1040    
1041    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
1042    
1043            * DESCRIPTION (Version): 0.95-2  released to CRAN
1044    
1045            * src/dgBCMatrix.c:
1046            * src/lmer.c: many changes
1047            * ...
1048    
1049    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1050    
1051            * R/Matrix.R: add more sophisticated show() method.
1052    
1053    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
1054    
1055            * */* : almost complete reorganization of classes.
1056    
1057    2005-01-26  Douglas Bates  <bates@wisc.edu>
1058    
1059            * R/AllGeneric.R: Added matrix exponential generic expm and a method
1060            for the geMatrix class.
1061    
1062    2005-01-24  Douglas Bates  <bates@wisc.edu>
1063    
1064            * src/Makefile (clean): Remove *.a and *.so
1065    
1066            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1067    
1068    2005-01-23  Douglas Bates  <bates@wisc.edu>
1069    
1070            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1071            had an effect in cases with more than 2 grouping factors.
1072    
1073    2005-01-03  Douglas Bates  <bates@wisc.edu>
1074    
1075            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1076    
1077    2004-12-23  Douglas Bates  <bates@wisc.edu>
1078    
1079            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1080            and R_useDynamicSymbols (suggested by B.D.Ripley).
1081    
1082    2004-12-14  Douglas Bates  <bates@wisc.edu>
1083    
1084            * R/sscMatrix.R: Add determinant methods
1085    
1086            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1087            for tripletMatrix to matrix.
1088    
1089    2004-12-13  Douglas Bates  <bates@wisc.edu>
1090    
1091            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1092            no longer used.
1093    
1094          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files          * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1095          with dynamic allocation of scratch arrays.          with dynamic allocation of scratch arrays.
# Line 7  Line 1098 
1098          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1099          Fixes part but not all of #15.          Fixes part but not all of #15.
1100    
1101  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1102    
1103          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1104          scalar grouping factors corrected.          scalar grouping factors corrected.
1105    
1106  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1107    
1108          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1109    
1110  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1111    
1112          * 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
1113          .h file can be included.          .h file can be included.
1114    
1115  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1116    
1117          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1118          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1119    
1120          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1121    
1122  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1123    
1124          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1125    
1126  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1127    
1128          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1129    
1130  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1131    
1132          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1133    
1134  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1135    
1136          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1137    
1138  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1139    
1140          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1141          routines.          routines.
1142    
1143  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1144    
1145          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1146    
1147  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1148    
1149          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1150    

Legend:
Removed from v.388  
changed lines
  Added in v.1543

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge