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 726, Thu May 12 14:59:04 2005 UTC revision 1544, Sat Sep 9 14:04:24 2006 UTC
# Line 1  Line 1 
1  2005-05-11  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    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
9    
10            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
11            * man/tcrossprod.Rd: dito
12    
13    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
14    
15            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
16            for exported functions
17            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
18            Remove partitioning algorithms for sparse matrix reordering.  The
19            copyright on the Metis code was problematic and the methods were
20            rarely used.
21            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
22            operations are now done entirely in CHOLMOD code.
23    
24    2006-09-06  Douglas Bates  <bates@R-project.org>
25    
26            * src/Mutils.h: Remove functions that are no longer used.
27    
28    2006-09-04  Douglas Bates  <bates@R-project.org>
29    
30            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
31            * src/DEPS.mkf: update
32    
33    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * created branches/Matrix-for-R-2.3.x;  on trunk: do
36            * DESCRIPTION (Version): 0.9975-0
37            (Depends): R (>= 2.4.0)
38    
39    2006-09-01  Douglas Bates  <bates@R-project.org>
40    
41            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
42    
43    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
46            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
47    
48            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
49    
50    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
53            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
54            * R/dsparseMatrix.R: dito
55            * R/Csparse.R: dito
56    
57    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/dMatrix.R (Compare): improve availability of "<", etc
60            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
61    
62    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
65            of a 0-index which was used as 1-index (..hmm)
66    
67            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
68    
69            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
70            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
71            (.is.diagonal): dito
72    
73            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
74    
75            * R/Matrix.R (Matrix): also work for NA data
76    
77    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
80            in all cases.
81    
82    2006-08-27  Douglas Bates  <bates@R-project.org>
83    
84            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
85            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
86    
87    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
90            subclasses of "ddenseMatrix"
91            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
92            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
93            instead of half dozen specialized ones.
94    
95    2006-08-25  Douglas Bates  <bates@R-project.org>
96    
97            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
98            <tillard@cirad.fr> - ordering standard errors to match effects.
99    
100    2006-08-24  Douglas Bates  <bates@R-project.org>
101    
102            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
103            on R_ldl.
104            * R/lCholCMatrix.R,
105            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
106            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
107            * many files in ./R and ./src: Use more general version of
108            dup_mMatrix_as_dgeMatrix to simplify method definitions.
109            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
110            dtpMatrix, dspMatrix and dppMatrix conversions.
111    
112    
113    2006-08-23  Douglas Bates  <bates@R-project.org>
114    
115            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
116            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
117            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
118            dgeMatrix_crossprod (may need to do this in other places).
119            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
120            generic and method for dsCMatrix.  Use CHOLMOD for chol().
121    
122    2006-08-22  Douglas Bates  <bates@R-project.org>
123    
124            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
125            types of classed Matrices, matrices or numeric or logical vectors.
126            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
127            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
128            to Mutils.h (as an inline) and change name to Matrix_check_class;
129            fixes in as_cholmod_factor and chm_factor_to_SEXP.
130            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
131            dsCMatrix_matrix_solve.  Comment out vestigial functions.
132            * src/Csparse.c: use diag_P and uplo_P macros.
133    
134    2006-08-21  Douglas Bates  <bates@R-project.org>
135    
136            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
137            valgrind.
138            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
139            inverses.
140            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
141            -Wall warnings.
142            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
143            Use dup_mMatrix_as_dgeMatrix.
144    
145    2006-08-20  Douglas Bates  <bates@R-project.org>
146    
147            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
148            * tests/sparseQR.R: Added
149            * man/sparseQR-class.Rd: Document methods for qr.* generics
150            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
151    
152    2006-08-19  Douglas Bates  <bates@R-project.org>
153    
154            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
155            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
156            and qr.fitted.
157            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
158            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
159    
160    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
163            the base version has no "..." argument.
164    
165            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
166    
167            * R/Matrix.R: define and
168            * NAMESPACE: export as.numeric() and as.logical() methods.
169                    Let's hope these do not badly slow down something...
170            Finally export the zapsmall() method.
171    
172    2006-08-17  Douglas Bates  <bates@R-project.org>
173    
174            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
175            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
176            * src/dtCMatrix.c :Remove code that is no longer used
177            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
178    
179    2006-08-14  Douglas Bates  <bates@R-project.org>
180    
181            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
182            Csparse_to_logical and Csparse_symmetric_to_general.
183            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
184            coercion methods between CsparseMatrix and TsparseMatrix.
185    
186    2006-08-14  Douglas Bates  <bates@R-project.org>
187    
188            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
189            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
190            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
191            possible.
192    
193    2006-08-12  Douglas Bates  <bates@R-project.org>
194    
195            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
196              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
197              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
198              generalize conversions between TsparseMatrix, CsparseMatrix,
199              denseMatrix and matrix.  Preserve triangularity property and
200              propagate Dimnames in the easy cases.
201    
202    2006-08-10  Douglas Bates  <bates@R-project.org>
203    
204            * src/lmer.c: adjust checks in glmer_init for S4SXP
205            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
206            before S4SXP but for the wrong reasons.
207    
208    2006-08-08  Douglas Bates  <bates@R-project.org>
209    
210            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
211            Later modified to return the upper triangle only.
212            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
213    
214    2006-08-07  Douglas Bates  <bates@R-project.org>
215    
216            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
217            R-level conversion to a sparse symmetric class.
218            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
219            Remove conversion to sparse symmetric classes (now done in C code).
220    
221    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
224            * man/band.Rd:  adapt the \dontshow{} unit test.
225    
226    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * DESCRIPTION (Version): 0.995-14  for CRAN
229    
230            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
231    
232            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
233            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
234    
235            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
236            * R/Tsparse.R (tril, triu, band): methods
237            * R/dgRMatrix.R (tril, ...):    ditto
238            * man/band.Rd:                  ditto
239    
240    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Matrix.R (head, tail): directly use utils:::head.matrix
243                    to be up-to-date automatically.
244    
245    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
248    
249            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
250            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
251            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
252            such that the S4 objects are always created by the current version
253            of R and 'Matrix' class definitions.
254    
255    2006-08-01  Douglas Bates  <bates@R-project.org>
256    
257            * R/lmer.R (LMEoptimize method), tests/lmer.R,
258            inst/external/test3comp.rda: Added warnings for convergence on
259            boundary and test cases.
260    
261            * src/lmer.c (mer_postVar): Modified to return the variances that
262            are marginal to the fixed effects, not conditional on them (which
263            is what the bVar slot contents represent).
264    
265    2006-07-31  Douglas Bates  <bates@R-project.org>
266    
267            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
268            function which calls the C function mer_hat_trace2.
269    
270            * man/ranef.Rd: Include description of "postVar" argument and
271            producing a caterpillar plot.
272    
273    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * NAMESPACE:    change  "correlation" to "corMatrix"
276            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
277            * R/dpoMatrix.R: ditto
278            * R/lmer.R:      ditto
279    
280    2006-07-28  Douglas Bates  <bates@R-project.org>
281    
282            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
283            RZXinv slot's contents into a separate internal function that can
284            be used in mer_hat_trace.
285    
286    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
289            via new smart
290            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
291            utility functions.
292    
293    
294    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/Csparse.R (tril, triu, band): do return *triangular* classed
297            matrices when appropriate; band() even symmetric ones.
298            (replCmat): extend to potentially all "CsparseMatrix"
299            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
300            allow subassignment for special sparse matrices.
301    
302            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
303    
304            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
305            argument; in glmer_*(): print only if(verbose).
306    
307            speed-optimize a few places by moving REAL(.) out of loops.
308    
309            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
310    
311    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
314                    since that wrongly triggers also for M[ logi , ]
315    
316            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
317            a symmetric matrix that results in a non-symmetric one.
318            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
319    
320            * R/dMatrix.R: make round(M) work as round(M, 0)
321    
322            * R/dgTMatrix.R (image): coordinate system and axis now use
323            1-based indices, not 0-based ones.
324    
325            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
326            * tests/indexing.R: test it.
327    
328            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
329            * man/isSymmetric-methods.Rd: and document it.
330    
331            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
332            * man/SparseM-conv.Rd: docu them
333    
334            * tests/other-pkgs.R: renamed from tests/graph.R and add example
335                    for 'SparseM' conversions
336    
337    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
338    
339            * R/Matrix.R (head): added head() and tail() methods.
340    
341    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * DESCRIPTION (Version): 0.995-12 released to CRAN
344    
345    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * tests/simple.R: add check for correct dsT -> dgT coercion;
348                    add check for correct printing of symmetric sparse matrices.
349    
350            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
351            for sparse symmetric matrices.
352    
353            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
354            diagonal twice.
355    
356    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
357    
358            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
359            being applied to the x slot (detected by Brian Ripley).
360    
361    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
364    
365            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
366    
367    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * src/lgCMatrix.c (lgCMatrix_diag): new function
370            * R/lgCMatrix.R (diag): for new method
371    
372            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
373                 ==> construction of illegal "*gTMatrix" via new() should
374                 now be much less easy:
375            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
376    
377            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
378                    directly.
379            * man/Matrix.Rd: documents it.
380    
381    2006-07-06  Douglas Bates  <bates@R-project.org>
382    
383            * src/pedigree.c (pedigree_inbreeding): Correction in
384            initialization.  This function is not currently being used and is
385            not fully tested.
386    
387            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
388            Introduced the glmer class.  Added code for mcmcmsamp on glmer
389            objects.  Modified validity check on pedigree objects to account
390            for nonparallel patterns of missingness of parents.
391    
392            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
393            class.
394    
395    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/pMatrix.R: coercion pMatrix -> Tsparse
398    
399    2006-06-12  Douglas Bates  <bates@R-project.org>
400    
401            * DESCRIPTION (Version): 0.995-11 released to CRAN
402    
403            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
404            the output from mcmcsamp.
405    
406    2006-06-10  Douglas Bates  <bates@R-project.org>
407    
408            * R/lmer.R (simulestimate): added C code for calculating the trace
409            of the hat matrix.
410    
411    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
414            classes.
415            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
416    
417    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
418    
419            * R/dgTMatrix.R (colSums): etc. All four of
420            colSums(), rowSums(), colMeans(), rowMeans() now should work for
421            all "Matrices".
422    
423    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
424    
425            * R/lmer.R (panel.ci): Add a reference line at zero and a
426            background grid to the qqmath plot of ranef.lmer.
427    
428    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
429    
430            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
431            grouping factors to be specified in the formula as (1|foo/bar).
432    
433    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
434    
435            * R/lmer.R (findbars and others): Change check of is.numeric to
436            !is.language to resolve the bug reported by Jacob Wegelin.
437    
438            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
439            code to evaluate inbreeding coefficients without calculating T,
440            based on code in Sargolzaei and Iwaisaki's paper.
441    
442    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
443    
444            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
445            generic and mer methods for isNested and denomDF. This denomDF was
446            an attempt to emulate that in lme but I don't think that makes
447            sense.  Use the trace of the hat matrix instead.
448    
449    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
452            the C code depending on a slot structure that's no longer valid.
453            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
454    
455    
456    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
457    
458            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
459            of lowerTriMatrix generic and methods to tril (also upper to triu)
460            and added a general band extractor.
461    
462    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
463    
464            * R/pedigree.R (pedigree): Replace sire and dam values outside the
465            allowable range with NAs. Added a corresponding check in the
466            validity check for the pedigree class.
467    
468            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
469            crossprod methods now inherits from symmetricMatrix.
470    
471    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
472    
473            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
474            generics lowerTriMatrix and upperTriMatrix along with methods for
475            the Csparse virtual class.  Also added a C function Csparse_band
476            that implements these methods by calling cholmod_band.
477    
478    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
481            erased when it was NULL.  This led to invalid subselections!
482    
483    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
484    
485            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
486            in method for "t" so as not to lose the unit diagonal property.
487    
488    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
489    
490            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
491            and methods.  This is now an option to the ranef method for the
492            mer class.
493    
494            * src/cs_utils.c: Ensure that the nz component is -1 for a
495            compressed column-oriented matrix.  Minor formatting cleanup.
496    
497            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
498            objects.
499    
500    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
503            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
504    
505    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
506    
507            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
508            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
509    
510            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
511            for the dtCMatrix class.
512    
513    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
514    
515            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
516            and methods for it.
517    
518    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
521            arguments, such that M %*% 1:6 now works
522            * Tests/matprod.R: test the above
523    
524    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
525    
526            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
527            the ranef.lmer class.
528    
529            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
530            methods to extract the posterior variances from the bVar slot.
531    
532    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
535            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
536    
537            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
538            * tests/simple: (extended)
539    
540            * R/sparseMatrix.R (isTriangular): now using much improved
541            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
542    
543    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
544    
545            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
546            (problem report from Franklin Parlamis).  This should be done
547            generally.
548    
549    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
550    
551            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
552            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
553            update the plot methods.
554    
555    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
556    
557            * R/lmer.R (resid and ranef methods):  Added methods for the
558            "residuals" and "resid" generic but only for linear mixed model
559            fits.  Changed the ranef method to return a list of data frames so
560            that the plot methods now work.
561    
562    2006-03-16  Douglas Bates  <bates@bates2>
563    
564            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
565            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
566    
567            * DESCRIPTION (Date): New release
568    
569    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
572    
573            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
574            * man/KNex.Rd: and other help files
575            * tests/*.R: several ones needed adaption
576            * inst/doc/Comparisons.Rnw: ditto
577    
578    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
581    
582            * tests/indexing.R: tests for new [<- methods for sparse matrices.
583    
584    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
587    
588            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
589    
590    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * R/dMatrix.R: enable things like  M [ M < 10 ]
593            * R/dgeMatrix.R: implement it
594    
595    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * R/AllClass.R: define "summary.mer" and "*.lmer"
598            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
599            * R/lmer.R (show): now works with summary()
600    
601    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
604            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
605                    support the above
606    
607    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
608    
609            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
610            Use glmFit$prior.weights for weights in a glmm.
611            Allow an option usePQL = FALSE to skip the PQL steps for the
612            Laplace method (and, in time, the AGQ method).
613    
614            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
615            into a separate function internal_mer_Xfactor to be able to call
616            it from internal_bhat.
617    
618    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * tests/Class+Meth.R (tstMatrixClass): function for much better
621            testing; now again of all actual classes.
622    
623            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
624                    use macros and define make_d_matrix_* and make_i_matrix_*
625                    where _i_ is for the ldense routines:
626    
627            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
628            * src/ldense.c (lsyMatrix_as_lgeMatrix):
629    
630            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
631    
632    
633    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
636                    many different kinds of matrices.
637            * R/*.R: quite a few new methods were needed for R CMD check with
638                    new Matrix().  Very good for users playing around.
639    
640    
641    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * src/dgeMatrix.c (dMatrix_validate): new
644            * src/Mutils.c (dense_nonpacked_validate): new
645    
646            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
647    
648    
649    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
650    
651            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
652    
653    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
654    
655            * DESCRIPTION (Version): 0.99-6 released to CRAN
656    
657            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
658            segfault in cases with multiple non-nested grouping factors.
659    
660    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
663                    (Depends): also on 'utils'
664    
665            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
666            * R/diagMatrix.R (Diagonal): constructor and methods for
667            diagonal matrices
668    
669            * R/ltTMatrix.R: new "minimal methods"
670    
671    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
674            all methods (and help files).
675    
676    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
679                    for case (dimn.  op  no_dimn.)
680    
681    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
682    
683            * DESCRIPTION (Version): 0.99-2  released to CRAN
684    
685    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
686    
687            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
688            by Julian Faraway.
689    
690    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/Auxiliaries.R (try_as): new utility
693            * R/sparseMatrix.R: use try_as() in coercion to original class
694    
695    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
698    
699    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/Auxiliaries.R (dimNamesCheck): added
702    
703            * R/Matrix.R (as.array), (as.vector): new
704    
705    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
708                    default.
709            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
710                    "pMatrix" now contains "sparseMatrix"
711    
712    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * tests/Class+Meth.R: new tests; t(t(m)) == m
715    
716            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
717    
718            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
719            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
720    
721            * R/dspMatrix.R: typo in "t" method
722    
723    2005-09-18  Douglas Bates  <bates@wisc.edu>
724    
725            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
726            * R/Tsparse.R: instead of R/gTMatrix.R
727            * R/Csparse.R: new
728            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
729            * src/Tsparse.c: new; many trivial methods calling cholmod_()
730            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
731                            via cholmod
732    
733    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/Auxiliaries.R (non0ind): new function using new C code
736            * src/dgCMatrix.c (compressed_non_0_ij): new utility
737    
738    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
739    
740            * src/chm_common.h: header file required by all C sources that
741            call CHOLMOD functions.  It defines a cholmod_common structure
742            called 'c' whose address is passed as the last argument to
743            (virtually) every CHOLMOD function.
744    
745            * src/Pattern.c: Simple example of the use of CHOLMOD.
746    
747            * src/init.c: initialize and finalize the cholmod_common structure.
748    
749            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
750            LDL and CCOLAMD from the U. of Florida sparse matrix library.
751    
752    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * inst/test-tools.R: new file collecting the utility functions used
755                    in ./tests/*.R
756    
757            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
758            * R/Matrix.R (cbind2): methods for NULL and missing
759    
760    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * R/AllClass.R: new "index" class for "[" and "[<-":
763                    First cut at "symmetricMatrix" and "triangularMatrix"
764            * R/gTMatrix.R (.ind.prep): new function;
765                    Logical and character indexing now work too.
766            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
767            * tests/indexing.R: new, including *.Rout.save
768            * tests/dgTMatrix.R: new
769    
770    2005-08-29  Douglas Bates  <bates@wisc.edu>
771    
772            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
773            indicator pos not being updated.  Also enforced upper triangular
774            for symmetric case.  Need to coerce edges component of elements of
775            edge list - grr! (Why don't they define their classes cleanly?)
776    
777    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * R/Matrix.R:  added first "[<-" methods; not yet functional
780            * R/denseMatrix.R: ditto
781            * man/Subassign-methods.Rd: new help file for these
782    
783    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * DESCRIPTION (Version): 0.98-6
786    
787            * R/denseMatrix.R: new file for "[" fallback methods for all dense
788            matrices.
789    
790    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
793                    as( <logical>, "matrix")
794    
795            * R/pMatrix.R: coercion to "lgTMatrix"
796    
797            * R/gTMatrix.R: new virtual class to define "[" methods for.
798            * man/gTMatrix-class.Rd:
799            * General slight re-organization of where "[" methods are defined.
800              more to come.
801    
802    2005-08-18  Douglas Bates  <bates@wisc.edu>
803    
804            * DESCRIPTION (Version): 0.98-5  released to CRAN
805    
806            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
807            * .....
808    
809    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
810    
811            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
812            or glmer objects.
813    
814    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
815    
816            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
817    
818    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
819    
820            * R/HBMM.R: finish re-writing R-only code.
821    
822    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
823    
824            * man/externalFormats.Rd: move documentation for writeHB and
825            writeMM here.
826    
827            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
828            (suggested by Paul Roecker).
829    
830            * tests/validObj.R (assertError): Comment out test that is failing
831            after recent changes in r-devel.
832    
833    
834    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/AllClass.R: intermediate virtual class "denseMatrix"
837            * man/denseMatrix-class.Rd
838            * NAMESPACE: export it, and also export
839            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
840    
841    2005-08-10  Douglas Bates  <bates@wisc.edu>
842    
843            * DESCRIPTION (Version): 0.98-3 to CRAN
844    
845            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
846            matrix_solve code (which was really, really wrong).
847    
848    2005-08-07  Douglas Bates  <bates@wisc.edu>
849    
850            * DESCRIPTION (Version): 0.98-2
851    
852            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
853    
854            * R/lmer.R (abbrvNms): new
855            * R/lmer.R (mcmcsamp): allow transformed parameters
856            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
857            for the Harwell-Boeing and the MatrixMarket formats.
858    
859    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * man/dtrMatrix-class.Rd: add examples
862            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
863    
864            * TODO: note the dtpMatrix (docu) bug
865    
866            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
867            in order to ensure that new as.matrix() is used by old functions,
868            e.g., svd(), qr(), eigen(), dist(),..;
869                  apply(), also matplot() or pairs().
870    
871    
872    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
873    
874            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
875              add comments about 'control' / lmerControl() arguments
876    
877    2005-07-27  Douglas Bates  <bates@wisc.edu>
878    
879            * man/sleepstudy.Rd: Added the sleep data set.
880            * DESCRIPTION (Version): 0.98-1  released to CRAN
881    
882    2005-07-12  Douglas Bates  <bates@wisc.edu>
883            * man/sleepstudy.Rd: Added the sleep data set.
884    
885            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
886            .Call calls that were producing spurious output.
887    
888    2005-07-05  Douglas Bates  <bates@wisc.edu>
889    
890            * R/lmer.R (lmer): stored updated variance component estimates in
891            mer object for the generalized model.  (Bug reported by Renaud
892            Lancelot).
893    
894    2005-07-03  Douglas Bates  <bates@wisc.edu>
895    
896            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
897            unidimensional case.
898    
899    2005-06-08  Douglas Bates  <bates@wisc.edu>
900    
901            * DESCRIPTION (Version): 0.96-1
902    
903            * moved  lmer-class' R and C code moved from lme4 to here
904    
905    2005-06-04  Douglas Bates  <bates@wisc.edu>
906    
907            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
908            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
909    
910    2005-06-02  Douglas Bates  <bates@wisc.edu>
911    
912            * src/Makefile.win: Forgot to update this when Makefile changed.
913    
914    2005-05-11  Douglas Bates  <bates@wisc.edu>
915    
916          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a          * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
917          bug reported by Kurt Hornik and Michael Hahsler.          bug reported by Kurt Hornik and Michael Hahsler.
918    
919  2005-05-10  Douglas Bates  <bates@bates1-home>  2005-05-10  Douglas Bates  <bates@wisc.edu>
920    
921          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for          * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
922          logical sparse matrices.  These will also be used in the symbolic          logical sparse matrices.  These will also be used in the symbolic
# Line 12  Line 925 
925          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions          * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
926          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr          of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
927    
928  2005-05-06  Douglas Bates  <bates@bates1-home>  2005-05-06  Douglas Bates  <bates@wisc.edu>
929    
930          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of          * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
931          colMeans, colSums, rowMeans and rowSums.          colMeans, colSums, rowMeans and rowSums.
932    
933  2005-04-18  Douglas Bates  <bates@bates1-home>  2005-04-18  Douglas Bates  <bates@wisc.edu>
934    
935          * src/lgCMatrix.[ch]: code for _validate method and stub for          * src/lgCMatrix.[ch]: code for _validate method and stub for
936          multiplication operation.          multiplication operation.
# Line 30  Line 943 
943    
944          * src/{many files}: Tighten code by using ALLOC_SLOT.          * src/{many files}: Tighten code by using ALLOC_SLOT.
945    
946  2005-04-15  Douglas Bates  <bates@bates1-home>  2005-04-15  Douglas Bates  <bates@wisc.edu>
947    
948          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes          * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
949    
950          * DESCRIPTION: Eliminate import of stats.          * DESCRIPTION: Eliminate import of stats.
951    
952    
953  2005-04-06  Douglas Bates  <bates@bates1-home>  2005-04-06  Douglas Bates  <bates@wisc.edu>
954    
955          * R/AllClass.R : add logical sparse matrix classes          * R/AllClass.R : add logical sparse matrix classes
956    
# Line 46  Line 959 
959          * R/dgTMatrix.R: add "[" method for triplet matrices          * R/dgTMatrix.R: add "[" method for triplet matrices
960          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse          * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
961    
962  2005-03-31  Douglas Bates  <bates@bates1-home>  2005-03-31  Douglas Bates  <bates@wisc.edu>
963    
964          * DESCRIPTION (Version): release 0.95-5 to CRAN          * DESCRIPTION (Version): release 0.95-5 to CRAN
965    
# Line 72  Line 985 
985          * tests/dpoMatrix.R: tests should now be less platform dependent;          * tests/dpoMatrix.R: tests should now be less platform dependent;
986            also run for R 2.1.0; using as.matrix()            also run for R 2.1.0; using as.matrix()
987    
988  2005-03-15  Douglas Bates  <bates@bates1-home>  2005-03-15  Douglas Bates  <bates@wisc.edu>
989    
990          * R/pMatrix.R: "pMatrix" class added          * R/pMatrix.R: "pMatrix" class added
991          * ....          * ....
992    
993  2005-03-14  Douglas Bates  <bates@bates1-home>  2005-03-14  Douglas Bates  <bates@wisc.edu>
994    
995          * R/dtpMatrix.R: Add unpack method and an example.          * R/dtpMatrix.R: Add unpack method and an example.
996    
# Line 92  Line 1005 
1005            crossprod() and "%*%" methods added; tests, too.            crossprod() and "%*%" methods added; tests, too.
1006          * tests/matprod.R: new, for testing these          * tests/matprod.R: new, for testing these
1007    
1008  2005-03-03  Douglas Bates  <bates@bates1-home>  2005-03-03  Douglas Bates  <bates@wisc.edu>
1009    
1010          * src/lmer.c (lmer_fitted): Added.          * src/lmer.c (lmer_fitted): Added.
1011    
1012  2005-03-02  Douglas Bates  <bates@bates1-home>  2005-03-02  Douglas Bates  <bates@wisc.edu>
1013    
1014          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix          * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1015    
1016  2005-02-28  Douglas Bates  <bates@bates1-home>  2005-02-28  Douglas Bates  <bates@wisc.edu>
1017    
1018          * src/*.c,po/,inst/po: Internationalization and localization of          * src/*.c,po/,inst/po: Internationalization and localization of
1019          the package.          the package.
# Line 148  Line 1061 
1061    
1062          * */* : almost complete reorganization of classes.          * */* : almost complete reorganization of classes.
1063    
1064  2005-01-26  Douglas Bates  <bates@bates7>  2005-01-26  Douglas Bates  <bates@wisc.edu>
1065    
1066          * R/AllGeneric.R: Added matrix exponential generic expm and a method          * R/AllGeneric.R: Added matrix exponential generic expm and a method
1067          for the geMatrix class.          for the geMatrix class.
1068    
1069  2005-01-24  Douglas Bates  <bates@bates7>  2005-01-24  Douglas Bates  <bates@wisc.edu>
1070    
1071          * src/Makefile (clean): Remove *.a and *.so          * src/Makefile (clean): Remove *.a and *.so
1072    
1073          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.          * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1074    
1075  2005-01-23  Douglas Bates  <bates@bates7>  2005-01-23  Douglas Bates  <bates@wisc.edu>
1076    
1077          * src/lmer.c (Lind): Definition of Lind was backwards.  This only          * src/lmer.c (Lind): Definition of Lind was backwards.  This only
1078          had an effect in cases with more than 2 grouping factors.          had an effect in cases with more than 2 grouping factors.
1079    
1080  2005-01-03  Douglas Bates  <bates@bates1-home>  2005-01-03  Douglas Bates  <bates@wisc.edu>
1081    
1082          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer          * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1083    
1084  2004-12-23  Douglas Bates  <bates@bates1-home>  2004-12-23  Douglas Bates  <bates@wisc.edu>
1085    
1086          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines          * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1087          and R_useDynamicSymbols (suggested by B.D.Ripley).          and R_useDynamicSymbols (suggested by B.D.Ripley).
1088    
1089  2004-12-14  Douglas Bates  <bates@bates1-home>  2004-12-14  Douglas Bates  <bates@wisc.edu>
1090    
1091          * R/sscMatrix.R: Add determinant methods          * R/sscMatrix.R: Add determinant methods
1092    
1093          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion          * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1094          for tripletMatrix to matrix.          for tripletMatrix to matrix.
1095    
1096  2004-12-13  Douglas Bates  <bates@bates1-home>  2004-12-13  Douglas Bates  <bates@wisc.edu>
1097    
1098          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is          * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1099          no longer used.          no longer used.
# Line 192  Line 1105 
1105          for multivariate random effects with multiple grouping factors.          for multivariate random effects with multiple grouping factors.
1106          Fixes part but not all of #15.          Fixes part but not all of #15.
1107    
1108  2004-12-03  Douglas Bates  <bates@bates1-home>  2004-12-03  Douglas Bates  <bates@wisc.edu>
1109    
1110          * src/lmeRep.c (lmeRep_factor): order of operations for multiple          * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1111          scalar grouping factors corrected.          scalar grouping factors corrected.
1112    
1113  2004-11-29  Douglas Bates  <bates@bates1-home>  2004-11-29  Douglas Bates  <bates@wisc.edu>
1114    
1115          * src/bCrosstab.c: remove diag_update which is no longer used          * src/bCrosstab.c: remove diag_update which is no longer used
1116    
1117  2004-11-16  Douglas Bates  <bates@bates1-home>  2004-11-16  Douglas Bates  <bates@wisc.edu>
1118    
1119          * 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
1120          .h file can be included.          .h file can be included.
1121    
1122  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1123    
1124          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1125          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1126    
1127          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1128    
1129  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1130    
1131          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1132    
1133  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1134    
1135          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1136    
1137  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1138    
1139          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1140    
1141  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1142    
1143          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1144    
1145  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1146    
1147          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1148          routines.          routines.
1149    
1150  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1151    
1152          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1153    
1154  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1155    
1156          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1157    

Legend:
Removed from v.726  
changed lines
  Added in v.1544

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