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 1312, Thu Jul 6 15:29:56 2006 UTC revision 1565, Fri Sep 15 14:02:48 2006 UTC
# Line 1  Line 1 
1    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * tests/other-pkgs.R (graph): small extenion in "graph" checks.
4    
5            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
6            (Tsp2grNEL): other fixes needed
7    
8    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
11                    Matrices, since "lMatrix", also "lsparseM" can have NA
12            * R/ndenseMatrix.R, etc: new source files
13            * man/nsparseMatrix-classes.Rd, etc: new help files
14            * tests/: adaptions
15            * src/chm_common.c (chm_dense_to_SEXP): and others:
16                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
17            * src/Csparse.c, etc: dito
18    
19    2006-09-11  Douglas Bates  <bates@R-project.org>
20    
21            * src/Mutils.[ch],init.c inst/include/*.h: Move the
22            alloc_d**Matrix functions to the lme4 package.
23    
24    2006-09-09  Douglas Bates  <bates@R-project.org>
25    
26            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
27            fixed
28    
29    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/lMatrix.R: new
32    
33            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
34    
35            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
36            * man/tcrossprod.Rd: dito
37    
38    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
39    
40            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
41            for exported functions
42            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
43            Remove partitioning algorithms for sparse matrix reordering.  The
44            copyright on the Metis code was problematic and the methods were
45            rarely used.
46            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
47            operations are now done entirely in CHOLMOD code.
48    
49    2006-09-06  Douglas Bates  <bates@R-project.org>
50    
51            * src/Mutils.h: Remove functions that are no longer used.
52    
53    2006-09-04  Douglas Bates  <bates@R-project.org>
54    
55            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
56            * src/DEPS.mkf: update
57    
58    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * created branches/Matrix-for-R-2.3.x;  on trunk: do
61            * DESCRIPTION (Version): 0.9975-0
62            (Depends): R (>= 2.4.0)
63    
64    2006-09-01  Douglas Bates  <bates@R-project.org>
65    
66            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
67    
68    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
71            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
72    
73            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
74    
75    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
78            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
79            * R/dsparseMatrix.R: dito
80            * R/Csparse.R: dito
81    
82    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/dMatrix.R (Compare): improve availability of "<", etc
85            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
86    
87    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
90            of a 0-index which was used as 1-index (..hmm)
91    
92            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
93    
94            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
95            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
96            (.is.diagonal): dito
97    
98            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
99    
100            * R/Matrix.R (Matrix): also work for NA data
101    
102    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
105            in all cases.
106    
107    2006-08-27  Douglas Bates  <bates@R-project.org>
108    
109            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
110            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
111    
112    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
115            subclasses of "ddenseMatrix"
116            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
117            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
118            instead of half dozen specialized ones.
119    
120    2006-08-25  Douglas Bates  <bates@R-project.org>
121    
122            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
123            <tillard@cirad.fr> - ordering standard errors to match effects.
124    
125    2006-08-24  Douglas Bates  <bates@R-project.org>
126    
127            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
128            on R_ldl.
129            * R/lCholCMatrix.R,
130            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
131            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
132            * many files in ./R and ./src: Use more general version of
133            dup_mMatrix_as_dgeMatrix to simplify method definitions.
134            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
135            dtpMatrix, dspMatrix and dppMatrix conversions.
136    
137    
138    2006-08-23  Douglas Bates  <bates@R-project.org>
139    
140            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
141            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
142            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
143            dgeMatrix_crossprod (may need to do this in other places).
144            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
145            generic and method for dsCMatrix.  Use CHOLMOD for chol().
146    
147    2006-08-22  Douglas Bates  <bates@R-project.org>
148    
149            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
150            types of classed Matrices, matrices or numeric or logical vectors.
151            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
152            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
153            to Mutils.h (as an inline) and change name to Matrix_check_class;
154            fixes in as_cholmod_factor and chm_factor_to_SEXP.
155            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
156            dsCMatrix_matrix_solve.  Comment out vestigial functions.
157            * src/Csparse.c: use diag_P and uplo_P macros.
158    
159    2006-08-21  Douglas Bates  <bates@R-project.org>
160    
161            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
162            valgrind.
163            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
164            inverses.
165            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
166            -Wall warnings.
167            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
168            Use dup_mMatrix_as_dgeMatrix.
169    
170    2006-08-20  Douglas Bates  <bates@R-project.org>
171    
172            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
173            * tests/sparseQR.R: Added
174            * man/sparseQR-class.Rd: Document methods for qr.* generics
175            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
176    
177    2006-08-19  Douglas Bates  <bates@R-project.org>
178    
179            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
180            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
181            and qr.fitted.
182            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
183            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
184    
185    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
188            the base version has no "..." argument.
189    
190            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
191    
192            * R/Matrix.R: define and
193            * NAMESPACE: export as.numeric() and as.logical() methods.
194                    Let's hope these do not badly slow down something...
195            Finally export the zapsmall() method.
196    
197    2006-08-17  Douglas Bates  <bates@R-project.org>
198    
199            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
200            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
201            * src/dtCMatrix.c :Remove code that is no longer used
202            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
203    
204    2006-08-14  Douglas Bates  <bates@R-project.org>
205    
206            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
207            Csparse_to_logical and Csparse_symmetric_to_general.
208            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
209            coercion methods between CsparseMatrix and TsparseMatrix.
210    
211    2006-08-14  Douglas Bates  <bates@R-project.org>
212    
213            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
214            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
215            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
216            possible.
217    
218    2006-08-12  Douglas Bates  <bates@R-project.org>
219    
220            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
221              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
222              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
223              generalize conversions between TsparseMatrix, CsparseMatrix,
224              denseMatrix and matrix.  Preserve triangularity property and
225              propagate Dimnames in the easy cases.
226    
227    2006-08-10  Douglas Bates  <bates@R-project.org>
228    
229            * src/lmer.c: adjust checks in glmer_init for S4SXP
230            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
231            before S4SXP but for the wrong reasons.
232    
233    2006-08-08  Douglas Bates  <bates@R-project.org>
234    
235            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
236            Later modified to return the upper triangle only.
237            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
238    
239    2006-08-07  Douglas Bates  <bates@R-project.org>
240    
241            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
242            R-level conversion to a sparse symmetric class.
243            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
244            Remove conversion to sparse symmetric classes (now done in C code).
245    
246    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
249            * man/band.Rd:  adapt the \dontshow{} unit test.
250    
251    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * DESCRIPTION (Version): 0.995-14  for CRAN
254    
255            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
256    
257            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
258            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
259    
260            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
261            * R/Tsparse.R (tril, triu, band): methods
262            * R/dgRMatrix.R (tril, ...):    ditto
263            * man/band.Rd:                  ditto
264    
265    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Matrix.R (head, tail): directly use utils:::head.matrix
268                    to be up-to-date automatically.
269    
270    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
273    
274            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
275            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
276            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
277            such that the S4 objects are always created by the current version
278            of R and 'Matrix' class definitions.
279    
280    2006-08-01  Douglas Bates  <bates@R-project.org>
281    
282            * R/lmer.R (LMEoptimize method), tests/lmer.R,
283            inst/external/test3comp.rda: Added warnings for convergence on
284            boundary and test cases.
285    
286            * src/lmer.c (mer_postVar): Modified to return the variances that
287            are marginal to the fixed effects, not conditional on them (which
288            is what the bVar slot contents represent).
289    
290    2006-07-31  Douglas Bates  <bates@R-project.org>
291    
292            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
293            function which calls the C function mer_hat_trace2.
294    
295            * man/ranef.Rd: Include description of "postVar" argument and
296            producing a caterpillar plot.
297    
298    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * NAMESPACE:    change  "correlation" to "corMatrix"
301            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
302            * R/dpoMatrix.R: ditto
303            * R/lmer.R:      ditto
304    
305    2006-07-28  Douglas Bates  <bates@R-project.org>
306    
307            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
308            RZXinv slot's contents into a separate internal function that can
309            be used in mer_hat_trace.
310    
311    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
314            via new smart
315            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
316            utility functions.
317    
318    
319    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Csparse.R (tril, triu, band): do return *triangular* classed
322            matrices when appropriate; band() even symmetric ones.
323            (replCmat): extend to potentially all "CsparseMatrix"
324            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
325            allow subassignment for special sparse matrices.
326    
327            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
328    
329            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
330            argument; in glmer_*(): print only if(verbose).
331    
332            speed-optimize a few places by moving REAL(.) out of loops.
333    
334            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
335    
336    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
339                    since that wrongly triggers also for M[ logi , ]
340    
341            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
342            a symmetric matrix that results in a non-symmetric one.
343            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
344    
345            * R/dMatrix.R: make round(M) work as round(M, 0)
346    
347            * R/dgTMatrix.R (image): coordinate system and axis now use
348            1-based indices, not 0-based ones.
349    
350            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
351            * tests/indexing.R: test it.
352    
353            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
354            * man/isSymmetric-methods.Rd: and document it.
355    
356            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
357            * man/SparseM-conv.Rd: docu them
358    
359            * tests/other-pkgs.R: renamed from tests/graph.R and add example
360                    for 'SparseM' conversions
361    
362    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
363    
364            * R/Matrix.R (head): added head() and tail() methods.
365    
366    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * DESCRIPTION (Version): 0.995-12 released to CRAN
369    
370    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * tests/simple.R: add check for correct dsT -> dgT coercion;
373                    add check for correct printing of symmetric sparse matrices.
374    
375            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
376            for sparse symmetric matrices.
377    
378            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
379            diagonal twice.
380    
381    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
382    
383            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
384            being applied to the x slot (detected by Brian Ripley).
385    
386    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
389    
390            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
391    
392    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * src/lgCMatrix.c (lgCMatrix_diag): new function
395            * R/lgCMatrix.R (diag): for new method
396    
397            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
398                 ==> construction of illegal "*gTMatrix" via new() should
399                 now be much less easy:
400            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
401    
402            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
403                    directly.
404            * man/Matrix.Rd: documents it.
405    
406  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
407    
408          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 414 
414          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
415          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
416    
417            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
418            class.
419    
420    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/pMatrix.R: coercion pMatrix -> Tsparse
423    
424  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
425    
426            * DESCRIPTION (Version): 0.995-11 released to CRAN
427    
428          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
429          the output from mcmcsamp.          the output from mcmcsamp.
430    
# Line 23  Line 437 
437    
438          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
439          classes.          classes.
440            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
441    
442  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
# Line 60  Line 475 
475    
476          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
477          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
478          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
479    
480    
481  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 598 
598          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
599          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
600          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
601          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
602    
603  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
# Line 387  Line 802 
802  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
803    
804          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
805          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
806          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
807    
808  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

Legend:
Removed from v.1312  
changed lines
  Added in v.1565

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