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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2236, Wed Jul 23 16:48:14 2008 UTC
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1    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
4            "x@p[ncol(x)]" instead of length(x@i).
5            * R/Auxiliaries.R (nnzero): ditto
6    
7            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
8            since that fails for over-allocated i.
9    
10            * tests/validObj.R: more testing of over-allocated (i,x) slots
11    
12    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
15            'sort_in_place' and set it to TRUE in call from
16            * src/Csparse.c (Csparse_validate): sort in place, making sure that
17            validObject() continues sort the columns if needed.
18    
19            * tests/validObj.R: now tests that more thoroughly, and
20            * man/CsparseMatrix-class.Rd: documents it.
21    
22    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
25            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
26            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
27            diagU2N().
28    
29            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
30            .spDiagonal() and new .trDiagonal().
31    
32            * R/dtCMatrix.R (solve): make use of .trDiagonal()
33    
34    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
37            stumbled upon by Michael H.
38    
39            * tests/validObj.R: testing the bug-fix
40    
41            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
42            versions.
43    
44            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
45            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
46    
47            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
48              AS_CHM_SP() which includes diagU2N.
49    
50            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
51            adapt to 3 arguments.
52    
53    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
54    
55            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
56              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
57              new solve method
58            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
59              Csparse_diagU2N functionality into Matrix_as_cs
60    
61    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
64    
65    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
68              argument with default TRUE
69            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
70              Csparse_diagU2N
71            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
72              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
73              parent array; new solve method for signature(a = "dtCMatrix", b =
74              "sparseMatrix")
75    
76    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/diagMatrix.R (.bdiag): also keep result triangular
79    
80    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
81    
82            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
83              messages
84    
85    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
88            symmetric- or nsparse-Matrix, also fixing the bug introduced with
89            the new version (.999375-10).
90    
91            * tests/Simple.R: regression test for the bugs.
92    
93    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/sparseVector.R (spV2M): fix for "isparseVector".
96            Further, fix <diag> -> <sparseVector> coercion
97            (repSpV): add rep(<sparseVector>, .) method
98    
99            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
100            use as.vector(.).
101    
102            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
103    
104            * R/AllClass.R: new (hidden) class union "scarceMatrix"
105            * R/AllClass.R: sparseVector: add prototype
106    
107            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
108            Kasper Kristensen
109    
110    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * tests/other-pkgs.R: add more interesting Matrix -> graph
113    
114    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
117            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
118    
119    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * DESCRIPTION: release 0.999375-10 to CRAN
122    
123            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
124            .bdiag().
125            * man/bdiag.Rd: update, including test.
126    
127    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * tests/Simple.R: add minimal bdiag() checks
130    
131            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
132              factor out the Tsparse - internal computation into new .bdiag()
133    
134    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/nsparseMatrix.R: specific fast all() and any() methods.
137    
138            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
139            when trying to produce too large result.
140    
141            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
142            very large matrices.
143    
144            * R/sparseMatrix.R (printSpMatrix2): new function, used by
145            show(<sparseMatrix>).
146    
147            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
148    
149    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * src/Mutils.c (m_encodeInd, m_encodeInd2):
152            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
153    
154            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
155            big matrices): -> 2nd argument 'di' instead of 'nr' !
156    
157    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/dtCMatrix.R: faster dgC* -> dtC* method
160            * tests/Simple.R: (hence removed "FIXME")
161    
162            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
163            which can be be turned off for possible speed gains.
164    
165    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
168    
169            * R/not.R: fix !<ldiMatrix>
170            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
171    
172            * R/diagMatrix.R (Ops): fix one-off thinko in
173            <diagonal> o <numeric> methods
174    
175            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
176    
177    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
180            * tests/Simple.R: testing the above
181    
182    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
185    
186    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
189            * NAMESPACE (unname): finally exported
190    
191    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Auxiliaries.R (cholMat): possibly keep packed
194    
195            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
196            for R < 2.7.0.
197    
198            * R/Tsparse.R ([): for triangularMatrix, check if result may be
199            triangular.
200            * tests/indexing.R: regression test
201    
202    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
205            * R/Ops.R: more methods, for lMatrix/nMatrix
206    
207    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/expm.R: new file for all expm() methods; notably new ones for
210            diagonal*, triangular*, symmetric* and also simple "matrix".
211    
212    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
215    
216            * inst/test-tools.R (assert.EQ.mat): better message when not equal
217    
218            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
219    
220            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
221            [dl]denseMatrix {identical slots; but more logical method dispatch}
222    
223    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
226    
227            * R/diagMatrix.R (determinant): method
228    
229    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
232    
233            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
234    
235            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
236            its diagonal
237    
238    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
241    
242            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
243    
244            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
245    
246            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
247    
248    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
251    
252            * R/Ops.R (.do.Logic.lsparse): fix NA case
253    
254            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
255    
256            * R/Auxiliaries.R (nnzero): fix special cases, using
257            * R/Auxiliaries.R (indDiag): new utility
258            * R/Auxiliaries.R (indTri): new argument 'diag'
259    
260            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
261    
262    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
265    
266            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
267            ".tCMatrix" triangular matrix.
268    
269            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
270            'clx' can be class *or* class representation.
271            (nnzSparse): new.
272            (non0ind): new 'xtendSymm' argument; used in
273            * R/Ops.R:
274    
275            * R/pMatrix.R: more efficient determinant() method
276    
277    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
280            * [disactivated] NAMESPACE: export(det)
281    
282            * R/diagMatrix.R (mkDiag): new substitute for diag()
283    
284            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
285            (as0, as1): new utility.
286    
287            * R/Csparse.R (diag, band): need diagU2N()
288    
289            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
290    
291            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
292    
293            * R/Ops.R (Compare): fix <nsp> o <nsp> case
294    
295            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
296    
297    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/Auxiliaries.R (signPerm): new utility for
300            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
301    
302            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
303            since we have our own error handler (and can use tryCatch() from R).
304    
305    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
308    
309            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
310            when not positive definite.
311    
312            * R/Auxiliaries.R (asTri): new auxiliary
313            (non0.i): make *much* faster for Tsparse with many non-zero
314            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
315    
316            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
317            test-tools.R , see below
318    
319            * R/dMatrix.R: fix "Summary" method: + diagU2N()
320    
321            * NAMESPACE, R/Matrix.R: add mean() method
322    
323    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
326            cold-hot colors; try *changed* default useAbs = FALSE
327            * man/image-methods.Rd:  nice examples
328    
329    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * inst/test-tools.R (checkMatrix): new function for modularizing part
332            of tstMatrixClass() in tests/Class+Meth.R
333    
334            * R/dsCMatrix.R: coercion from "matrix"
335            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
336    
337            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
338            add test for as(matrix(,0,0), <class>)
339    
340    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
343            work as determinant(matrix(,0,0)).
344    
345            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
346            * man/sparseLU-class.Rd: ditto
347    
348            * R/dgCMatrix.R (determinant): method building on lu()
349            * R/sparseMatrix.R, Matrix.R, ...: ditto
350    
351            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
352    
353    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
356            pattern matrices.
357    
358    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * src/dense.c (dense_to_Csparse): all declarations *before*
361            R_CheckStack(); needed e.g. for ancient gcc 2.96.
362    
363    
364  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
367          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
368    
369            * R/AllClass.R: drop "double" from "atomicVector" class union
370    
371            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
372            * R/dgeMatrix.R: ditto
373    
374          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
375    
376            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
377    
378  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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