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revision 2159, Sat Mar 29 08:09:05 2008 UTC revision 2218, Thu Jul 17 20:26:19 2008 UTC
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1    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
4              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
5              new solve method
6            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
7              Csparse_diagU2N functionality into Matrix_as_cs
8    
9    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
12              vignette
13            * [r2214] R/AllGeneric.R: cosmetic
14            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
15    
16    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
17    
18            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
19              argument with default TRUE
20            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
21              Csparse_diagU2N
22            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
23              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
24              parent array; new solve method for signature(a = "dtCMatrix", b =
25              "sparseMatrix")
26    
27    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/diagMatrix.R (.bdiag): also keep triangular
30            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
31              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
32              bdiag() improvements of last week
33    
34    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
35    
36            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
37              messages
38    
39    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
42            symmetric- or nsparse-Matrix, also fixing the bug introduced with
43            the new version (.999375-10).
44    
45            * tests/Simple.R: regression test for the bugs.
46    
47    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/sparseVector.R (spV2M): fix for "isparseVector".
50            Further, fix <diag> -> <sparseVector> coercion
51            (repSpV): add rep(<sparseVector>, .) method
52    
53            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
54            use as.vector(.).
55    
56            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
57    
58            * R/AllClass.R: new (hidden) class union "scarceMatrix"
59            * R/AllClass.R: sparseVector: add prototype
60    
61            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
62            Kasper Kristensen
63    
64    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * tests/other-pkgs.R: add more interesting Matrix -> graph
67    
68    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
71            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
72    
73    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * DESCRIPTION: release 0.999375-10 to CRAN
76    
77            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
78            .bdiag().
79            * man/bdiag.Rd: update, including test.
80    
81    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * tests/Simple.R: add minimal bdiag() checks
84    
85            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
86              factor out the Tsparse - internal computation into new .bdiag()
87    
88    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/nsparseMatrix.R: specific fast all() and any() methods.
91    
92            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
93            when trying to produce too large result.
94    
95            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
96            very large matrices.
97    
98            * R/sparseMatrix.R (printSpMatrix2): new function, used by
99            show(<sparseMatrix>).
100    
101            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
102    
103    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * src/Mutils.c (m_encodeInd, m_encodeInd2):
106            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
107    
108            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
109            big matrices): -> 2nd argument 'di' instead of 'nr' !
110    
111    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/dtCMatrix.R: faster dgC* -> dtC* method
114            * tests/Simple.R: (hence removed "FIXME")
115    
116            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
117            which can be be turned off for possible speed gains.
118    
119    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
122    
123            * R/not.R: fix !<ldiMatrix>
124            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
125    
126            * R/diagMatrix.R (Ops): fix one-off thinko in
127            <diagonal> o <numeric> methods
128    
129            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
130    
131    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
134            * tests/Simple.R: testing the above
135    
136    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
139    
140    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
143            * NAMESPACE (unname): finally exported
144    
145    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/Auxiliaries.R (cholMat): possibly keep packed
148    
149            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
150            for R < 2.7.0.
151    
152            * R/Tsparse.R ([): for triangularMatrix, check if result may be
153            triangular.
154            * tests/indexing.R: regression test
155    
156    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
159            * R/Ops.R: more methods, for lMatrix/nMatrix
160    
161    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/expm.R: new file for all expm() methods; notably new ones for
164            diagonal*, triangular*, symmetric* and also simple "matrix".
165    
166    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
169    
170            * inst/test-tools.R (assert.EQ.mat): better message when not equal
171    
172            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
173    
174            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
175            [dl]denseMatrix {identical slots; but more logical method dispatch}
176    
177    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
180    
181            * R/diagMatrix.R (determinant): method
182    
183    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
186    
187            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
188    
189            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
190            its diagonal
191    
192    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
195    
196            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
197    
198            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
199    
200            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
201    
202    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
205    
206            * R/Ops.R (.do.Logic.lsparse): fix NA case
207    
208            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
209    
210            * R/Auxiliaries.R (nnzero): fix special cases, using
211            * R/Auxiliaries.R (indDiag): new utility
212            * R/Auxiliaries.R (indTri): new argument 'diag'
213    
214            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
215    
216    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
219    
220            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
221            ".tCMatrix" triangular matrix.
222    
223            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
224            'clx' can be class *or* class representation.
225            (nnzSparse): new.
226            (non0ind): new 'xtendSymm' argument; used in
227            * R/Ops.R:
228    
229            * R/pMatrix.R: more efficient determinant() method
230    
231    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
234            * [disactivated] NAMESPACE: export(det)
235    
236            * R/diagMatrix.R (mkDiag): new substitute for diag()
237    
238            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
239            (as0, as1): new utility.
240    
241            * R/Csparse.R (diag, band): need diagU2N()
242    
243            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
244    
245            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
246    
247            * R/Ops.R (Compare): fix <nsp> o <nsp> case
248    
249            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
250    
251    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Auxiliaries.R (signPerm): new utility for
254            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
255    
256            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
257            since we have our own error handler (and can use tryCatch() from R).
258    
259    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
262    
263            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
264            when not positive definite.
265    
266            * R/Auxiliaries.R (asTri): new auxiliary
267            (non0.i): make *much* faster for Tsparse with many non-zero
268            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
269    
270            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
271            test-tools.R , see below
272    
273            * R/dMatrix.R: fix "Summary" method: + diagU2N()
274    
275            * NAMESPACE, R/Matrix.R: add mean() method
276    
277    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
280            cold-hot colors; try *changed* default useAbs = FALSE
281            * man/image-methods.Rd:  nice examples
282    
283    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * inst/test-tools.R (checkMatrix): new function for modularizing part
286            of tstMatrixClass() in tests/Class+Meth.R
287    
288            * R/dsCMatrix.R: coercion from "matrix"
289            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
290    
291            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
292            add test for as(matrix(,0,0), <class>)
293    
294    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
297            work as determinant(matrix(,0,0)).
298    
299            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
300            * man/sparseLU-class.Rd: ditto
301    
302            * R/dgCMatrix.R (determinant): method building on lu()
303            * R/sparseMatrix.R, Matrix.R, ...: ditto
304    
305            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
306    
307    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
310            pattern matrices.
311    
312    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * src/dense.c (dense_to_Csparse): all declarations *before*
315            R_CheckStack(); needed e.g. for ancient gcc 2.96.
316    
317    
318  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320          * DESCRIPTION (Version): 0.999375-9 --- need to release          * DESCRIPTION (Version): 0.999375-9 --- need to release
321          for R-devel (and R 2.7.0 alpha soon).          for R-devel (and R 2.7.0 alpha soon).
322    
323            * R/AllClass.R: drop "double" from "atomicVector" class union
324    
325            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
326            * R/dgeMatrix.R: ditto
327    
328          * R/sparseMatrix.R (summary): count NAs          * R/sparseMatrix.R (summary): count NAs
329    
330            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
331    
332  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in          * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in

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