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Annotation of /pkg/ChangeLog

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1 : maechler 2108 2008-01-24 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/Ops.R (.Arith.Csparse): new utility factored out of former
4 :     <dgC> o <dgC>, extended for triangular and also used in <dtC> o <dtC>.
5 :    
6 : maechler 2106 2008-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
7 :    
8 :     * tests/factorizing.R (checkSchur): and more tests for checking Schur()
9 :    
10 : maechler 2108 * inst/test-tools.R (isOrthogonal): new function; also file restructured
11 : maechler 2106
12 :     2008-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
13 :    
14 :     * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
15 :     coercion to "nMatrix" and "pMatrix"
16 :    
17 :     * R/AllClass.R: "Schur" class; "number" class union
18 :     * man/number-class.Rd:
19 :     * man/Schur-class.Rd:
20 :    
21 :     * R/eigen.R (.dgeSchur): utility, and return "Schur" class
22 :     (.simpleSchur): Schur() method for diagonal matrices
23 :     (.triSchur): Schur() method for triangular matrices
24 :     (Schur.sym): Schur() for symmetric matrices {building on eigen()}.
25 :    
26 :    
27 :     2008-01-21 Martin Maechler <maechler@stat.math.ethz.ch>
28 :    
29 :     * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
30 :    
31 : maechler 2105 2008-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
32 :    
33 :     * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
34 :     in order to ensure 'system = *' is not lost;
35 :     formals()$system instead of cut&paste.
36 :     * tests/factorizing.R: test solve(<CHM..>, <numeric>)
37 :    
38 : maechler 2102 2008-01-11 Martin Maechler <maechler@stat.math.ethz.ch>
39 : maechler 2096
40 : maechler 2105 * DESCRIPTION (Date): make ready for release --> 0.999375-4
41 : maechler 2096
42 : maechler 2102 * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
43 : maechler 2096
44 : maechler 2098 2007-12-08 Martin Maechler <maechler@stat.math.ethz.ch>
45 : maechler 2096
46 : maechler 2098 * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
47 :     and hence does as.vector(.).
48 :     * man/pMatrix-class.Rd: docs
49 :     * R/sparseMatrix.R: fix for printing "integer sparse"
50 :    
51 :     * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
52 :    
53 :     * R/Matrix.R and others: use "exact" function argument list for
54 :     both "[" : (x, i,j, ..., drop)
55 :     and "[<-" : (x, i,j, ..., value)
56 :    
57 :     * R/denseMatrix.R: M[i] and M[i] <- v (i vector) now work
58 :     * R/Tsparse.R (replTmat): ditto
59 :     * R/diagMatrix.R (replDiag): ditto
60 :     * R/Csparse.R (replCmat): ditto {was it worth the pain?}
61 :     * tests/indexing.R: testing the above
62 :    
63 : maechler 2096 2007-12-07 Martin Maechler <maechler@stat.math.ethz.ch>
64 :    
65 :     * R/sparseMatrix.R (cov2cor): method for sparse matrices
66 :    
67 :     * R/diagMatrix.R ([<-): fix D[ cbind(i,j) ] <- v
68 :    
69 :     * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
70 :    
71 :     * tests/Class+Meth.R: test cbind2, rbind2 and diag<-
72 :    
73 :     2007-12-06 Martin Maechler <maechler@stat.math.ethz.ch>
74 :    
75 :     * R/Matrix.R: "generic" cov2cor() method
76 :    
77 :     * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
78 :     speed up Q %*% D %*% t(Q)
79 :     * tests/dpoMatrix.R: test nearPD()
80 :    
81 :     2007-12-05 Doug Bates and Martin Maechler
82 :    
83 :     * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
84 :     stats::xtabs() allowing to create sparse matrices.
85 :    
86 :     2007-10-08 Martin Maechler <maechler@stat.math.ethz.ch>
87 :    
88 :     * DESCRIPTION (Version): *-4 (released *-3 two days ago)
89 :    
90 : maechler 2081 2007-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
91 :    
92 :     * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
93 :    
94 :     2007-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
95 :    
96 :     * R/LU.R: solve() method for "denseLU"
97 :    
98 :     2007-10-01 Martin Maechler <maechler@stat.math.ethz.ch>
99 :    
100 :     * DESCRIPTION (Version): 0.999375-3 preparing for release
101 :    
102 :     * R/AllGeneric.R: simplify if(.) .. else .. for R <= 2.5.1
103 :    
104 :     * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
105 :    
106 : maechler 2073 2007-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
107 :    
108 :     * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
109 :     thanks to Kasper Kristensen.
110 :     * tests/matprod.R: regression test for that.
111 :    
112 : bates 2069 2007-09-23 17:32 Douglas Bates <bates@stat.wisc.edu>
113 :    
114 :     * [r4778] R/AllGeneric.R: Check R version before defining generics for
115 :     primitives
116 :    
117 : maechler 2073 2007-09-13 Martin Maechler <maechler@stat.math.ethz.ch>
118 :    
119 :     * R/denseMatrix.R (rcond): method
120 :     * R/sparseQR.R (rcond): method, use x or t(x)
121 :    
122 :     2007-09-12 Martin Maechler <maechler@stat.math.ethz.ch>
123 :    
124 :     * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
125 :     matrices.
126 :     * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
127 :    
128 :     * man/rcond.Rd: mention the more general definition, and add
129 :     example for non-square matrices.
130 :    
131 :     * man/chol.Rd: new file, for the S4 chol() generic and all methods.
132 :    
133 :     2007-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
134 :    
135 :     * R/sparseQR.R: add qr.R() method [to be used for rcond()]
136 :    
137 : maechler 2062 2007-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
138 :    
139 :     * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
140 :     * tests/indexing.R: add new regression for the above cases.
141 :    
142 : maechler 2061 2007-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
143 :    
144 :     * src/Mutils.h (__sun): clause for alloca.h on Solaris
145 :    
146 : maechler 2056 2007-08-16 Martin Maechler <maechler@stat.math.ethz.ch>
147 :    
148 :     * DESCRIPTION (Date, Version): 0.999375-2
149 :    
150 :     2007-08-15 Martin Maechler <maechler@stat.math.ethz.ch>
151 :    
152 :     * R/HBMM.R (readMM): make work for pattern matrices as well
153 :    
154 : bates 2050 2007-08-14 13:07 Douglas Bates <bates@stat.wisc.edu>
155 :    
156 :     * [r4730] src/Mutils.h: declare alloca
157 :     * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
158 :     R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
159 :     man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
160 :     src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
161 :     src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
162 :     methods; switch writeMM to use CHOLMOD code; repair readMM
163 :    
164 : maechler 2048 2007-08-14 Martin Maechler <maechler@stat.math.ethz.ch>
165 :    
166 :     * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
167 :     Oehlschlaegel's ... result type still to be discussed!
168 :    
169 : maechler 2043 2007-08-10 Martin Maechler <maechler@stat.math.ethz.ch>
170 :    
171 :     * man/image-methods.Rd: new, combining all image() methods
172 :    
173 :     2007-08-09 Martin Maechler <maechler@stat.math.ethz.ch>
174 :    
175 :     * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
176 :     to work via dgC...
177 :    
178 :     * R/Matrix.R (Matrix): special treatment for "table" (S3)
179 :    
180 :     2007-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
181 :    
182 :     * R/dgTMatrix.R (image): change defaults to
183 :     aspect = "iso", colorkey = FALSE
184 :    
185 : maechler 2039 2007-08-06 Martin Maechler <maechler@stat.math.ethz.ch>
186 :    
187 :     * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
188 :     must copy its *expanded* x slot before LAPACK call.
189 :    
190 :     * tests/matprod.R: test the last days' changes.
191 :    
192 : bates 2041 2007-08-06 16:43 Douglas Bates <bates@stat.wisc.edu>
193 :    
194 :     * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
195 :     as well as in sources
196 : bates 2050 * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
197 :     Lapack call
198 : maechler 2043
199 : maechler 2036 2007-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
200 :    
201 :     * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
202 : maechler 2039 ("Matrix", "matrix") which is needed in some cases.
203 :     Ditto for solve().
204 : maechler 2036
205 :     * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
206 :     infinite recursion in dispatch for some cases.
207 :    
208 : bates 2041 2007-08-02 08:48 Martin Maechler <maechler@stat.math.ethz.ch>
209 : maechler 2036
210 : bates 2041 * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
211 :     so pointers match
212 :    
213 : maechler 2024 2007-08-02 Martin Maechler <maechler@stat.math.ethz.ch>
214 :    
215 : maechler 2036 * DESCRIPTION (Date): set ready for release -- 0.999375-1
216 : maechler 2024
217 : bates 2020 2007-08-01 15:44 Douglas Bates <bates@stat.wisc.edu>
218 :    
219 :     * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
220 :     src/chm_common.c, src/chm_common.h: Change API for
221 :     numeric_as_chm_dense and N_AS_CHM_DN
222 : maechler 2024
223 : maechler 2018 2007-08-01 Martin Maechler <maechler@stat.math.ethz.ch>
224 :    
225 :     * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
226 :     * tests/matprod.R: regr.test for it
227 :    
228 : maechler 2011 2007-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
229 :    
230 :     * R/dMatrix.R: fix from Brian for Math2(., digits = "missing")
231 :     * tests/group-methods.R: and regression-test it
232 :    
233 : bates 2008 2007-07-19 19:45 Douglas Bates <bates@stat.wisc.edu>
234 :    
235 :     * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
236 :     inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
237 :     triplet_to_sparse, documentation, use typedefs
238 : maechler 2011
239 : maechler 2005 2007-07-18 Martin Maechler <maechler@stat.math.ethz.ch>
240 :    
241 :     * man/dpoMatrix-class.Rd: added 'corMatrix' example
242 :    
243 :     * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
244 :     * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
245 :     * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
246 :    
247 :     * R/lsparseMatrix.R: bug fix in "all" method
248 :     * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
249 :    
250 :     * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
251 :     * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
252 :     + matrix |-> nMatrix coercion
253 :     * R/pMatrix.R: + setAs() to dMatrix and from nMatrix
254 :     * man/pMatrix-class.Rd: ditto
255 :    
256 :     * R/Matrix.R (Summary): method for non-dMatrix
257 :    
258 :     * tests/Class+Meth.R (extraValid): new check about "dirty" slots
259 :     * tests/Class+Meth.R (tstMatrixClass): test norm(.);
260 :     test all Summary methods.
261 :    
262 :     2007-07-16 Martin Maechler <maechler@stat.math.ethz.ch>
263 :    
264 :     * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
265 :    
266 :     2007-07-14 Martin Maechler <maechler@stat.math.ethz.ch>
267 :    
268 :     * R/sparseMatrix.R (norm): simple methods for sparseMatrix
269 :    
270 :     * R/pMatrix.R (t?crossprod): methods for pMatrix
271 :    
272 : bates 1987 2007-07-10 Douglas Bates <bates@stat.wisc.edu>
273 :    
274 :     * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
275 :    
276 : bates 1975 2007-07-09 20:45 Douglas Bates <bates@stat.wisc.edu>
277 :    
278 :     * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
279 : maechler 2005 trying to fix a subtle bug - which has been somewhere else.
280 : bates 1975
281 :     2007-07-09 19:43 Martin Maechler <maechler@stat.math.ethz.ch>
282 :    
283 :     * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
284 :     solve the bug
285 :    
286 : maechler 1968 2007-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
287 : bates 1964
288 : maechler 1968 * src/dgCMatrix.c (compressed_to_TMatrix):
289 :    
290 :     2007-07-07 Martin Maechler <maechler@stat.math.ethz.ch>
291 :    
292 :     * src/Csparse.c (Rsparse_validate): new, to have some validity
293 :     checking for RsparseMatrix
294 :     * src/dgCMatrix.c (xRMatrix_validate): ditto
295 :     * src/dtCMatrix.c (tRMatrix_validate): ditto
296 :    
297 :     2007-07-07 Douglas Bates <bates@stat.wisc.edu>
298 :    
299 : bates 1964 * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
300 :     lgRMatrix
301 :     * [r4568] DESCRIPTION: Prepare for bug-fix release
302 : bates 1966 * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
303 :     for declaration of cholmod_symmetry
304 : maechler 1968
305 : maechler 1961 2007-07-06 Martin Maechler <maechler@stat.math.ethz.ch>
306 :    
307 :     * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
308 :     release.
309 :    
310 : maechler 1960 2007-07-06 14:11 Douglas Bates <bates@stat.wisc.edu>
311 :    
312 :     * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
313 :     functions - no longer used
314 :     * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
315 :     src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
316 :     src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
317 :     Alloca
318 :    
319 :     2007-07-06 13:14 Martin Maechler <maechler@stat.math.ethz.ch>
320 :    
321 :     * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
322 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
323 :     src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
324 :     src/t_gCMatrix_colSums.c: more R_CheckStack()s
325 :    
326 :     2007-07-05 18:12 Douglas Bates <bates@stat.wisc.edu>
327 :    
328 :     * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
329 :     the required amount of memory then call M_numeric_as_chm_dense.
330 :     * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
331 :     (like Calloc but calling alloca)
332 :    
333 : maechler 1947 2007-07-05 Martin Maechler <maechler@stat.math.ethz.ch>
334 :    
335 :     * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
336 :     and extended with more sophisticated 'col.names' option.
337 :     * NAMESPACE: export printSparseMatrix()
338 :     * man/printSpMatrix.Rd: document, incl. examples
339 :    
340 : maechler 1960 2007-07-04 16:21 Douglas Bates <bates@stat.wisc.edu>
341 :    
342 :     * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
343 :     src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
344 :     AS_CSP. API change - pass the empty structure to Matrix_as_cs.
345 :    
346 : maechler 1945 2007-07-04 Martin Maechler <maechler@stat.math.ethz.ch>
347 :    
348 :     * DESCRIPTION (Version): 0.99875-4
349 :    
350 :     * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
351 :     some dimnames perservation.
352 :    
353 :     * R/dsTMatrix.R (t-method): keep dimnames
354 :     * R/dtTMatrix.R: ditto
355 :    
356 :     * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
357 :     and ncol(.) < 10
358 :    
359 :     * src/cs_utils.c: drop check_class() and use Matrix_check_class()
360 :     from Mutils.h
361 :    
362 :     * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
363 :     e.g. in as(<ngCMatrix>, "matrix")
364 :    
365 : maechler 1960 2007-07-01 13:27 Douglas Bates <bates@stat.wisc.edu>
366 :    
367 :     * [r4529] .: Create a branch for the API changes from the 0.99875
368 :     series to the 0.999375 series
369 :     * [r4530] DESCRIPTION, inst/include/Matrix.h,
370 :     inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
371 :     src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
372 :     src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
373 :     src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
374 :     as_cholmod_x functions
375 :    
376 :     2007-06-30 09:05 Martin Maechler <maechler@stat.math.ethz.ch>
377 :    
378 :     * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
379 :     trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
380 :     to Comparisons
381 :    
382 :     >>>>>>> .merge-right.r4561
383 : maechler 1932 2007-06-29 Martin Maechler <maechler@stat.math.ethz.ch>
384 :    
385 :     * DESCRIPTION (Version): 0.99875-3 ready to be released.
386 :    
387 :     * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
388 :    
389 :     * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
390 :     that should also work in a future version of R.
391 :    
392 : maechler 1922 2007-06-21 Martin Maechler <maechler@stat.math.ethz.ch>
393 :    
394 :     * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
395 :    
396 :     * R/sparseVector.R: more *sparseVector coercions, notably for
397 :     non - double ones.
398 :    
399 : maechler 1911 2007-06-19 Martin Maechler <maechler@stat.math.ethz.ch>
400 :    
401 :     * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
402 :     notably the new ones building on the new .Call(.)s:
403 :    
404 :     * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
405 :     all 4 of [dlin]gCMatrix_colSums().
406 :    
407 : bates 1909 2007-06-18 16:12 Douglas Bates <bates@stat.wisc.edu>
408 :    
409 :     * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
410 :     * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
411 :     result
412 : maechler 1911
413 : maechler 1903 2007-06-16 Martin Maechler <maechler@stat.math.ethz.ch>
414 :    
415 : maechler 1904 * R/kronecker.R: fix typo (could lead to inf.recursion)
416 :     * test/simple.R: testing that
417 :    
418 : maechler 1903 * R/sparseMatrix.R (prSpMatrix): change to be used as print()
419 : maechler 1922 method as well (which can have arguments, show() can't).
420 : maechler 1903
421 : bates 1902 2007-06-16 15:52 Douglas Bates <bates@stat.wisc.edu>
422 :    
423 :     * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
424 :     added dgCMatrix_colSums for [col,row][Sums,Means]
425 :    
426 : bates 1899 2007-06-15 23:15 Douglas Bates <bates@stat.wisc.edu>
427 : bates 1897
428 :     * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
429 :     src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
430 :     coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
431 :     * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
432 :     class
433 : bates 1899 * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
434 :     man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
435 :     row names to store the levels - duh! Added an example.
436 : maechler 1903
437 : maechler 1893 2007-06-14 Martin Maechler <maechler@stat.math.ethz.ch>
438 :    
439 :     * src/Csparse.c (Csparse_validate): check for *repeated* entries
440 :     thanks to example from Christian Buchta; with a test here:
441 :     * tests/simple.R:
442 :    
443 : maechler 1886 2007-06-07 Martin Maechler <maechler@stat.math.ethz.ch>
444 :    
445 :     * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
446 :     of colSums(*, sparseResult = TRUE)
447 :    
448 : maechler 1883 2007-06-06 Martin Maechler <maechler@stat.math.ethz.ch>
449 :    
450 :     * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
451 :     'na.rm = FALSE' as "everywhere" else in R.
452 :    
453 : bates 1877 2007-06-05 Douglas Bates <bates@stat.wisc.edu>
454 :    
455 : bates 1878 * [r4421] src/CSparse_install.sh: Modify for new organization of
456 : maechler 1883 CSparse package
457 : bates 1877 * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
458 :     SuiteSparse
459 :     * [r4426] src/Makefile: add ./UFconfig to the include path for
460 :     compilation
461 : maechler 1883 * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
462 :     * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
463 :     src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
464 :    
465 : maechler 1870 2007-06-05 Martin Maechler <maechler@stat.math.ethz.ch>
466 :    
467 :     * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
468 :     * R/sparseMatrix.R (prSpMatrix): now gives a message about
469 :     suppressed column names.
470 :    
471 : bates 1868 2007-06-04 17:13 Douglas Bates <bates@stat.wisc.edu>
472 :    
473 :     * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
474 :     src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
475 :     src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
476 :     src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
477 :     src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
478 :     Remove warnings after change to const char* CHAR
479 :    
480 :     2007-06-04 17:11 Douglas Bates <bates@stat.wisc.edu>
481 :    
482 :     * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
483 :     type of M_cholmod_ssmult
484 :    
485 : bates 1863 2007-06-03 14:42 Douglas Bates <bates@stat.wisc.edu>
486 :    
487 :     * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
488 :     src/init.c: Yet another cholmod export - cholmod_ssmult
489 :    
490 : maechler 1855 2007-05-23 Martin Maechler <maechler@stat.math.ethz.ch>
491 :    
492 :     * NAMESPACE: exported drop0(), since
493 :     * man/drop0.Rd: I have seen several cases, I really wanted to use
494 :     it, so our users may want too.
495 :    
496 :     2007-05-22 Martin Maechler <maechler@stat.math.ethz.ch>
497 :    
498 :     * man/colSums.Rd: separately document colSums() etc, since these
499 :     have the extra argument 'sparseResult'.
500 :    
501 : maechler 1852 2007-05-21 Martin Maechler <maechler@stat.math.ethz.ch>
502 :    
503 :     * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
504 :     * man/spMatrix.Rd: docu., including examples
505 :    
506 :     * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
507 :     in order to make colMeans() etc fast *and* correct.
508 :     * R/sparseVector.R (replSPvec): "[<-" functionality for
509 :     sparseVectors; tested in
510 :     * tests/simple.R:
511 :    
512 :     2007-05-19 Martin Maechler <maechler@stat.math.ethz.ch>
513 :    
514 :     * R/sparseMatrix.R (print.sparseSummary): and summary() method for
515 :     (very) sparse Matrices; output similar to Matlab's print().
516 :    
517 : bates 1847 2007-05-17 Douglas Bates <bates@stat.wisc.edu>
518 :    
519 :     * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
520 :     0-based, indices (Jose Quesada <quesada@gmail.com>).
521 :    
522 : bates 1844 2007-05-16 Douglas Bates <bates@stat.wisc.edu>
523 :    
524 :     * R/CHMfactor.R: Added solve methods for a CHMfactor object.
525 :    
526 : maechler 1845 2007-05-16 Martin Maechler <maechler@stat.math.ethz.ch>
527 :    
528 :     * R/Auxiliaries.R (sparsapply): new utility, much faster than
529 :     tapply1() for large sparse matrices.
530 :    
531 :     2007-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
532 :    
533 :     * R/Matrix.R (dim<-): reshape now via sparseVector.
534 :    
535 :     * R/sparseVector.R: methods and function for
536 :     * R/AllClass.R: new "sparseVector" class and daughters.
537 :     * NAMESPACE: export new classes
538 :    
539 : maechler 1837 2007-05-14 Martin Maechler <maechler@stat.math.ethz.ch>
540 :    
541 :     * DESCRIPTION (Version): 0.99875-1
542 :     * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
543 :    
544 : maechler 1834 2007-05-11 Martin Maechler <maechler@stat.math.ethz.ch>
545 :    
546 :     * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
547 :     indexing
548 :     * tests/indexing.R: test set for that.
549 :    
550 : maechler 1833 2007-05-08 Martin Maechler <maechler@stat.math.ethz.ch>
551 :    
552 :     * R/Tsparse.R (replTmat): fix the case of *duplicated* index
553 :     entries.
554 :     * tests/indexing.R(out): add regression test for it
555 :    
556 :     2007-04-30 Martin Maechler <maechler@stat.math.ethz.ch>
557 :    
558 :     * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
559 :     name for "!" method definitions.
560 :    
561 : maechler 1829 2007-04-26 Martin Maechler <maechler@stat.math.ethz.ch>
562 :    
563 :     * R/Tsparse.R (intI): new utility, used for "[" :
564 :     Cleanup up there, and fixes for duplicated indices - more TODO!
565 :    
566 :     * tests/indexing.R(out): more tests
567 :    
568 : bates 1827 2007-04-25 Douglas Bates <bates@stat.wisc.edu>
569 :    
570 :     * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
571 :     code that is now part of the R Lapack library.
572 : maechler 1829
573 : bates 1827 * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
574 :     cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
575 :    
576 : maechler 1829 2007-04-21 Martin Maechler <maechler@stat.math.ethz.ch>
577 :    
578 :     * R/Matrix.R (image): method for all Matrices, not just sparse ones.
579 :    
580 :     2007-04-17 Martin Maechler <maechler@stat.math.ethz.ch>
581 :    
582 :     * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
583 :     up with extraneous names '0'...'<n-1>'
584 :    
585 : maechler 1825 2007-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
586 :    
587 :     * R/dgTMatrix.R (mat2dgT): care about NAs
588 :    
589 :     2007-04-11 Martin Maechler <maechler@stat.math.ethz.ch>
590 :    
591 :     * R/kronecker.R: triangularity preserving methods
592 :    
593 : maechler 1803 2007-03-27 Martin Maechler <maechler@stat.math.ethz.ch>
594 :    
595 :     * R/kronecker.R: new file collecting kronecker() methods in one
596 :     place. Goal: become much faster!
597 :    
598 : maechler 1799 2007-03-23 Martin Maechler <maechler@stat.math.ethz.ch>
599 :    
600 :     * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
601 :     Kristensen based cs_spsolve() instead of _lsolve & _usolve which
602 :     can be much faster.
603 :    
604 :     * tests/matprod.R: add regression tests for these (upper & lower).
605 :    
606 :     2007-03-19 Martin Maechler <maechler@stat.math.ethz.ch>
607 :    
608 :     * R/Matrix.R (diff): method for our Matrices.
609 :    
610 :     * R/sparseMatrix.R (isDiagonal): check dim()!
611 :    
612 :     2007-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
613 :    
614 :     * R/Matrix.R (dim<-): new method for "reshape()" built on a
615 :     proposal from Tamas Papp.
616 :    
617 :     2007-03-16 Martin Maechler <maechler@stat.math.ethz.ch>
618 :    
619 :     * R/AllGeneric.R: remove all if(!isGeneric(.)) clauses
620 :    
621 :     * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
622 : maechler 1803 rather define and export cBind() and rBind() only.
623 :     --> useRs *must* change code that used to have cbind()/rbind() !!
624 : maechler 1799
625 : maechler 1803 * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
626 :     * R/bind.Rout.save: ditto
627 : maechler 1799
628 : bates 1787 2007-02-16 Douglas Bates <bates@r-project.org>
629 :    
630 :     * DESCRIPTION (Date, Version): 0.9975-11 with new date
631 :     * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
632 :     const modifier on declaration of the array 'valid'
633 :    
634 : bates 1786 2007-02-12 Douglas Bates <bates@stat.wisc.edu>
635 :    
636 :     * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
637 :    
638 : maechler 1765 2007-02-05 Martin Maechler <maechler@stat.math.ethz.ch>
639 :    
640 : maechler 1768 * DESCRIPTION (Date, Version): 0.9975-10 with new date.
641 :    
642 : maechler 1767 * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
643 :     * tests/simple.R: test the above and some of these coercions:
644 :    
645 :     * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
646 :     be careful to avoid infinite recursion, using new coercions in
647 :     * R/ngCMatrix.R and nsC... and ntC...
648 :     * R/lsparseMatrix.R: ditto
649 :    
650 : maechler 1765 * R/SparseM-conv.R: more conversion, notably for triplet matrices.
651 :    
652 : maechler 1767 * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
653 :     * R/Rsparse.R: reactivate .Call()s
654 : maechler 1765
655 : maechler 1767 * tests/Class+Meth.R: a bit more on actual classes
656 :    
657 :     2007-02-04 Douglas Bates <bates@stat.wisc.edu>
658 :    
659 :     * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
660 :    
661 : maechler 1760 2007-02-03 Martin Maechler <maechler@stat.math.ethz.ch>
662 : maechler 1758
663 :     * DESCRIPTION (Version): 0.9975-10 to upload
664 :    
665 : maechler 1760 * tests/Class+Meth.R (tstMatrixClass): require coercions to
666 :     specific classes less unconditionally.
667 :    
668 :     * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
669 :    
670 :     * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
671 :    
672 :     * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
673 : maechler 1758 * R/Rsparse.R (.R.2.C): R-level workaround since C-level
674 :     R_to_CMatrix segfaults on one platform.
675 : maechler 1760 Eliminate most coercion method to *specific* classes, and replace
676 :     with virtual classes coercions.
677 : maechler 1758
678 : maechler 1760
679 : maechler 1758 2007-02-01 Martin Maechler <maechler@stat.math.ethz.ch>
680 :    
681 :     * src/init.c: export the CHM...._validate() placeholders, since
682 :     they *are* called.
683 :    
684 : maechler 1760 * tests/Class+Meth.R (classCanCoerce): and starting to test
685 : maechler 1758 all as(<from>, <to>)
686 :    
687 : maechler 1751 2007-01-30 Martin Maechler <maechler@stat.math.ethz.ch>
688 :    
689 :     * R/Tsparse.R ([): more care when subsetting triangular Tsparse
690 :     * tests/indexing.R: tested now
691 :     * tests/indexing.Rout.save: updated
692 :    
693 :     * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
694 :     * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
695 :     appropriate.
696 :    
697 :     * NAMESPACE: export a trivial
698 :     * R/Matrix.R: drop() Matrix-method
699 :    
700 :     * R/AllClass.R: moved all prototypes to virtual super classes.
701 :    
702 :     * R/Rsparse.R: many more coercions to have less exceptions in
703 :     * tests/Class+Meth.R:
704 :    
705 :     * R/Ops.R (Compare): tweak for case with NA
706 :     * tests/simpl.R: hence another 'FIXME' eliminated
707 :    
708 : maechler 1747 2007-01-29 Martin Maechler <maechler@stat.math.ethz.ch>
709 :    
710 : maechler 1748 * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
711 :     objects.
712 :    
713 : maechler 1747 * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
714 :     and more of "!", "&", "|", all, any; coercions
715 :    
716 :     * R/Rsparse.R: many coercions (which enable quite a few other
717 :     methods), thanks to enhancements in
718 :     * src/dgCMatrix.c (R_to_CMatrix): new, and
719 :     * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
720 :     symmetric & triangular and ..RMatrix objects.
721 :    
722 :     * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
723 :     renamed file from src/dsTMatrix.c;
724 :     now dealing with symmetric and triangular Tsparse coercions, both
725 :     to dense and general.
726 :    
727 :     2007-01-27 Martin Maechler <maechler@stat.math.ethz.ch>
728 :    
729 :     * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
730 :    
731 :     * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
732 :     where sensible when the <numeric> is of length > 1.
733 :    
734 :     2007-01-26 Martin Maechler <maechler@stat.math.ethz.ch>
735 :    
736 :     * R/Matrix.R ([<-): for M[] <- value: fix length
737 :    
738 :     2007-01-25 Martin Maechler <maechler@stat.math.ethz.ch>
739 :    
740 :     * R/Auxiliaries.R (n2l_Matrix): new, to be used in
741 :     * R/ndenseMatrix.R: new coercions n* -> l*
742 :    
743 : maechler 1738 2007-01-22 Martin Maechler <maechler@stat.math.ethz.ch>
744 :    
745 :     * R/triangularMatrix.R: new file; simple triu() and tril() methods.
746 :    
747 :     * R/Ops.R ("Logic"): and other "Ops", many updates
748 :    
749 :     2007-01-18 Martin Maechler <maechler@stat.math.ethz.ch>
750 :    
751 :     * src/Mutils.h (SET_DimNames): new utility
752 :    
753 :     * R/Auxiliaries.R (nnzero): improved and now exported via
754 :    
755 :     * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
756 :    
757 : maechler 1725 2007-01-17 Martin Maechler <maechler@stat.math.ethz.ch>
758 :    
759 :     * R/diagMatrix.R (!): fix typo.
760 :    
761 :     2007-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
762 :    
763 :     * R/Auxiliaries.R (as_Csparse): and quite a few others:
764 :     allow to pass class definition --> speedup
765 :     * R/sparseMatrix.R: apply the above
766 :    
767 :     * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
768 :    
769 :     * src/Mutils.h (mMatrix_as_geMatrix): new, based on
770 :     * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
771 :     old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
772 :    
773 :     * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
774 :    
775 :     * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
776 :     and use it for "sparse*" as well, since it's faster than the
777 :     as_Csparse(.) way.
778 :    
779 :     2007-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
780 :    
781 :     * R/Ops.R ("Logic"): more methods, notably an <lgC> o <lgC> one.
782 :    
783 : maechler 1724 2007-01-12 Martin Maechler <maechler@stat.math.ethz.ch>
784 :    
785 :     * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
786 :     as method for M[ ij ] <- v
787 :     * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
788 :    
789 :     * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
790 :     FALSE answer
791 :    
792 :     * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
793 :     * tests/indexing.R: test it, and some of the above
794 :    
795 :     2007-01-05 Martin Maechler <maechler@stat.math.ethz.ch>
796 :    
797 :     * R/Auxiliaries.R (is_duplicatedT): new utility
798 :    
799 : bates 1716 2007-01-05 Douglas Bates <bates@stat.wisc.edu>
800 :    
801 :     * src/init.c (R_init_Matrix): export cholmod_scale
802 :    
803 : maechler 1724 2006-12-30 Martin Maechler <maechler@stat.math.ethz.ch>
804 :    
805 :     * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
806 :     base::as.matrix to (x, ...)
807 :    
808 : maechler 1714 2006-12-28 Martin Maechler <maechler@stat.math.ethz.ch>
809 :    
810 :     * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
811 :     file; start using "Logic", hence
812 :    
813 :     * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
814 :     * NAMESPACE: import and export "Logic"
815 :    
816 :     2006-12-27 Martin Maechler <maechler@stat.math.ethz.ch>
817 :    
818 :     * src/zpotfr.f and dependencies: use LAPACK 3.1 version
819 :     only needed previously to R version 2.5.0.
820 : maechler 1724
821 : maechler 1710 2006-12-26 Martin Maechler <maechler@stat.math.ethz.ch>
822 :    
823 :     * DESCRIPTION (Date, Version): 0.9975-8, ready for release
824 :    
825 :     * R/Tsparse.R (replTmat): fix subassignment of triangular
826 :     * R/Csparse.R (replCmat): ditto
827 :     * tests/indexing.R: more tests, incl the above fix
828 :    
829 :     2006-12-23 Martin Maechler <maechler@stat.math.ethz.ch>
830 :    
831 :     * R/Auxiliaries.R (drop0): extend for non CSparse
832 :     * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
833 :    
834 :     * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
835 :     use uplo correctly (!); other places: use uplo_P() macro
836 :    
837 :     * R/Csparse.R (replCmat): call diagU2N() when needed
838 :     * R/Tsparse.R (replTmat): ditto
839 :    
840 :     * src/dtCMatrix.c (tCMatrix_validate): new
841 :     * src/dtTMatrix.c (tTMatrix_validate): new, used in
842 :     * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
843 :    
844 :     * R/diagMatrix.R (replDiag): to use in [<-
845 :    
846 : maechler 1708 2006-12-22 Martin Maechler <maechler@stat.math.ethz.ch>
847 :    
848 :     * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
849 :     also more general diagU2N().
850 :    
851 :     2006-12-21 Martin Maechler <maechler@stat.math.ethz.ch>
852 :    
853 :     * R/bind2.R: new file for all cbind2(), rbind() methods moved here
854 :     from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
855 :    
856 : maechler 1707 2006-12-20 Martin Maechler <maechler@stat.math.ethz.ch>
857 :    
858 :     * tests/bind.R: a few more cases
859 :     * R/Auxiliaries.R (.M.kind): also work for atomic vectors
860 :    
861 :     * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
862 :     * R/ddenseMatrix.R (cbind2/rbind2)
863 :     * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
864 :     * tests/indexing.R
865 :     * tests/indexing.Rout.save: updated
866 :    
867 :     2006-12-18 Martin Maechler <maechler@stat.math.ethz.ch>
868 :    
869 :     * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
870 :     * tests/indexing.R
871 :    
872 : maechler 1705 2006-12-15 Martin Maechler <maechler@stat.math.ethz.ch>
873 :    
874 :     * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
875 :     align with proper position of "0", i.e., right for integers.
876 :     argument 'align' by default is "fancy".
877 :    
878 :     2006-12-14 Martin Maechler <maechler@stat.math.ethz.ch>
879 :    
880 :     * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
881 :     * R/Csparse.R: and fix "Compare" for more cases.
882 :     * tests/Class+Meth.R: test some of these (m == m, m != m)
883 :    
884 :     2006-12-13 Martin Maechler <maechler@stat.math.ethz.ch>
885 :    
886 :     * R/lsparseMatrix.R: all() and any() methods
887 :     * R/ldenseMatrix.R: ditto
888 :     * NAMESPACE, R/Matrix.R: ditto
889 :    
890 :     * man/all-methods.Rd: document them minimally
891 :    
892 :     * tests/simple.R: add a few examples for these
893 :    
894 : maechler 1696 2006-12-11 Martin Maechler <maechler@stat.math.ethz.ch>
895 :    
896 :     * R/Tsparse.R ([): fix long standing typo in symmetric case
897 :     * man/dsCMatrix-class.Rd: add example exhibiting the above case
898 :    
899 : bates 1691 2006-12-10 Douglas Bates <bates@stat.wisc.edu>
900 :    
901 :     * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
902 :     to LL before converting to a sparse matrix. (The LDL form can be
903 :     converted to a sparse matrix but it is implicitly a unit
904 :     triangular matrix and a diagonal matrix overwritten on the diagonal.)
905 :    
906 :     2006-12-09 Douglas Bates <bates@stat.wisc.edu>
907 :    
908 :     * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
909 :    
910 : bates 1688 2006-12-08 Douglas Bates <bates@stat.wisc.edu>
911 :    
912 :     * DESCRIPTION (Version): updated -> release 0.9975-7
913 :     * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
914 :    
915 : maechler 1682 2006-11-30 Martin Maechler <maechler@stat.math.ethz.ch>
916 :    
917 :     * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
918 :    
919 : bates 1681 2006-11-29 Douglas Bates <bates@stat.wisc.edu>
920 :    
921 :     * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
922 :     * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
923 :     is exactly singular.
924 :    
925 : maechler 1674 2006-11-07 Martin Maechler <maechler@stat.math.ethz.ch>
926 :    
927 :     * DESCRIPTION (Date): updated -> release 0.9975-6
928 :    
929 : maechler 1673 2006-11-06 Martin Maechler <maechler@stat.math.ethz.ch>
930 :    
931 :     * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
932 :     now returns symmetric.
933 :    
934 :     * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
935 :    
936 :     * R/Matrix.R (.M.sub.i.2col): new, for M[ cbind(i,j) ] indexing.
937 :     * R/Matrix.R (.M.repl.i.2col): new, for M[ cbind(i,j) ] <- value
938 :    
939 :     * R/Auxiliaries.R (.type.kind): added
940 :    
941 :     2006-11-04 Martin Maechler <maechler@stat.math.ethz.ch>
942 :    
943 :     * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
944 :     running src/CSparse_install.sh
945 :    
946 :     * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
947 :    
948 : maechler 1665 2006-11-03 Martin Maechler <maechler@stat.math.ethz.ch>
949 :    
950 :     * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
951 :     * R/dsCMatrix.R (solve): "fully-sparse" using the above.
952 :    
953 :     * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
954 :    
955 :     * tests/Class+Meth.R (tstMatrixClass): now assure
956 :     the (important in method programming) property :
957 :    
958 :     ###>> Every "Matrix" is either
959 :     ###>> "general*", "symmetric*", "triangular*" or "diagonal*"
960 :    
961 :     (where "*" stands for "Matrix")
962 :    
963 :     * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
964 :    
965 :     * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
966 :     * tests/validObj.R: checks for "comparison"
967 :    
968 :     * R/sparseMatrix.R ([): improved indexing for sparse;
969 :     trying to keep <symmetric>[ n, n] symmmetric
970 :    
971 :     * tests/indexing.R: indexing for logical sparse now ok
972 :    
973 :    
974 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
975 :    
976 : maechler 1661 * src/Tsparse.c: use xTsparse_validate() , and hence remove
977 :    
978 :     * src/{ltC,lsC,lgT}Matrix.[ch]: removed
979 :    
980 :     2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
981 :    
982 : maechler 1660 * R/AllClass.R (Matrix-class): check length of dimnames in validity.
983 :    
984 :     * tests/simple.R: validObject() checking the above.
985 :    
986 : maechler 1665 * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
987 : maechler 1660 replacing both dgCMatrix_validate and lgCM*.
988 :    
989 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
990 :     fix dimnames setting in other places.
991 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
992 :    
993 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
994 :    
995 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
996 :    
997 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
998 :     symmetry test, via
999 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
1000 :    
1001 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
1002 :    
1003 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1004 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1005 :     <CsparseMatrix>) added
1006 :    
1007 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
1008 :    
1009 :     * tests/matprod.R: add a variation of Harri's example
1010 :    
1011 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1012 :     recursive infinitely.
1013 :    
1014 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1015 :    
1016 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1017 :    
1018 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
1019 :    
1020 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1021 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
1022 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1023 :     satisfy the above test.
1024 :    
1025 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
1026 :    
1027 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
1028 :    
1029 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
1030 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1031 :     RHS = NULL.
1032 :    
1033 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1034 :     add more (needed) [t]crossprod() methods.
1035 :    
1036 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1037 :    
1038 :     * R/Auxiliaries.R (as_CspClass): cleanup
1039 :     (drop0): internal utility for "Csparse_drop(*, 0)"
1040 :     (.bail.out.2): encourage active feedback
1041 :    
1042 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
1043 :    
1044 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
1045 :    
1046 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1047 :     non-valid or 'sorted' case).
1048 :    
1049 :     * R/dsparseMatrix.R: add "chol" method.
1050 :     * R/ddenseMatrix.R: ditto
1051 :    
1052 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
1053 :     * NAMESPACE (Ops)
1054 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
1055 :     coercion; deprecating direct lower level coercions.
1056 :    
1057 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
1058 :    
1059 :    
1060 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
1061 :    
1062 :     * DESCRIPTION (Version): 0.9975-5 ready for release
1063 :    
1064 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
1065 :    
1066 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1067 :    
1068 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
1069 :    
1070 :     * R/AllClass.R (corMatrix): add 'validity' check;
1071 :     comment out unused "LDL" class definition
1072 :     * NAMESPACE: mention, but do not export "LDL" class
1073 :     * R/corMatrix.R: new (simple), needed for R-devel with
1074 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1075 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1076 :    
1077 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
1078 :    
1079 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1080 :     use Rprintf and R's error handling.
1081 :    
1082 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
1083 :    
1084 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1085 :     * tests/matprod.R: add tests for the bug fixed.
1086 :    
1087 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
1088 :    
1089 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1090 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1091 :    
1092 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
1093 :    
1094 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
1095 : bates 1624
1096 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1097 :    
1098 :     * DESCRIPTION (Version): 0.9975-3
1099 :    
1100 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
1101 :     (sparse) matrices.
1102 :     * man/bdiag.Rd: docu + examples
1103 :    
1104 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1105 :    
1106 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1107 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1108 :    
1109 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1110 :     that result is sparse or diagonal (and not dense).
1111 :    
1112 :     * man/Subassign-methods.Rd: fix examples
1113 :    
1114 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
1115 :     should always return a sparse (and not sometimes a diagonal) matrix.
1116 :    
1117 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
1118 :    
1119 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1120 :    
1121 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
1122 :    
1123 :     * DESCRIPTION (Version): 0.9975-2
1124 : maechler 1615
1125 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1126 :    
1127 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
1128 :    
1129 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
1130 :    
1131 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1132 :    
1133 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1134 :    
1135 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
1136 :     * R/nsTMatrix.R: " 'for completeness'
1137 :    
1138 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
1139 :    
1140 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1141 :    
1142 :    
1143 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
1144 :    
1145 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1146 :     included.
1147 :    
1148 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1149 :     Export C-callable functions used in Zt_create in lme4.
1150 :    
1151 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1152 :    
1153 :     * DESCRIPTION (Version): 0.9975-1
1154 :    
1155 :     * tests/simple.R: less checks fail; using NA, found that our
1156 :     kronecker() is not base-compatible with NA's.
1157 :    
1158 :     * R/dMatrix.R: "Compare" method now implemented for all cases
1159 :    
1160 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1161 :    
1162 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
1163 :    
1164 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
1165 :     * src/dspMatrix.c (dspMatrix_validate): ditto
1166 :    
1167 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1168 :     including coercion to [nl]tTMatrix.
1169 :    
1170 :     * R/diagMatrix.R (show): print a header line as for other classes.
1171 :    
1172 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
1173 :    
1174 :     * src/Makefile.win (SUBDIRS): fix typo
1175 :    
1176 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
1177 :    
1178 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1179 :    
1180 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
1181 :    
1182 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1183 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
1184 :     accept a symmetric matrix).
1185 :     * tests/group-methods.R: Uncomment test of crossprod applied to
1186 :     lsCMatrix objects.
1187 :    
1188 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
1189 :    
1190 :     * R/AllClass.R (symmetricMatrix): add validity method (available
1191 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1192 :    
1193 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1194 :    
1195 :     * tests/indexing.Rout.save:
1196 :     * tests/indexing.R: additions, mainly for 'lsparse'
1197 :    
1198 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1199 :     case.
1200 :    
1201 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1202 :    
1203 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1204 :    
1205 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1206 :     as 'N' (1-letter - Ok?)
1207 :    
1208 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
1209 :    
1210 :     * R/dMatrix.R ("Compare"): fix to work with NA's
1211 :    
1212 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1213 :    
1214 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1215 :     which is implemented.
1216 :    
1217 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
1218 :    
1219 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
1220 :     typecasting; needed for "l" matrix handling in cholmod.
1221 : maechler 1565
1222 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
1223 :    
1224 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1225 :     (Tsp2grNEL): other fixes needed
1226 :    
1227 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
1228 :    
1229 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1230 :     Matrices, since "lMatrix", also "lsparseM" can have NA
1231 :     * R/ndenseMatrix.R, etc: new source files
1232 :     * man/nsparseMatrix-classes.Rd, etc: new help files
1233 :     * tests/: adaptions
1234 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
1235 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1236 : maechler 1582 * src/Csparse.c, etc: ditto
1237 : maechler 1548
1238 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
1239 :    
1240 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
1241 :     alloc_d**Matrix functions to the lme4 package.
1242 :    
1243 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
1244 :    
1245 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1246 : maechler 1544 fixed
1247 : bates 1543
1248 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
1249 :    
1250 : maechler 1548 * R/lMatrix.R: new
1251 :    
1252 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1253 :    
1254 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1255 : maechler 1582 * man/tcrossprod.Rd: ditto
1256 : maechler 1544
1257 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
1258 :    
1259 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1260 :     for exported functions
1261 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1262 :     Remove partitioning algorithms for sparse matrix reordering. The
1263 :     copyright on the Metis code was problematic and the methods were
1264 :     rarely used.
1265 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
1266 :     operations are now done entirely in CHOLMOD code.
1267 :    
1268 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
1269 :    
1270 :     * src/Mutils.h: Remove functions that are no longer used.
1271 :    
1272 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
1273 :    
1274 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1275 :     * src/DEPS.mkf: update
1276 :    
1277 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
1278 :    
1279 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
1280 :     * DESCRIPTION (Version): 0.9975-0
1281 :     (Depends): R (>= 2.4.0)
1282 :    
1283 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
1284 :    
1285 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1286 :    
1287 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
1288 :    
1289 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1290 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
1291 :    
1292 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1293 :    
1294 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1295 :    
1296 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1297 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1298 : maechler 1582 * R/dsparseMatrix.R: ditto
1299 :     * R/Csparse.R: ditto
1300 : maechler 1472
1301 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1302 :    
1303 :     * R/dMatrix.R (Compare): improve availability of "<", etc
1304 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1305 :    
1306 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
1307 :    
1308 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1309 :     of a 0-index which was used as 1-index (..hmm)
1310 :    
1311 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1312 :    
1313 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1314 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1315 : maechler 1582 (.is.diagonal): ditto
1316 : maechler 1467
1317 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1318 :    
1319 :     * R/Matrix.R (Matrix): also work for NA data
1320 :    
1321 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
1322 :    
1323 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1324 :     in all cases.
1325 :    
1326 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
1327 :    
1328 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1329 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1330 :    
1331 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1332 :    
1333 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1334 :     subclasses of "ddenseMatrix"
1335 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1336 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1337 :     instead of half dozen specialized ones.
1338 :    
1339 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
1340 :    
1341 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1342 :     <tillard@cirad.fr> - ordering standard errors to match effects.
1343 :    
1344 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
1345 : bates 1431
1346 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1347 :     on R_ldl.
1348 :     * R/lCholCMatrix.R,
1349 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1350 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1351 :     * many files in ./R and ./src: Use more general version of
1352 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
1353 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1354 :     dtpMatrix, dspMatrix and dppMatrix conversions.
1355 :    
1356 : maechler 1447
1357 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
1358 :    
1359 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1360 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1361 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1362 :     dgeMatrix_crossprod (may need to do this in other places).
1363 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1364 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
1365 :    
1366 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
1367 :    
1368 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1369 :     types of classed Matrices, matrices or numeric or logical vectors.
1370 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1371 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1372 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
1373 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
1374 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1375 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
1376 :     * src/Csparse.c: use diag_P and uplo_P macros.
1377 : maechler 1447
1378 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
1379 :    
1380 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1381 : maechler 1447 valgrind.
1382 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1383 :     inverses.
1384 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1385 :     -Wall warnings.
1386 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1387 :     Use dup_mMatrix_as_dgeMatrix.
1388 : maechler 1447
1389 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
1390 :    
1391 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1392 :     * tests/sparseQR.R: Added
1393 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
1394 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1395 :    
1396 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
1397 :    
1398 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1399 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1400 :     and qr.fitted.
1401 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1402 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1403 :    
1404 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
1405 :    
1406 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1407 :     the base version has no "..." argument.
1408 :    
1409 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1410 :    
1411 :     * R/Matrix.R: define and
1412 :     * NAMESPACE: export as.numeric() and as.logical() methods.
1413 :     Let's hope these do not badly slow down something...
1414 :     Finally export the zapsmall() method.
1415 :    
1416 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
1417 :    
1418 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1419 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1420 :     * src/dtCMatrix.c :Remove code that is no longer used
1421 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1422 :    
1423 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
1424 :    
1425 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1426 :     Csparse_to_logical and Csparse_symmetric_to_general.
1427 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1428 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
1429 : bates 1373
1430 :     2006-08-14 Douglas Bates <bates@R-project.org>
1431 :    
1432 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1433 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1434 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1435 :     possible.
1436 :    
1437 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
1438 :    
1439 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1440 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1441 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1442 :     generalize conversions between TsparseMatrix, CsparseMatrix,
1443 :     denseMatrix and matrix. Preserve triangularity property and
1444 :     propagate Dimnames in the easy cases.
1445 :    
1446 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
1447 :    
1448 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
1449 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1450 :     before S4SXP but for the wrong reasons.
1451 :    
1452 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
1453 :    
1454 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
1455 :     Later modified to return the upper triangle only.
1456 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
1457 : maechler 1389
1458 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
1459 :    
1460 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
1461 :     R-level conversion to a sparse symmetric class.
1462 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
1463 :     Remove conversion to sparse symmetric classes (now done in C code).
1464 :    
1465 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1466 :    
1467 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
1468 :     * man/band.Rd: adapt the \dontshow{} unit test.
1469 :    
1470 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
1471 :    
1472 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
1473 :    
1474 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
1475 :    
1476 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
1477 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
1478 :    
1479 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
1480 :     * R/Tsparse.R (tril, triu, band): methods
1481 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
1482 :     * man/band.Rd: ditto
1483 : maechler 1349
1484 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1485 :    
1486 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
1487 :     to be up-to-date automatically.
1488 :    
1489 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1490 :    
1491 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
1492 :    
1493 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
1494 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
1495 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
1496 :     such that the S4 objects are always created by the current version
1497 :     of R and 'Matrix' class definitions.
1498 :    
1499 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
1500 :    
1501 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
1502 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
1503 : bates 1342 boundary and test cases.
1504 :    
1505 :     * src/lmer.c (mer_postVar): Modified to return the variances that
1506 :     are marginal to the fixed effects, not conditional on them (which
1507 :     is what the bVar slot contents represent).
1508 :    
1509 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
1510 :    
1511 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
1512 :     function which calls the C function mer_hat_trace2.
1513 : maechler 1346
1514 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
1515 :     producing a caterpillar plot.
1516 : bates 1338
1517 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
1518 :    
1519 :     * NAMESPACE: change "correlation" to "corMatrix"
1520 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
1521 : bates 1352 * R/dpoMatrix.R: ditto
1522 :     * R/lmer.R: ditto
1523 : maechler 1335
1524 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
1525 :    
1526 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
1527 :     RZXinv slot's contents into a separate internal function that can
1528 :     be used in mer_hat_trace.
1529 :    
1530 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
1531 :    
1532 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
1533 :     via new smart
1534 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
1535 :     utility functions.
1536 :    
1537 :    
1538 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
1539 :    
1540 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
1541 :     matrices when appropriate; band() even symmetric ones.
1542 :     (replCmat): extend to potentially all "CsparseMatrix"
1543 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
1544 :     allow subassignment for special sparse matrices.
1545 :    
1546 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
1547 :    
1548 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
1549 :     argument; in glmer_*(): print only if(verbose).
1550 :    
1551 :     speed-optimize a few places by moving REAL(.) out of loops.
1552 :    
1553 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
1554 :    
1555 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
1556 :    
1557 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
1558 :     since that wrongly triggers also for M[ logi , ]
1559 :    
1560 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
1561 :     a symmetric matrix that results in a non-symmetric one.
1562 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
1563 :    
1564 :     * R/dMatrix.R: make round(M) work as round(M, 0)
1565 :    
1566 :     * R/dgTMatrix.R (image): coordinate system and axis now use
1567 :     1-based indices, not 0-based ones.
1568 :    
1569 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
1570 :     * tests/indexing.R: test it.
1571 :    
1572 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
1573 :     * man/isSymmetric-methods.Rd: and document it.
1574 :    
1575 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
1576 :     * man/SparseM-conv.Rd: docu them
1577 :    
1578 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
1579 :     for 'SparseM' conversions
1580 :    
1581 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
1582 :    
1583 :     * R/Matrix.R (head): added head() and tail() methods.
1584 :    
1585 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
1586 :    
1587 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
1588 :    
1589 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
1590 :    
1591 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
1592 :     add check for correct printing of symmetric sparse matrices.
1593 :    
1594 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
1595 :     for sparse symmetric matrices.
1596 :    
1597 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
1598 :     diagonal twice.
1599 :    
1600 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
1601 :    
1602 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
1603 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
1604 : bates 1316
1605 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
1606 :    
1607 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
1608 :    
1609 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
1610 :    
1611 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
1612 :    
1613 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
1614 :     * R/lgCMatrix.R (diag): for new method
1615 :    
1616 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
1617 :     ==> construction of illegal "*gTMatrix" via new() should
1618 :     now be much less easy:
1619 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
1620 :    
1621 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
1622 :     directly.
1623 :     * man/Matrix.Rd: documents it.
1624 :    
1625 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
1626 :    
1627 :     * src/pedigree.c (pedigree_inbreeding): Correction in
1628 :     initialization. This function is not currently being used and is
1629 :     not fully tested.
1630 :    
1631 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
1632 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
1633 :     objects. Modified validity check on pedigree objects to account
1634 :     for nonparallel patterns of missingness of parents.
1635 : bates 1311
1636 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
1637 :     class.
1638 : maechler 1315
1639 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
1640 :    
1641 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
1642 :    
1643 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
1644 :    
1645 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
1646 :    
1647 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
1648 :     the output from mcmcsamp.
1649 :    
1650 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
1651 :    
1652 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
1653 :     of the hat matrix.
1654 : bates 1298
1655 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
1656 :    
1657 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
1658 :     classes.
1659 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
1660 : maechler 1295
1661 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
1662 :    
1663 :     * R/dgTMatrix.R (colSums): etc. All four of
1664 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
1665 :     all "Matrices".
1666 :    
1667 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
1668 :    
1669 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
1670 :     background grid to the qqmath plot of ranef.lmer.
1671 :    
1672 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
1673 : bates 1284
1674 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
1675 :     grouping factors to be specified in the formula as (1|foo/bar).
1676 :    
1677 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1678 :    
1679 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
1680 :     !is.language to resolve the bug reported by Jacob Wegelin.
1681 :    
1682 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
1683 :     code to evaluate inbreeding coefficients without calculating T,
1684 :     based on code in Sargolzaei and Iwaisaki's paper.
1685 :    
1686 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
1687 :    
1688 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
1689 :     generic and mer methods for isNested and denomDF. This denomDF was
1690 :     an attempt to emulate that in lme but I don't think that makes
1691 :     sense. Use the trace of the hat matrix instead.
1692 :    
1693 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
1694 :    
1695 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
1696 :     the C code depending on a slot structure that's no longer valid.
1697 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
1698 : maechler 1271
1699 :    
1700 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
1701 :    
1702 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
1703 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
1704 :     and added a general band extractor.
1705 :    
1706 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
1707 :    
1708 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
1709 :     allowable range with NAs. Added a corresponding check in the
1710 :     validity check for the pedigree class.
1711 :    
1712 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
1713 :     crossprod methods now inherits from symmetricMatrix.
1714 :    
1715 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
1716 :    
1717 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
1718 :     generics lowerTriMatrix and upperTriMatrix along with methods for
1719 :     the Csparse virtual class. Also added a C function Csparse_band
1720 :     that implements these methods by calling cholmod_band.
1721 :    
1722 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
1723 :    
1724 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
1725 :     erased when it was NULL. This led to invalid subselections!
1726 :    
1727 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
1728 :    
1729 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
1730 :     in method for "t" so as not to lose the unit diagonal property.
1731 :    
1732 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
1733 :    
1734 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
1735 :     and methods. This is now an option to the ranef method for the
1736 :     mer class.
1737 :    
1738 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
1739 :     compressed column-oriented matrix. Minor formatting cleanup.
1740 :    
1741 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
1742 :     objects.
1743 :    
1744 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
1745 :    
1746 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
1747 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
1748 :    
1749 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
1750 :    
1751 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
1752 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
1753 :    
1754 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
1755 :     for the dtCMatrix class.
1756 : maechler 1253
1757 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
1758 :    
1759 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
1760 :     and methods for it.
1761 :    
1762 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
1763 :    
1764 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
1765 :     arguments, such that M %*% 1:6 now works
1766 :     * Tests/matprod.R: test the above
1767 :    
1768 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
1769 : bates 1243
1770 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
1771 :     the ranef.lmer class.
1772 :    
1773 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
1774 :     methods to extract the posterior variances from the bVar slot.
1775 :    
1776 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
1777 :    
1778 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
1779 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
1780 :    
1781 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
1782 :     * tests/simple: (extended)
1783 :    
1784 :     * R/sparseMatrix.R (isTriangular): now using much improved
1785 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
1786 :    
1787 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
1788 :    
1789 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
1790 :     (problem report from Franklin Parlamis). This should be done
1791 : maechler 1238 generally.
1792 : bates 1236
1793 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
1794 :    
1795 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
1796 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
1797 :     update the plot methods.
1798 :    
1799 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
1800 :    
1801 :     * R/lmer.R (resid and ranef methods): Added methods for the
1802 :     "residuals" and "resid" generic but only for linear mixed model
1803 :     fits. Changed the ranef method to return a list of data frames so
1804 :     that the plot methods now work.
1805 :    
1806 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
1807 :    
1808 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
1809 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
1810 :    
1811 :     * DESCRIPTION (Date): New release
1812 :    
1813 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
1814 :    
1815 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
1816 :    
1817 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
1818 :     * man/KNex.Rd: and other help files
1819 :     * tests/*.R: several ones needed adaption
1820 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
1821 : maechler 1228
1822 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
1823 :    
1824 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
1825 :    
1826 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
1827 :    
1828 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1829 :    
1830 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
1831 :    
1832 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
1833 :    
1834 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
1835 :    
1836 :     * R/dMatrix.R: enable things like M [ M < 10 ]
1837 :     * R/dgeMatrix.R: implement it
1838 :    
1839 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
1840 :    
1841 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
1842 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
1843 :     * R/lmer.R (show): now works with summary()
1844 :    
1845 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
1846 :    
1847 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
1848 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
1849 :     support the above
1850 :    
1851 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
1852 :    
1853 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
1854 :     Use glmFit$prior.weights for weights in a glmm.
1855 :     Allow an option usePQL = FALSE to skip the PQL steps for the
1856 :     Laplace method (and, in time, the AGQ method).
1857 :    
1858 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
1859 :     into a separate function internal_mer_Xfactor to be able to call
1860 :     it from internal_bhat.
1861 :    
1862 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
1863 :    
1864 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
1865 :     testing; now again of all actual classes.
1866 :    
1867 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
1868 :     use macros and define make_d_matrix_* and make_i_matrix_*
1869 :     where _i_ is for the ldense routines:
1870 :    
1871 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
1872 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
1873 :    
1874 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
1875 :    
1876 :    
1877 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
1878 :    
1879 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
1880 :     many different kinds of matrices.
1881 :     * R/*.R: quite a few new methods were needed for R CMD check with
1882 :     new Matrix(). Very good for users playing around.
1883 :    
1884 :    
1885 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
1886 :    
1887 :     * src/dgeMatrix.c (dMatrix_validate): new
1888 :     * src/Mutils.c (dense_nonpacked_validate): new
1889 :    
1890 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
1891 :    
1892 :    
1893 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
1894 :    
1895 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
1896 :    
1897 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
1898 : bates 1119
1899 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
1900 :    
1901 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
1902 :     segfault in cases with multiple non-nested grouping factors.
1903 :    
1904 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
1905 :    
1906 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
1907 :     (Depends): also on 'utils'
1908 :    
1909 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
1910 :     * R/diagMatrix.R (Diagonal): constructor and methods for
1911 :     diagonal matrices
1912 :    
1913 :     * R/ltTMatrix.R: new "minimal methods"
1914 :    
1915 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
1916 :    
1917 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
1918 :     all methods (and help files).
1919 :    
1920 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
1921 :    
1922 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
1923 :     for case (dimn. op no_dimn.)
1924 :    
1925 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
1926 :    
1927 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
1928 : maechler 1084
1929 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
1930 :    
1931 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
1932 :     by Julian Faraway.
1933 :    
1934 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
1935 :    
1936 :     * R/Auxiliaries.R (try_as): new utility
1937 :     * R/sparseMatrix.R: use try_as() in coercion to original class
1938 :    
1939 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
1940 :    
1941 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
1942 :    
1943 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
1944 :    
1945 :     * R/Auxiliaries.R (dimNamesCheck): added
1946 :    
1947 :     * R/Matrix.R (as.array), (as.vector): new
1948 :    
1949 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
1950 :    
1951 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
1952 : maechler 956 default.
1953 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
1954 :     "pMatrix" now contains "sparseMatrix"
1955 : maechler 954
1956 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
1957 :    
1958 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
1959 :    
1960 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
1961 :    
1962 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
1963 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
1964 :    
1965 :     * R/dspMatrix.R: typo in "t" method
1966 :    
1967 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
1968 :    
1969 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
1970 :     * R/Tsparse.R: instead of R/gTMatrix.R
1971 :     * R/Csparse.R: new
1972 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
1973 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
1974 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
1975 :     via cholmod
1976 :    
1977 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
1978 :    
1979 :     * R/Auxiliaries.R (non0ind): new function using new C code
1980 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
1981 :    
1982 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
1983 :    
1984 :     * src/chm_common.h: header file required by all C sources that
1985 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
1986 : bates 917 called 'c' whose address is passed as the last argument to
1987 :     (virtually) every CHOLMOD function.
1988 :    
1989 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
1990 :    
1991 :     * src/init.c: initialize and finalize the cholmod_common structure.
1992 :    
1993 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1994 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
1995 :    
1996 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
1997 :    
1998 :     * inst/test-tools.R: new file collecting the utility functions used
1999 :     in ./tests/*.R
2000 :    
2001 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
2002 :     * R/Matrix.R (cbind2): methods for NULL and missing
2003 :    
2004 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
2005 :    
2006 :     * R/AllClass.R: new "index" class for "[" and "[<-":
2007 :     First cut at "symmetricMatrix" and "triangularMatrix"
2008 :     * R/gTMatrix.R (.ind.prep): new function;
2009 : maechler 1174 Logical and character indexing now work too.
2010 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
2011 :     * tests/indexing.R: new, including *.Rout.save
2012 :     * tests/dgTMatrix.R: new
2013 :    
2014 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
2015 :    
2016 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
2017 :     indicator pos not being updated. Also enforced upper triangular
2018 :     for symmetric case. Need to coerce edges component of elements of
2019 :     edge list - grr! (Why don't they define their classes cleanly?)
2020 :    
2021 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
2022 :    
2023 :     * R/Matrix.R: added first "[<-" methods; not yet functional
2024 : bates 1352 * R/denseMatrix.R: ditto
2025 : maechler 871 * man/Subassign-methods.Rd: new help file for these
2026 :    
2027 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
2028 :    
2029 :     * DESCRIPTION (Version): 0.98-6
2030 :    
2031 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
2032 :     matrices.
2033 :    
2034 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
2035 :    
2036 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
2037 :     as( <logical>, "matrix")
2038 :    
2039 :     * R/pMatrix.R: coercion to "lgTMatrix"
2040 :    
2041 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
2042 :     * man/gTMatrix-class.Rd:
2043 :     * General slight re-organization of where "[" methods are defined.
2044 :     more to come.
2045 :    
2046 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
2047 : maechler 868
2048 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
2049 : maechler 871
2050 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
2051 :     * .....
2052 :    
2053 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
2054 :    
2055 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
2056 :     or glmer objects.
2057 :    
2058 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
2059 :    
2060 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
2061 :    
2062 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
2063 :    
2064 :     * R/HBMM.R: finish re-writing R-only code.
2065 :    
2066 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
2067 :    
2068 :     * man/externalFormats.Rd: move documentation for writeHB and
2069 :     writeMM here.
2070 :    
2071 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
2072 :     (suggested by Paul Roecker).
2073 :    
2074 :     * tests/validObj.R (assertError): Comment out test that is failing
2075 :     after recent changes in r-devel.
2076 :    
2077 : maechler 860
2078 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
2079 :    
2080 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
2081 :     * man/denseMatrix-class.Rd
2082 :     * NAMESPACE: export it, and also export
2083 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
2084 :    
2085 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
2086 :    
2087 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
2088 :    
2089 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
2090 :     matrix_solve code (which was really, really wrong).
2091 :    
2092 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
2093 : maechler 834
2094 :     * DESCRIPTION (Version): 0.98-2
2095 :    
2096 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
2097 :    
2098 :     * R/lmer.R (abbrvNms): new
2099 :     * R/lmer.R (mcmcsamp): allow transformed parameters
2100 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
2101 :     for the Harwell-Boeing and the MatrixMarket formats.
2102 : maechler 834
2103 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
2104 :    
2105 :     * man/dtrMatrix-class.Rd: add examples
2106 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
2107 : maechler 834
2108 :     * TODO: note the dtpMatrix (docu) bug
2109 :    
2110 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
2111 :     in order to ensure that new as.matrix() is used by old functions,
2112 :     e.g., svd(), qr(), eigen(), dist(),..;
2113 :     apply(), also matplot() or pairs().
2114 :    
2115 :    
2116 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
2117 :    
2118 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
2119 :     add comments about 'control' / lmerControl() arguments
2120 :    
2121 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
2122 : bates 820
2123 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
2124 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
2125 : bates 820
2126 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
2127 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
2128 :    
2129 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
2130 :     .Call calls that were producing spurious output.
2131 :    
2132 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
2133 : bates 801
2134 :     * R/lmer.R (lmer): stored updated variance component estimates in
2135 :     mer object for the generalized model. (Bug reported by Renaud
2136 :     Lancelot).
2137 :    
2138 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
2139 : bates 794
2140 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
2141 :     unidimensional case.
2142 :    
2143 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
2144 : maechler 791
2145 :     * DESCRIPTION (Version): 0.96-1
2146 :    
2147 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
2148 : maechler 791
2149 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
2150 : bates 763
2151 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
2152 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
2153 :    
2154 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
2155 : bates 763
2156 :     * src/Makefile.win: Forgot to update this when Makefile changed.
2157 :    
2158 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
2159 : bates 726
2160 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
2161 :     bug reported by Kurt Hornik and Michael Hahsler.
2162 :    
2163 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
2164 : bates 725
2165 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
2166 :     logical sparse matrices. These will also be used in the symbolic
2167 :     analysis for lmer objects.
2168 :    
2169 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
2170 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
2171 : maechler 791
2172 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
2173 : bates 714
2174 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
2175 :     colMeans, colSums, rowMeans and rowSums.
2176 :    
2177 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
2178 : bates 692
2179 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
2180 :     multiplication operation.
2181 :    
2182 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
2183 :     to dgetrs.
2184 :    
2185 :     * src/init.c: Fix cut-and-paste error in definition of
2186 :     dgeMatrix_matrix_solve
2187 :    
2188 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
2189 :    
2190 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
2191 : bates 692
2192 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
2193 :    
2194 :     * DESCRIPTION: Eliminate import of stats.
2195 :    
2196 : maechler 791
2197 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
2198 : bates 692
2199 :     * R/AllClass.R : add logical sparse matrix classes
2200 :    
2201 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
2202 :    
2203 :     * R/dgTMatrix.R: add "[" method for triplet matrices
2204 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
2205 :    
2206 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
2207 : maechler 687
2208 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
2209 :    
2210 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
2211 :     * R/sparseMatrix.R: %*%, crossprod()
2212 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
2213 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
2214 :     * src/lmer.c (lmer_fitted): fix thinko
2215 :    
2216 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
2217 :    
2218 :     * R/AllClass.R: add two virtual sparse classes ``on top''
2219 :    
2220 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
2221 :    
2222 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
2223 :     correspondingly fix examples and tests/ since new()
2224 :     doesn't work for virtual classes.
2225 :    
2226 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
2227 :    
2228 :     * R/Matrix.R (as.matrix): method and one for unname()
2229 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
2230 :     also run for R 2.1.0; using as.matrix()
2231 :    
2232 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
2233 : maechler 658
2234 :     * R/pMatrix.R: "pMatrix" class added
2235 :     * ....
2236 :    
2237 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
2238 : bates 645
2239 :     * R/dtpMatrix.R: Add unpack method and an example.
2240 :    
2241 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
2242 :     of general symmetric matrices and associated S4 methods.
2243 :    
2244 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
2245 :     +
2246 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
2247 :    
2248 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
2249 :     crossprod() and "%*%" methods added; tests, too.
2250 :     * tests/matprod.R: new, for testing these
2251 :    
2252 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
2253 : bates 599
2254 :     * src/lmer.c (lmer_fitted): Added.
2255 :    
2256 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
2257 : bates 596
2258 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
2259 :    
2260 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
2261 : bates 582
2262 :     * src/*.c,po/,inst/po: Internationalization and localization of
2263 :     the package.
2264 :    
2265 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
2266 :     R_ldl.c file.
2267 :    
2268 :     * src/flame.[ch]: Removed these source files.
2269 : maechler 658
2270 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
2271 :    
2272 :     * src/LU.[ch],src/init.c: absorb in factorizations
2273 :    
2274 :     * src/Mutils.h: prepare for internationalization
2275 :    
2276 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
2277 :     this file
2278 :    
2279 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
2280 :    
2281 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
2282 :    
2283 :     * R/dtrMatrix.R: fix t() method
2284 :    
2285 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
2286 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
2287 : maechler 578 * tests/group-methods.R : and test them.
2288 :    
2289 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
2290 :     border case
2291 :    
2292 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
2293 :    
2294 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
2295 : maechler 578
2296 :     * src/dgBCMatrix.c:
2297 :     * src/lmer.c: many changes
2298 :     * ...
2299 :    
2300 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
2301 :    
2302 :     * R/Matrix.R: add more sophisticated show() method.
2303 :    
2304 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
2305 :    
2306 :     * */* : almost complete reorganization of classes.
2307 :    
2308 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
2309 : bates 460
2310 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
2311 :     for the geMatrix class.
2312 :    
2313 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
2314 : bates 460
2315 :     * src/Makefile (clean): Remove *.a and *.so
2316 :    
2317 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
2318 :    
2319 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
2320 : bates 460
2321 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
2322 : bates 460 had an effect in cases with more than 2 grouping factors.
2323 :    
2324 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
2325 : bates 415
2326 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
2327 :    
2328 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
2329 : bates 410
2330 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
2331 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
2332 :    
2333 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
2334 : bates 392
2335 :     * R/sscMatrix.R: Add determinant methods
2336 :    
2337 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
2338 :     for tripletMatrix to matrix.
2339 :    
2340 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
2341 : bates 388
2342 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
2343 :     no longer used.
2344 :    
2345 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
2346 :     with dynamic allocation of scratch arrays.
2347 :    
2348 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
2349 :     for multivariate random effects with multiple grouping factors.
2350 :     Fixes part but not all of #15.
2351 :    
2352 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
2353 : bates 375
2354 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
2355 :     scalar grouping factors corrected.
2356 :    
2357 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
2358 : bates 375
2359 :     * src/bCrosstab.c: remove diag_update which is no longer used
2360 :    
2361 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
2362 : bates 350
2363 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
2364 :     .h file can be included.
2365 :    
2366 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
2367 : bates 342
2368 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
2369 : bates 342 Complete allocation of slots in NEW_OBJECT.
2370 :    
2371 :     * src/Mutils.h: Moved list of symbols to an include file
2372 :    
2373 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
2374 : bates 342
2375 :     * src/geMutils.c (Matrix_init): remove unused function
2376 :    
2377 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
2378 : bates 342
2379 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
2380 :    
2381 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
2382 : bates 327
2383 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
2384 :    
2385 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
2386 : bates 303
2387 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
2388 :    
2389 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
2390 : bates 296
2391 :     * src/init.c: Created R_init_Matrix and added registration of C
2392 :     routines.
2393 :    
2394 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
2395 : bates 283
2396 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
2397 :    
2398 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
2399 : bates 229
2400 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
2401 :    
2402 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
2403 :    
2404 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
2405 :    
2406 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
2407 :    
2408 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
2409 :     ssclme_update_mm
2410 :    
2411 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
2412 :    
2413 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
2414 :     in the order of unconstrained and constrained parameters.
2415 :     (ssclme_gradient): Added the gradients (not yet correct for
2416 :     multidimensional, unconstrained case).
2417 :    
2418 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
2419 :    
2420 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
2421 :    
2422 :     * src/Makefile.win: Remove unneeded ranlib call
2423 :    
2424 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
2425 :    
2426 :     * DESCRIPTION (Version): New release
2427 :    
2428 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
2429 :    
2430 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
2431 :    
2432 :     * src/triplet_to_col.c: Create triplet_to_col as a native
2433 : maechler 658 function, not the version from umfpack. There were problems with
2434 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
2435 :     only one umfpack routine being used so I moved it here.
2436 :    
2437 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
2438 :    
2439 :     * src/ssclme.c (ssclme_variances): New function.
2440 :    
2441 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
2442 :    
2443 :     * src/ssclme.c (ssclme_fitted): Added function.
2444 :    
2445 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
2446 :    
2447 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
2448 :     store the dimnames in the XtX and bVar slots
2449 :     (ssclme_update_mm): Change the dimensions of the bVar slot
2450 :     components and the returned value from ssclme_ranef.
2451 :    
2452 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
2453 :    
2454 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
2455 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
2456 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
2457 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
2458 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
2459 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
2460 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
2461 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
2462 :     Moved the pdMat classes from the lme4 package.
2463 :    
2464 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
2465 :    
2466 :     * man/ssclme-class.Rd: Update definition and documentation of the
2467 :     ssclme class to include the DIsqrt slot.
2468 :    
2469 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
2470 :     (much faster using dsyrk, a level 3 BLAS routine).
2471 :    
2472 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
2473 :    
2474 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
2475 :    
2476 :     * tests/ssclme.R: Modify the test to account for the permutation
2477 :     of the levels of the grouping factors.
2478 :    
2479 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
2480 :    
2481 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
2482 :     directly into the ssclme class definition.
2483 :    
2484 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
2485 :    
2486 :     * DESCRIPTION (Date): New release
2487 :    
2488 :     * man/ssclme-class.Rd: new file.
2489 :    
2490 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
2491 :     works and it's fast!
2492 :    
2493 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
2494 :    
2495 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
2496 :    
2497 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
2498 :    
2499 :     * DESCRIPTION (Date): New release
2500 :    
2501 :     * NAMESPACE: Don't export ssclme.
2502 :    
2503 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
2504 :     school data.
2505 :    
2506 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
2507 :    
2508 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
2509 :     keep track of the fixed-effects and the response. Counts also
2510 :     gets an extra element, which is always one.
2511 :    
2512 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
2513 :    
2514 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
2515 :    
2516 :     * src/cscMatrix.c (csc_transpose): new function
2517 :    
2518 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
2519 :     (csc_components_transpose): new function
2520 :    
2521 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
2522 :    
2523 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
2524 :     triplets
2525 :    
2526 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
2527 :    
2528 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
2529 :    
2530 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
2531 :     and all other .h files in src.
2532 :    
2533 :     * src/Makefile.win: This and other Makefile.win files contributed
2534 :     by Brian Ripley.
2535 :    
2536 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
2537 :    
2538 :     * R/syMatrix.R: Added methods for "%*%".
2539 :    
2540 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
2541 :     poMatrix object.
2542 :    
2543 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
2544 :    
2545 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
2546 :    
2547 :     2004-01-25 Douglas Bates <bates@bates2_home>
2548 :    
2549 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
2550 :    
2551 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
2552 :     of nrow.
2553 :    
2554 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
2555 :    
2556 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
2557 :     subdirectories.
2558 :    
2559 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
2560 :    
2561 :     * src/taucs.h: Accidently referred to global header files
2562 :     instead of local files.
2563 :    
2564 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
2565 :    
2566 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
2567 :     and methods and replaced all classes with S4 classes.
2568 :    
2569 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
2570 :    
2571 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
2572 :    
2573 :     * src/R_LapackPP.cc: Change method of calculating determinants
2574 :    
2575 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
2576 :    
2577 :     * DESCRIPTION (Version): removed empty data directory as requested
2578 :     by CRAN maintainers. Changed version number and date.
2579 :    
2580 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
2581 :    
2582 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
2583 :     under Windows.
2584 :    
2585 :     * Added configure.win and src/Makevars.win as requested by Brian
2586 :     Ripley.
2587 :    
2588 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
2589 :    
2590 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
2591 :     Hornik.
2592 :    
2593 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
2594 :    
2595 :     * configure.ac: Replaced configure.in with configure.ac
2596 :     contributed by Kurt Hornik.
2597 :    
2598 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
2599 :     version for R-1.5.0
2600 :    
2601 : maechler 512
2602 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
2603 :    
2604 :     * man/eigen.Rd: Removed the .Alias in the example

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