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Annotation of /pkg/ChangeLog

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

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