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1 : maechler 1660 2006-11-02 Martin Maechler <maechler@stat.math.ethz.ch>
2 :    
3 :     * R/AllClass.R (Matrix-class): check length of dimnames in validity.
4 :    
5 :     * tests/simple.R: validObject() checking the above.
6 :    
7 :     * src/dgCMatrix.c (gCMatrix_validate): new, small and simple,
8 :     replacing both dgCMatrix_validate and lgCM*.
9 :    
10 :     * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
11 :     fix dimnames setting in other places.
12 :     * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
13 :    
14 : maechler 1659 2006-11-01 Martin Maechler <maechler@stat.math.ethz.ch>
15 :    
16 : maechler 1660 * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
17 :    
18 :     * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
19 :     symmetry test, via
20 : maechler 1659 * R/Auxiliaries.R (.as.dgC.0.factors):
21 :    
22 : bates 1657 2006-11-01 Douglas Bates <bates@r-project.org>
23 :    
24 :     * R/Csparse.R,src/Csparse.c,tests/matprod.R,
25 :     man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
26 :     <CsparseMatrix>) added
27 :    
28 : maechler 1655 2006-10-30 Martin Maechler <maechler@stat.math.ethz.ch>
29 :    
30 :     * tests/matprod.R: add a variation of Harri's example
31 :    
32 :     * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
33 :     recursive infinitely.
34 :    
35 :     * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
36 :    
37 :     * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
38 :    
39 :     2006-10-28 Martin Maechler <maechler@stat.math.ethz.ch>
40 :    
41 :     * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
42 :     matrix if possible; test m+m == 2*m; now test dgRMatrix.
43 :     * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
44 :     satisfy the above test.
45 :    
46 : maechler 1654 2006-10-27 Martin Maechler <maechler@stat.math.ethz.ch>
47 :    
48 : maechler 1655 * R/Matrix.R (Ops): <Matrix> o <matrix> method added
49 :    
50 : maechler 1654 * R/dgCMatrix.R: solve(a, b="missing") based on
51 :     * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
52 :     RHS = NULL.
53 :    
54 :     * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
55 :     add more (needed) [t]crossprod() methods.
56 :    
57 :     * man/ddiMatrix-class.Rd: more info, notably on 'diag'
58 :    
59 :     * R/Auxiliaries.R (as_CspClass): cleanup
60 :     (drop0): internal utility for "Csparse_drop(*, 0)"
61 :     (.bail.out.2): encourage active feedback
62 :    
63 :     2006-10-26 Martin Maechler <maechler@stat.math.ethz.ch>
64 :    
65 :     * R/dMatrix.R(Compare): new(), then slots [no validity check]
66 :    
67 :     * src/Csparse.c (Csparse_validate): fixed (and more efficient in
68 :     non-valid or 'sorted' case).
69 :    
70 :     * R/dsparseMatrix.R: add "chol" method.
71 :     * R/ddenseMatrix.R: ditto
72 :    
73 :     * R/diagMatrix.R (Ops): group methods for <diagonal> o <sparse>
74 :     * NAMESPACE (Ops)
75 :     * R/diagMatrix.R (diag2T): simple utility used "higher level"
76 :     coercion; deprecating direct lower level coercions.
77 :    
78 :     * R/*.R (seq): use seq_len() and seq_along() where possible.
79 :    
80 :    
81 : maechler 1647 2006-10-23 Martin Maechler <maechler@stat.math.ethz.ch>
82 :    
83 :     * DESCRIPTION (Version): 0.9975-5 ready for release
84 :    
85 : bates 1646 2006-10-20 Douglas Bates <bates@stat.wisc.edu>
86 :    
87 :     * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
88 :    
89 : maechler 1642 2006-10-20 Martin Maechler <maechler@stat.math.ethz.ch>
90 :    
91 :     * R/AllClass.R (corMatrix): add 'validity' check;
92 :     comment out unused "LDL" class definition
93 :     * NAMESPACE: mention, but do not export "LDL" class
94 :     * R/corMatrix.R: new (simple), needed for R-devel with
95 :     * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
96 :     coerce and t() exceptions for all 5 'Mat.MatFact' classes.
97 :    
98 : bates 1641 2006-10-19 Douglas Bates <bates@stat.wisc.edu>
99 :    
100 :     * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
101 :     use Rprintf and R's error handling.
102 :    
103 : maechler 1635 2006-10-17 Martin Maechler <maechler@stat.math.ethz.ch>
104 :    
105 :     * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
106 :     * tests/matprod.R: add tests for the bug fixed.
107 :    
108 : bates 1624 2006-10-11 Douglas Bates <bates@stat.wisc.edu>
109 :    
110 :     * src/HBMM.[ch]: remove HarwellBoeing format for writing.
111 :     * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
112 :    
113 :     2006-10-06 Douglas Bates <bates@stat.wisc.edu>
114 :    
115 : bates 1629 * R/d[gs]CMatrix.R: deprecate the writeHB function. Use writeMM instead.
116 : bates 1624
117 : maechler 1618 2006-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
118 :    
119 :     * DESCRIPTION (Version): 0.9975-3
120 :    
121 :     * R/diagMatrix.R (bdiag): new function constructing block diagonal
122 :     (sparse) matrices.
123 :     * man/bdiag.Rd: docu + examples
124 :    
125 : maechler 1619 * R/Csparse.R (replCmat): calling new Csparse_drop() now.
126 :    
127 : maechler 1618 * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
128 :     * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
129 :    
130 :     * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
131 :     that result is sparse or diagonal (and not dense).
132 :    
133 :     * man/Subassign-methods.Rd: fix examples
134 :    
135 :     * R/Matrix.R (Matrix): Matrix(0, *) or Matrix(*, sparse=TRUE)
136 :     should always return a sparse (and not sometimes a diagonal) matrix.
137 :    
138 : maechler 1615 2006-10-05 Martin Maechler <maechler@stat.math.ethz.ch>
139 :    
140 :     * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
141 :    
142 : bates 1613 2006-10-04 Douglas Bates <bates@stat.wisc.edu>
143 :    
144 :     * DESCRIPTION (Version): 0.9975-2
145 : maechler 1615
146 : bates 1613 * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
147 :    
148 : bates 1611 2006-10-02 Douglas Bates <bates@R-project.org>
149 :    
150 :     * tests/dg_Matrix.R: Simplify test taking into account new code.
151 :    
152 : maechler 1599 2006-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
153 :    
154 : maechler 1600 * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
155 :    
156 : maechler 1599 * R/lsTMatrix.R: new files w/ missing methods
157 :     * R/nsTMatrix.R: " 'for completeness'
158 :    
159 :     * tests/Class+Meth.R: a bit less 'not.ok.classes'
160 :    
161 :     * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
162 :    
163 :    
164 : bates 1595 2006-09-28 Douglas Bates <bates@R-project.org>
165 :    
166 :     * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
167 :     included.
168 :    
169 :     * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
170 :     Export C-callable functions used in Zt_create in lme4.
171 :    
172 : maechler 1592 2006-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
173 :    
174 :     * DESCRIPTION (Version): 0.9975-1
175 :    
176 :     * tests/simple.R: less checks fail; using NA, found that our
177 :     kronecker() is not base-compatible with NA's.
178 :    
179 :     * R/dMatrix.R: "Compare" method now implemented for all cases
180 :    
181 :     * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
182 :    
183 :     * man/dtpMatrix-class.Rd: mention length of 'x' slot
184 :    
185 :     * src/dtpMatrix.c (dtpMatrix_validate): fix check
186 :     * src/dspMatrix.c (dspMatrix_validate): ditto
187 :    
188 :     * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
189 :     including coercion to [nl]tTMatrix.
190 :    
191 :     * R/diagMatrix.R (show): print a header line as for other classes.
192 :    
193 :     2006-09-27 Martin Maechler <maechler@stat.math.ethz.ch>
194 :    
195 :     * src/Makefile.win (SUBDIRS): fix typo
196 :    
197 : maechler 1583 2006-09-19 Martin Maechler <maechler@stat.math.ethz.ch>
198 :    
199 :     * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
200 :    
201 : bates 1577 2006-09-18 Douglas Bates <bates@stat.wisc.edu>
202 :    
203 :     * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
204 :     symmetric and y missing in R code using %*% (cholmod_aat doesn't
205 :     accept a symmetric matrix).
206 :     * tests/group-methods.R: Uncomment test of crossprod applied to
207 :     lsCMatrix objects.
208 :    
209 : maechler 1575 2006-09-18 Martin Maechler <maechler@stat.math.ethz.ch>
210 :    
211 :     * R/AllClass.R (symmetricMatrix): add validity method (available
212 :     in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
213 :    
214 :     * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
215 :    
216 :     * tests/indexing.Rout.save:
217 :     * tests/indexing.R: additions, mainly for 'lsparse'
218 :    
219 :     * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
220 :     case.
221 :    
222 :     * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
223 :    
224 : maechler 1571 2006-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
225 :    
226 : maechler 1572 * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
227 :     as 'N' (1-letter - Ok?)
228 :    
229 : maechler 1571 * tests/group-methods.R: add test for logical + NAs
230 :    
231 :     * R/dMatrix.R ("Compare"): fix to work with NA's
232 :    
233 :     * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
234 :    
235 :     * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
236 :     which is implemented.
237 :    
238 : maechler 1565 2006-09-15 Martin Maechler <maechler@stat.math.ethz.ch>
239 :    
240 : maechler 1571 * src/chm_common.c: coerce logical <-> double instead of
241 :     typecasting; needed for "l" matrix handling in cholmod.
242 : maechler 1565
243 : maechler 1571 * tests/other-pkgs.R (graph): small extension in "graph" checks.
244 :    
245 : maechler 1565 * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
246 :     (Tsp2grNEL): other fixes needed
247 :    
248 : maechler 1548 2006-09-11 Martin Maechler <maechler@stat.math.ethz.ch>
249 :    
250 :     * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
251 :     Matrices, since "lMatrix", also "lsparseM" can have NA
252 :     * R/ndenseMatrix.R, etc: new source files
253 :     * man/nsparseMatrix-classes.Rd, etc: new help files
254 :     * tests/: adaptions
255 :     * src/chm_common.c (chm_dense_to_SEXP): and others:
256 :     new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
257 : maechler 1582 * src/Csparse.c, etc: ditto
258 : maechler 1548
259 : bates 1546 2006-09-11 Douglas Bates <bates@R-project.org>
260 :    
261 :     * src/Mutils.[ch],init.c inst/include/*.h: Move the
262 :     alloc_d**Matrix functions to the lme4 package.
263 :    
264 : bates 1543 2006-09-09 Douglas Bates <bates@R-project.org>
265 :    
266 :     * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
267 : maechler 1544 fixed
268 : bates 1543
269 : maechler 1544 2006-09-09 Martin Maechler <maechler@stat.math.ethz.ch>
270 :    
271 : maechler 1548 * R/lMatrix.R: new
272 :    
273 : maechler 1544 * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
274 :    
275 :     * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
276 : maechler 1582 * man/tcrossprod.Rd: ditto
277 : maechler 1544
278 : bates 1538 2006-09-08 Douglas Bates <bates@stat.wisc.edu>
279 :    
280 :     * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
281 :     for exported functions
282 :     * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
283 :     Remove partitioning algorithms for sparse matrix reordering. The
284 :     copyright on the Metis code was problematic and the methods were
285 :     rarely used.
286 :     * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col. Such
287 :     operations are now done entirely in CHOLMOD code.
288 :    
289 : bates 1517 2006-09-06 Douglas Bates <bates@R-project.org>
290 :    
291 :     * src/Mutils.h: Remove functions that are no longer used.
292 :    
293 : bates 1507 2006-09-04 Douglas Bates <bates@R-project.org>
294 :    
295 :     * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
296 :     * src/DEPS.mkf: update
297 :    
298 : maechler 1481 2006-09-02 Martin Maechler <maechler@stat.math.ethz.ch>
299 :    
300 :     * created branches/Matrix-for-R-2.3.x; on trunk: do
301 :     * DESCRIPTION (Version): 0.9975-0
302 :     (Depends): R (>= 2.4.0)
303 :    
304 : bates 1475 2006-09-01 Douglas Bates <bates@R-project.org>
305 :    
306 :     * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
307 :    
308 : maechler 1472 2006-09-01 Martin Maechler <maechler@stat.math.ethz.ch>
309 :    
310 :     * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
311 :     * R/denseMatrix.R: add coercion from "ANY" to "denseMatrix"
312 :    
313 :     * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
314 :    
315 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
316 :    
317 :     * R/sparseMatrix.R (Arith): moved Arith group method one-level up
318 :     from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
319 : maechler 1582 * R/dsparseMatrix.R: ditto
320 :     * R/Csparse.R: ditto
321 : maechler 1472
322 :     2006-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
323 :    
324 :     * R/dMatrix.R (Compare): improve availability of "<", etc
325 :     * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
326 :    
327 : maechler 1467 2006-08-30 Martin Maechler <maechler@stat.math.ethz.ch>
328 :    
329 :     * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
330 :     of a 0-index which was used as 1-index (..hmm)
331 :    
332 :     * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
333 :    
334 :     * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
335 :     * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
336 : maechler 1582 (.is.diagonal): ditto
337 : maechler 1467
338 :     * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
339 :    
340 :     * R/Matrix.R (Matrix): also work for NA data
341 :    
342 : maechler 1455 2006-08-28 Martin Maechler <maechler@stat.math.ethz.ch>
343 :    
344 :     * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
345 :     in all cases.
346 :    
347 : bates 1453 2006-08-27 Douglas Bates <bates@R-project.org>
348 :    
349 :     * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
350 :     (ddense_band): Added triu, tril and band for ddenseMatrix objects.
351 :    
352 : maechler 1447 2006-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
353 :    
354 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
355 :     subclasses of "ddenseMatrix"
356 :     * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
357 :     * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
358 :     instead of half dozen specialized ones.
359 :    
360 : bates 1445 2006-08-25 Douglas Bates <bates@R-project.org>
361 :    
362 :     * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
363 :     <tillard@cirad.fr> - ordering standard errors to match effects.
364 :    
365 : bates 1439 2006-08-24 Douglas Bates <bates@R-project.org>
366 : bates 1431
367 : bates 1439 * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
368 :     on R_ldl.
369 :     * R/lCholCMatrix.R,
370 :     src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
371 :     * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
372 :     * many files in ./R and ./src: Use more general version of
373 :     dup_mMatrix_as_dgeMatrix to simplify method definitions.
374 : bates 1442 * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
375 :     dtpMatrix, dspMatrix and dppMatrix conversions.
376 :    
377 : maechler 1447
378 : bates 1439 2006-08-23 Douglas Bates <bates@R-project.org>
379 :    
380 :     * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
381 :     Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
382 : bates 1431 * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
383 :     dgeMatrix_crossprod (may need to do this in other places).
384 :     * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
385 :     generic and method for dsCMatrix. Use CHOLMOD for chol().
386 :    
387 : bates 1414 2006-08-22 Douglas Bates <bates@R-project.org>
388 :    
389 :     * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
390 :     types of classed Matrices, matrices or numeric or logical vectors.
391 : bates 1423 * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
392 :     * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
393 :     to Mutils.h (as an inline) and change name to Matrix_check_class;
394 :     fixes in as_cholmod_factor and chm_factor_to_SEXP.
395 :     * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
396 :     dsCMatrix_matrix_solve. Comment out vestigial functions.
397 :     * src/Csparse.c: use diag_P and uplo_P macros.
398 : maechler 1447
399 : bates 1405 2006-08-21 Douglas Bates <bates@R-project.org>
400 :    
401 :     * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
402 : maechler 1447 valgrind.
403 : bates 1411 * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
404 :     inverses.
405 :     * src/sparseQR.c (sparseQR_validate): add new validation test, fix
406 :     -Wall warnings.
407 :     * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
408 :     Use dup_mMatrix_as_dgeMatrix.
409 : maechler 1447
410 : bates 1403 2006-08-20 Douglas Bates <bates@R-project.org>
411 :    
412 :     * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
413 :     * tests/sparseQR.R: Added
414 :     * man/sparseQR-class.Rd: Document methods for qr.* generics
415 :     * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
416 :    
417 : bates 1398 2006-08-19 Douglas Bates <bates@R-project.org>
418 :    
419 :     * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
420 :     Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
421 :     and qr.fitted.
422 :     * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
423 :     * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
424 :    
425 : maechler 1389 2006-08-18 Martin Maechler <maechler@stat.math.ethz.ch>
426 :    
427 :     * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
428 :     the base version has no "..." argument.
429 :    
430 :     * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
431 :    
432 :     * R/Matrix.R: define and
433 :     * NAMESPACE: export as.numeric() and as.logical() methods.
434 :     Let's hope these do not badly slow down something...
435 :     Finally export the zapsmall() method.
436 :    
437 : bates 1388 2006-08-17 Douglas Bates <bates@R-project.org>
438 :    
439 :     * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
440 :     R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
441 :     * src/dtCMatrix.c :Remove code that is no longer used
442 :     * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
443 :    
444 : bates 1370 2006-08-14 Douglas Bates <bates@R-project.org>
445 :    
446 : bates 1373 * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
447 :     Csparse_to_logical and Csparse_symmetric_to_general.
448 :     * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
449 : maechler 1389 coercion methods between CsparseMatrix and TsparseMatrix.
450 : bates 1373
451 :     2006-08-14 Douglas Bates <bates@R-project.org>
452 :    
453 : bates 1370 * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
454 :     Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
455 :     for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
456 :     possible.
457 :    
458 : bates 1368 2006-08-12 Douglas Bates <bates@R-project.org>
459 :    
460 :     * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
461 :     dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
462 :     Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
463 :     generalize conversions between TsparseMatrix, CsparseMatrix,
464 :     denseMatrix and matrix. Preserve triangularity property and
465 :     propagate Dimnames in the easy cases.
466 :    
467 : bates 1365 2006-08-10 Douglas Bates <bates@R-project.org>
468 :    
469 :     * src/lmer.c: adjust checks in glmer_init for S4SXP
470 :     * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
471 :     before S4SXP but for the wrong reasons.
472 :    
473 : bates 1354 2006-08-08 Douglas Bates <bates@R-project.org>
474 :    
475 : bates 1360 * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
476 :     Later modified to return the upper triangle only.
477 :     * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
478 : maechler 1389
479 : bates 1352 2006-08-07 Douglas Bates <bates@R-project.org>
480 :    
481 :     * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
482 :     R-level conversion to a sparse symmetric class.
483 :     * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
484 :     Remove conversion to sparse symmetric classes (now done in C code).
485 :    
486 : maechler 1349 2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
487 :    
488 : maechler 1351 * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
489 :     * man/band.Rd: adapt the \dontshow{} unit test.
490 :    
491 :     2006-08-07 Martin Maechler <maechler@stat.math.ethz.ch>
492 :    
493 : maechler 1349 * DESCRIPTION (Version): 0.995-14 for CRAN
494 :    
495 :     * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
496 :    
497 :     * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
498 :     * tests/other-pkgs.R: more checks, sparseMatrix -> graph
499 :    
500 :     * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
501 :     * R/Tsparse.R (tril, triu, band): methods
502 : bates 1352 * R/dgRMatrix.R (tril, ...): ditto
503 :     * man/band.Rd: ditto
504 : maechler 1349
505 :     2006-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
506 :    
507 :     * R/Matrix.R (head, tail): directly use utils:::head.matrix
508 :     to be up-to-date automatically.
509 :    
510 : maechler 1346 2006-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
511 :    
512 :     * DESCRIPTION (Version): 0.995-13 to be released to CRAN
513 :    
514 :     * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
515 :     * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
516 :     * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
517 :     such that the S4 objects are always created by the current version
518 :     of R and 'Matrix' class definitions.
519 :    
520 : bates 1342 2006-08-01 Douglas Bates <bates@R-project.org>
521 :    
522 :     * R/lmer.R (LMEoptimize method), tests/lmer.R,
523 : maechler 1346 inst/external/test3comp.rda: Added warnings for convergence on
524 : bates 1342 boundary and test cases.
525 :    
526 :     * src/lmer.c (mer_postVar): Modified to return the variances that
527 :     are marginal to the fixed effects, not conditional on them (which
528 :     is what the bVar slot contents represent).
529 :    
530 : bates 1338 2006-07-31 Douglas Bates <bates@R-project.org>
531 :    
532 :     * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace): Add the hatTrace
533 :     function which calls the C function mer_hat_trace2.
534 : maechler 1346
535 : bates 1342 * man/ranef.Rd: Include description of "postVar" argument and
536 :     producing a caterpillar plot.
537 : bates 1338
538 : maechler 1335 2006-07-31 Martin Maechler <maechler@stat.math.ethz.ch>
539 :    
540 :     * NAMESPACE: change "correlation" to "corMatrix"
541 :     * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
542 : bates 1352 * R/dpoMatrix.R: ditto
543 :     * R/lmer.R: ditto
544 : maechler 1335
545 : bates 1338 2006-07-28 Douglas Bates <bates@R-project.org>
546 :    
547 :     * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
548 :     RZXinv slot's contents into a separate internal function that can
549 :     be used in mer_hat_trace.
550 :    
551 : maechler 1331 2006-07-22 Martin Maechler <maechler@stat.math.ethz.ch>
552 :    
553 :     * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
554 :     via new smart
555 :     * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
556 :     utility functions.
557 :    
558 :    
559 : maechler 1330 2006-07-21 Martin Maechler <maechler@stat.math.ethz.ch>
560 :    
561 : maechler 1331 * R/Csparse.R (tril, triu, band): do return *triangular* classed
562 :     matrices when appropriate; band() even symmetric ones.
563 :     (replCmat): extend to potentially all "CsparseMatrix"
564 :     * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
565 :     allow subassignment for special sparse matrices.
566 :    
567 :     * R/Auxiliaries.R (as_geClass): factor out the .M.kind() functionality
568 :    
569 : maechler 1330 * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
570 :     argument; in glmer_*(): print only if(verbose).
571 :    
572 :     speed-optimize a few places by moving REAL(.) out of loops.
573 :    
574 :     * src/lmer.h, src/init.h, R/lmer.R: related to above.
575 :    
576 : maechler 1329 2006-07-20 Martin Maechler <maechler@stat.math.ethz.ch>
577 :    
578 :     * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
579 :     since that wrongly triggers also for M[ logi , ]
580 :    
581 :     * R/denseMatrix.R: "[" methods now also work e.g. when indexing
582 :     a symmetric matrix that results in a non-symmetric one.
583 :     * R/Auxiliaries.R (as_geClass): new function used in "[" above.
584 :    
585 :     * R/dMatrix.R: make round(M) work as round(M, 0)
586 :    
587 :     * R/dgTMatrix.R (image): coordinate system and axis now use
588 :     1-based indices, not 0-based ones.
589 :    
590 :     * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
591 :     * tests/indexing.R: test it.
592 :    
593 :     * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
594 :     * man/isSymmetric-methods.Rd: and document it.
595 :    
596 :     * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
597 :     * man/SparseM-conv.Rd: docu them
598 :    
599 :     * tests/other-pkgs.R: renamed from tests/graph.R and add example
600 :     for 'SparseM' conversions
601 :    
602 :     2006-07-17 Douglas Bates <Douglas.Bates@R-project.org>
603 :    
604 :     * R/Matrix.R (head): added head() and tail() methods.
605 :    
606 :     2006-07-17 Martin Maechler <maechler@stat.math.ethz.ch>
607 :    
608 :     * DESCRIPTION (Version): 0.995-12 released to CRAN
609 :    
610 : maechler 1319 2006-07-15 Martin Maechler <maechler@stat.math.ethz.ch>
611 :    
612 :     * tests/simple.R: add check for correct dsT -> dgT coercion;
613 :     add check for correct printing of symmetric sparse matrices.
614 :    
615 :     * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
616 :     for sparse symmetric matrices.
617 :    
618 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
619 :     diagonal twice.
620 :    
621 : bates 1316 2006-07-11 Douglas Bates <Douglas.Bates@R-project.org>
622 :    
623 :     * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
624 : maechler 1319 being applied to the x slot (detected by Brian Ripley).
625 : bates 1316
626 : maechler 1315 2006-07-10 Martin Maechler <maechler@stat.math.ethz.ch>
627 :    
628 :     * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
629 :    
630 :     * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
631 :    
632 :     2006-07-08 Martin Maechler <maechler@stat.math.ethz.ch>
633 :    
634 :     * src/lgCMatrix.c (lgCMatrix_diag): new function
635 :     * R/lgCMatrix.R (diag): for new method
636 :    
637 :     * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
638 :     ==> construction of illegal "*gTMatrix" via new() should
639 :     now be much less easy:
640 :     * tests/Class+Meth.R: assertError() for some illegal "dgT*"
641 :    
642 :     * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
643 :     directly.
644 :     * man/Matrix.Rd: documents it.
645 :    
646 : bates 1311 2006-07-06 Douglas Bates <bates@R-project.org>
647 :    
648 :     * src/pedigree.c (pedigree_inbreeding): Correction in
649 :     initialization. This function is not currently being used and is
650 :     not fully tested.
651 :    
652 : bates 1312 * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
653 :     Introduced the glmer class. Added code for mcmcmsamp on glmer
654 :     objects. Modified validity check on pedigree objects to account
655 :     for nonparallel patterns of missingness of parents.
656 : bates 1311
657 : bates 1313 * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
658 :     class.
659 : maechler 1315
660 :     2006-07-01 Martin Maechler <maechler@stat.math.ethz.ch>
661 :    
662 :     * R/pMatrix.R: coercion pMatrix -> Tsparse
663 :    
664 : bates 1300 2006-06-12 Douglas Bates <bates@R-project.org>
665 :    
666 : maechler 1319 * DESCRIPTION (Version): 0.995-11 released to CRAN
667 :    
668 : bates 1300 * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
669 :     the output from mcmcsamp.
670 :    
671 : bates 1298 2006-06-10 Douglas Bates <bates@R-project.org>
672 :    
673 : bates 1300 * R/lmer.R (simulestimate): added C code for calculating the trace
674 :     of the hat matrix.
675 : bates 1298
676 : maechler 1295 2006-06-09 Martin Maechler <maechler@stat.math.ethz.ch>
677 :    
678 :     * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
679 :     classes.
680 : maechler 1315 * R/sparseMatrix.R etc: multiplication of diagonal and sparse
681 : maechler 1295
682 : maechler 1290 2006-06-08 Martin Maechler <maechler@stat.math.ethz.ch>
683 :    
684 :     * R/dgTMatrix.R (colSums): etc. All four of
685 :     colSums(), rowSums(), colMeans(), rowMeans() now should work for
686 :     all "Matrices".
687 :    
688 : bates 1288 2006-06-01 Douglas Bates <bates@stat.wisc.edu>
689 :    
690 :     * R/lmer.R (panel.ci): Add a reference line at zero and a
691 :     background grid to the qqmath plot of ranef.lmer.
692 :    
693 : bates 1287 2006-05-30 Douglas Bates <bates@stat.wisc.edu>
694 : bates 1284
695 : bates 1287 * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
696 :     grouping factors to be specified in the formula as (1|foo/bar).
697 :    
698 :     2006-05-27 Douglas Bates <bates@stat.wisc.edu>
699 :    
700 : bates 1284 * R/lmer.R (findbars and others): Change check of is.numeric to
701 :     !is.language to resolve the bug reported by Jacob Wegelin.
702 :    
703 :     * src/pedigree.c (pedigree_inbreeding): Initial implementation of
704 :     code to evaluate inbreeding coefficients without calculating T,
705 :     based on code in Sargolzaei and Iwaisaki's paper.
706 :    
707 : bates 1283 2006-05-27 Douglas Bates <bates@stat.wisc.edu>
708 :    
709 :     * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
710 :     generic and mer methods for isNested and denomDF. This denomDF was
711 :     an attempt to emulate that in lme but I don't think that makes
712 :     sense. Use the trace of the hat matrix instead.
713 :    
714 : maechler 1271 2006-05-17 Martin Maechler <maechler@stat.math.ethz.ch>
715 :    
716 :     * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
717 :     the C code depending on a slot structure that's no longer valid.
718 : bates 1352 * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
719 : maechler 1271
720 :    
721 : bates 1268 2006-05-17 Douglas Bates <bates@stat.wisc.edu>
722 :    
723 :     * R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
724 :     of lowerTriMatrix generic and methods to tril (also upper to triu)
725 :     and added a general band extractor.
726 :    
727 : bates 1267 2006-05-16 Douglas Bates <bates@stat.wisc.edu>
728 :    
729 :     * R/pedigree.R (pedigree): Replace sire and dam values outside the
730 :     allowable range with NAs. Added a corresponding check in the
731 :     validity check for the pedigree class.
732 :    
733 :     * R/[CT]sparse.R ([t]crossprod): The result of single-argument
734 :     crossprod methods now inherits from symmetricMatrix.
735 :    
736 : bates 1265 2006-05-15 Douglas Bates <bates@stat.wisc.edu>
737 :    
738 :     * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
739 :     generics lowerTriMatrix and upperTriMatrix along with methods for
740 :     the Csparse virtual class. Also added a C function Csparse_band
741 :     that implements these methods by calling cholmod_band.
742 :    
743 : maechler 1264 2006-05-15 Martin Maechler <maechler@stat.math.ethz.ch>
744 :    
745 :     * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
746 :     erased when it was NULL. This led to invalid subselections!
747 :    
748 : bates 1259 2006-04-25 Douglas Bates <bates@stat.wisc.edu>
749 :    
750 :     * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
751 :     in method for "t" so as not to lose the unit diagonal property.
752 :    
753 : bates 1257 2006-04-19 Douglas Bates <bates@stat.wisc.edu>
754 :    
755 :     * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
756 :     and methods. This is now an option to the ranef method for the
757 :     mer class.
758 :    
759 :     * src/cs_utils.c: Ensure that the nz component is -1 for a
760 :     compressed column-oriented matrix. Minor formatting cleanup.
761 :    
762 :     * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
763 :     objects.
764 :    
765 : maechler 1253 2006-04-19 Martin Maechler <maechler@stat.math.ethz.ch>
766 :    
767 :     * R/Auxiliaries.R (diagU2N): new for the solve() methods in
768 :     * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
769 :    
770 : bates 1251 2006-04-15 Douglas Bates <bates@stat.wisc.edu>
771 :    
772 :     * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
773 :     in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
774 :    
775 :     * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
776 :     for the dtCMatrix class.
777 : maechler 1253
778 : bates 1247 2006-04-12 Douglas Bates <bates@stat.wisc.edu>
779 :    
780 :     * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
781 :     and methods for it.
782 :    
783 : maechler 1245 2006-04-12 Martin Maechler <maechler@stat.math.ethz.ch>
784 :    
785 :     * R/dgCMatrix.R: add storage.mode(.) <- "double" for "matrix"
786 :     arguments, such that M %*% 1:6 now works
787 :     * Tests/matprod.R: test the above
788 :    
789 : bates 1244 2006-04-03 Douglas Bates <bates@stat.wisc.edu>
790 : bates 1243
791 :     * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
792 :     the ranef.lmer class.
793 :    
794 :     * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
795 :     methods to extract the posterior variances from the bVar slot.
796 :    
797 : maechler 1238 2006-03-30 Martin Maechler <maechler@stat.math.ethz.ch>
798 :    
799 :     * R/dtCMatrix.R: allow coercion from dgC* to triangular (dtC*)
800 :     * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
801 :    
802 :     * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
803 :     * tests/simple: (extended)
804 :    
805 :     * R/sparseMatrix.R (isTriangular): now using much improved
806 :     * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
807 :    
808 : bates 1236 2006-03-23 Douglas Bates <bates@stat.wisc.edu>
809 :    
810 :     * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
811 :     (problem report from Franklin Parlamis). This should be done
812 : maechler 1238 generally.
813 : bates 1236
814 : bates 1234 2006-03-21 Douglas Bates <bates@stat.wisc.edu>
815 :    
816 :     * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
817 :     ranef.lmer (like summary.lmer). Add the coef.lmer class and
818 :     update the plot methods.
819 :    
820 : bates 1232 2006-03-20 Douglas Bates <bates@stat.wisc.edu>
821 :    
822 :     * R/lmer.R (resid and ranef methods): Added methods for the
823 :     "residuals" and "resid" generic but only for linear mixed model
824 :     fits. Changed the ranef method to return a list of data frames so
825 :     that the plot methods now work.
826 :    
827 : bates 1230 2006-03-16 Douglas Bates <bates@bates2>
828 :    
829 :     * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
830 :     dpotrf - otherwise the BLAS on Mac OS X complains and quits.
831 :    
832 :     * DESCRIPTION (Date): New release
833 :    
834 : maechler 1228 2006-03-15 Martin Maechler <maechler@stat.math.ethz.ch>
835 :    
836 :     * DESCRIPTION (Version): 0.995-6 -- to be released to CRAN
837 :    
838 :     * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
839 :     * man/KNex.Rd: and other help files
840 :     * tests/*.R: several ones needed adaption
841 : bates 1352 * inst/doc/Comparisons.Rnw: ditto
842 : maechler 1228
843 : maechler 1226 2006-03-11 Martin Maechler <maechler@stat.math.ethz.ch>
844 :    
845 :     * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
846 :    
847 :     * tests/indexing.R: tests for new [<- methods for sparse matrices.
848 :    
849 :     2006-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
850 :    
851 :     * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
852 :    
853 :     * R/Tsparse.R (.ind.prep): fix out-of-range indexing
854 :    
855 :     2006-03-08 Martin Maechler <maechler@stat.math.ethz.ch>
856 :    
857 :     * R/dMatrix.R: enable things like M [ M < 10 ]
858 :     * R/dgeMatrix.R: implement it
859 :    
860 : maechler 1222 2006-03-06 Martin Maechler <maechler@stat.math.ethz.ch>
861 :    
862 :     * R/AllClass.R: define "summary.mer" and "*.lmer"
863 :     * R/lmer.R (summary): summary(<mer>) computes & returns the above;
864 :     * R/lmer.R (show): now works with summary()
865 :    
866 :     2006-03-04 Martin Maechler <maechler@stat.math.ethz.ch>
867 :    
868 :     * R/dgCMatrix.R: finally direct "Arith" dgC o dgC
869 :     * R/Auxiliaries.R (WhichintersectInd): and other utilities to
870 :     support the above
871 :    
872 : bates 1213 2006-02-07 Douglas Bates <bates@stat.wisc.edu>
873 :    
874 :     * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
875 :     Use glmFit$prior.weights for weights in a glmm.
876 :     Allow an option usePQL = FALSE to skip the PQL steps for the
877 :     Laplace method (and, in time, the AGQ method).
878 :    
879 :     * src/lmer.c (mer_factor): Move downdating and factoring of XtX
880 :     into a separate function internal_mer_Xfactor to be able to call
881 :     it from internal_bhat.
882 :    
883 : maechler 1200 2006-01-23 Martin Maechler <maechler@stat.math.ethz.ch>
884 :    
885 :     * tests/Class+Meth.R (tstMatrixClass): function for much better
886 :     testing; now again of all actual classes.
887 :    
888 :     * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
889 :     use macros and define make_d_matrix_* and make_i_matrix_*
890 :     where _i_ is for the ldense routines:
891 :    
892 :     * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
893 :     * src/ldense.c (lsyMatrix_as_lgeMatrix):
894 :    
895 :     * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
896 :    
897 :    
898 : maechler 1174 2006-01-16 Martin Maechler <maechler@stat.math.ethz.ch>
899 :    
900 :     * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
901 :     many different kinds of matrices.
902 :     * R/*.R: quite a few new methods were needed for R CMD check with
903 :     new Matrix(). Very good for users playing around.
904 :    
905 :    
906 : maechler 1165 2006-01-15 Martin Maechler <maechler@stat.math.ethz.ch>
907 :    
908 :     * src/dgeMatrix.c (dMatrix_validate): new
909 :     * src/Mutils.c (dense_nonpacked_validate): new
910 :    
911 :     * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
912 :    
913 :    
914 :     2006-01-14 Douglas Bates <bates@stat.wisc.edu>
915 :    
916 :     * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
917 :    
918 : bates 1123 2006-01-07 Douglas Bates <bates@stat.wisc.edu>
919 : bates 1119
920 : maechler 1127 * DESCRIPTION (Version): 0.99-6 released to CRAN
921 :    
922 : bates 1119 * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
923 :     segfault in cases with multiple non-nested grouping factors.
924 :    
925 : maechler 1109 2006-01-03 Martin Maechler <maechler@stat.math.ethz.ch>
926 :    
927 :     * DESCRIPTION (Version): 0.99-4 to be released to CRAN
928 :     (Depends): also on 'utils'
929 :    
930 :     * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
931 :     * R/diagMatrix.R (Diagonal): constructor and methods for
932 :     diagonal matrices
933 :    
934 :     * R/ltTMatrix.R: new "minimal methods"
935 :    
936 : maechler 1091 2005-12-12 Martin Maechler <maechler@stat.math.ethz.ch>
937 :    
938 :     * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
939 :     all methods (and help files).
940 :    
941 : maechler 1084 2005-12-09 Martin Maechler <maechler@stat.math.ethz.ch>
942 :    
943 :     * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
944 :     for case (dimn. op no_dimn.)
945 :    
946 :     2005-11-14 Douglas Bates <bates@stat.wisc.edu>
947 :    
948 : maechler 1174 * DESCRIPTION (Version): 0.99-2 released to CRAN
949 : maechler 1084
950 : bates 988 2005-10-21 Douglas Bates <bates@stat.wisc.edu>
951 :    
952 :     * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
953 :     by Julian Faraway.
954 :    
955 : maechler 976 2005-10-06 Martin Maechler <maechler@stat.math.ethz.ch>
956 :    
957 :     * R/Auxiliaries.R (try_as): new utility
958 :     * R/sparseMatrix.R: use try_as() in coercion to original class
959 :    
960 : maechler 956 2005-09-30 Martin Maechler <maechler@stat.math.ethz.ch>
961 :    
962 :     * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
963 :    
964 :     2005-09-29 Martin Maechler <maechler@stat.math.ethz.ch>
965 :    
966 :     * R/Auxiliaries.R (dimNamesCheck): added
967 :    
968 :     * R/Matrix.R (as.array), (as.vector): new
969 :    
970 : maechler 954 2005-09-28 Martin Maechler <maechler@stat.math.ethz.ch>
971 :    
972 :     * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
973 : maechler 956 default.
974 :     * R/AllClass.R: move 'factors' slot toplevel "Matrix";
975 :     "pMatrix" now contains "sparseMatrix"
976 : maechler 954
977 : maechler 948 2005-09-26 Martin Maechler <maechler@stat.math.ethz.ch>
978 :    
979 :     * tests/Class+Meth.R: new tests; t(t(m)) == m
980 :    
981 :     * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
982 :    
983 :     * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
984 :     * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
985 :    
986 :     * R/dspMatrix.R: typo in "t" method
987 :    
988 : maechler 925 2005-09-18 Douglas Bates <bates@wisc.edu>
989 :    
990 :     * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
991 :     * R/Tsparse.R: instead of R/gTMatrix.R
992 :     * R/Csparse.R: new
993 :     * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
994 :     * src/Tsparse.c: new; many trivial methods calling cholmod_()
995 :     * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
996 :     via cholmod
997 :    
998 :     2005-09-16 Martin Maechler <maechler@stat.math.ethz.ch>
999 :    
1000 :     * R/Auxiliaries.R (non0ind): new function using new C code
1001 :     * src/dgCMatrix.c (compressed_non_0_ij): new utility
1002 :    
1003 : bates 917 2005-09-15 Douglas Bates <bates@localhost.localdomain>
1004 :    
1005 :     * src/chm_common.h: header file required by all C sources that
1006 : maechler 1174 call CHOLMOD functions. It defines a cholmod_common structure
1007 : bates 917 called 'c' whose address is passed as the last argument to
1008 :     (virtually) every CHOLMOD function.
1009 :    
1010 :     * src/Pattern.c: Simple example of the use of CHOLMOD.
1011 :    
1012 :     * src/init.c: initialize and finalize the cholmod_common structure.
1013 :    
1014 :     * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
1015 :     LDL and CCOLAMD from the U. of Florida sparse matrix library.
1016 :    
1017 : maechler 908 2005-09-08 Martin Maechler <maechler@stat.math.ethz.ch>
1018 :    
1019 :     * inst/test-tools.R: new file collecting the utility functions used
1020 :     in ./tests/*.R
1021 :    
1022 :     * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
1023 :     * R/Matrix.R (cbind2): methods for NULL and missing
1024 :    
1025 : maechler 886 2005-08-31 Martin Maechler <maechler@stat.math.ethz.ch>
1026 :    
1027 :     * R/AllClass.R: new "index" class for "[" and "[<-":
1028 :     First cut at "symmetricMatrix" and "triangularMatrix"
1029 :     * R/gTMatrix.R (.ind.prep): new function;
1030 : maechler 1174 Logical and character indexing now work too.
1031 : maechler 886 * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
1032 :     * tests/indexing.R: new, including *.Rout.save
1033 :     * tests/dgTMatrix.R: new
1034 :    
1035 : bates 876 2005-08-29 Douglas Bates <bates@wisc.edu>
1036 :    
1037 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
1038 :     indicator pos not being updated. Also enforced upper triangular
1039 :     for symmetric case. Need to coerce edges component of elements of
1040 :     edge list - grr! (Why don't they define their classes cleanly?)
1041 :    
1042 : maechler 871 2005-08-26 Martin Maechler <maechler@stat.math.ethz.ch>
1043 :    
1044 :     * R/Matrix.R: added first "[<-" methods; not yet functional
1045 : bates 1352 * R/denseMatrix.R: ditto
1046 : maechler 871 * man/Subassign-methods.Rd: new help file for these
1047 :    
1048 :     2005-08-25 Martin Maechler <maechler@stat.math.ethz.ch>
1049 :    
1050 :     * DESCRIPTION (Version): 0.98-6
1051 :    
1052 :     * R/denseMatrix.R: new file for "[" fallback methods for all dense
1053 :     matrices.
1054 :    
1055 : maechler 868 2005-08-19 Martin Maechler <maechler@stat.math.ethz.ch>
1056 :    
1057 :     * src/lgCMatrix.c (lcsc_to_matrix): new; need for
1058 :     as( <logical>, "matrix")
1059 :    
1060 :     * R/pMatrix.R: coercion to "lgTMatrix"
1061 :    
1062 :     * R/gTMatrix.R: new virtual class to define "[" methods for.
1063 :     * man/gTMatrix-class.Rd:
1064 :     * General slight re-organization of where "[" methods are defined.
1065 :     more to come.
1066 :    
1067 : maechler 871 2005-08-18 Douglas Bates <bates@wisc.edu>
1068 : maechler 868
1069 : maechler 1174 * DESCRIPTION (Version): 0.98-5 released to CRAN
1070 : maechler 871
1071 :     * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
1072 :     * .....
1073 :    
1074 : bates 863 2005-08-18 Douglas Bates <bates@localhost.localdomain>
1075 :    
1076 :     * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
1077 :     or glmer objects.
1078 :    
1079 : maechler 860 2005-08-17 Martin Maechler <maechler@stat.math.ethz.ch>
1080 :    
1081 :     * DESCRIPTION (Version): 0.98-4 : upload to CRAN
1082 :    
1083 :     2005-08-16 Douglas Bates <bates@localhost.localdomain>
1084 :    
1085 :     * R/HBMM.R: finish re-writing R-only code.
1086 :    
1087 : bates 854 2005-08-15 Douglas Bates <bates@localhost.localdomain>
1088 :    
1089 :     * man/externalFormats.Rd: move documentation for writeHB and
1090 :     writeMM here.
1091 :    
1092 :     * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
1093 :     (suggested by Paul Roecker).
1094 :    
1095 :     * tests/validObj.R (assertError): Comment out test that is failing
1096 :     after recent changes in r-devel.
1097 :    
1098 : maechler 860
1099 : maechler 848 2005-08-11 Martin Maechler <maechler@stat.math.ethz.ch>
1100 :    
1101 :     * R/AllClass.R: intermediate virtual class "denseMatrix"
1102 :     * man/denseMatrix-class.Rd
1103 :     * NAMESPACE: export it, and also export
1104 :     * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
1105 :    
1106 : bates 846 2005-08-10 Douglas Bates <bates@wisc.edu>
1107 :    
1108 : maechler 848 * DESCRIPTION (Version): 0.98-3 to CRAN
1109 :    
1110 : bates 846 * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
1111 :     matrix_solve code (which was really, really wrong).
1112 :    
1113 : bates 835 2005-08-07 Douglas Bates <bates@wisc.edu>
1114 : maechler 834
1115 :     * DESCRIPTION (Version): 0.98-2
1116 :    
1117 :     * R/HBMM.R (readHB), (readMM): read Matrix Market formats
1118 :    
1119 :     * R/lmer.R (abbrvNms): new
1120 :     * R/lmer.R (mcmcsamp): allow transformed parameters
1121 : bates 835 * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
1122 :     for the Harwell-Boeing and the MatrixMarket formats.
1123 : maechler 834
1124 :     2005-08-04 Martin Maechler <maechler@stat.math.ethz.ch>
1125 :    
1126 :     * man/dtrMatrix-class.Rd: add examples
1127 : bates 835 * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
1128 : maechler 834
1129 :     * TODO: note the dtpMatrix (docu) bug
1130 :    
1131 :     * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
1132 :     in order to ensure that new as.matrix() is used by old functions,
1133 :     e.g., svd(), qr(), eigen(), dist(),..;
1134 :     apply(), also matplot() or pairs().
1135 :    
1136 :    
1137 :     2005-08-03 Martin Maechler <maechler@stat.math.ethz.ch>
1138 :    
1139 :     * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
1140 :     add comments about 'control' / lmerControl() arguments
1141 :    
1142 : bates 835 2005-07-27 Douglas Bates <bates@wisc.edu>
1143 : bates 820
1144 : bates 835 * man/sleepstudy.Rd: Added the sleep data set.
1145 : maechler 1174 * DESCRIPTION (Version): 0.98-1 released to CRAN
1146 : bates 820
1147 : bates 835 2005-07-12 Douglas Bates <bates@wisc.edu>
1148 : maechler 834 * man/sleepstudy.Rd: Added the sleep data set.
1149 :    
1150 : bates 809 * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
1151 :     .Call calls that were producing spurious output.
1152 :    
1153 : bates 835 2005-07-05 Douglas Bates <bates@wisc.edu>
1154 : bates 801
1155 :     * R/lmer.R (lmer): stored updated variance component estimates in
1156 :     mer object for the generalized model. (Bug reported by Renaud
1157 :     Lancelot).
1158 :    
1159 : bates 835 2005-07-03 Douglas Bates <bates@wisc.edu>
1160 : bates 794
1161 :     * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
1162 :     unidimensional case.
1163 :    
1164 : bates 835 2005-06-08 Douglas Bates <bates@wisc.edu>
1165 : maechler 791
1166 :     * DESCRIPTION (Version): 0.96-1
1167 :    
1168 : maechler 1174 * moved lmer-class' R and C code moved from lme4 to here
1169 : maechler 791
1170 : bates 835 2005-06-04 Douglas Bates <bates@wisc.edu>
1171 : bates 763
1172 :     * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
1173 :     (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
1174 :    
1175 : bates 835 2005-06-02 Douglas Bates <bates@wisc.edu>
1176 : bates 763
1177 :     * src/Makefile.win: Forgot to update this when Makefile changed.
1178 :    
1179 : bates 835 2005-05-11 Douglas Bates <bates@wisc.edu>
1180 : bates 726
1181 :     * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
1182 :     bug reported by Kurt Hornik and Michael Hahsler.
1183 :    
1184 : bates 835 2005-05-10 Douglas Bates <bates@wisc.edu>
1185 : bates 725
1186 :     * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
1187 :     logical sparse matrices. These will also be used in the symbolic
1188 :     analysis for lmer objects.
1189 :    
1190 :     * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
1191 :     of b to the result. Fixes bug reported by Jean.Coursol@math.u-psud.fr
1192 : maechler 791
1193 : bates 835 2005-05-06 Douglas Bates <bates@wisc.edu>
1194 : bates 714
1195 :     * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
1196 :     colMeans, colSums, rowMeans and rowSums.
1197 :    
1198 : bates 835 2005-04-18 Douglas Bates <bates@wisc.edu>
1199 : bates 692
1200 :     * src/lgCMatrix.[ch]: code for _validate method and stub for
1201 :     multiplication operation.
1202 :    
1203 :     * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
1204 :     to dgetrs.
1205 :    
1206 :     * src/init.c: Fix cut-and-paste error in definition of
1207 :     dgeMatrix_matrix_solve
1208 :    
1209 :     * src/{many files}: Tighten code by using ALLOC_SLOT.
1210 :    
1211 : bates 835 2005-04-15 Douglas Bates <bates@wisc.edu>
1212 : bates 692
1213 :     * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
1214 :    
1215 :     * DESCRIPTION: Eliminate import of stats.
1216 :    
1217 : maechler 791
1218 : bates 835 2005-04-06 Douglas Bates <bates@wisc.edu>
1219 : bates 692
1220 :     * R/AllClass.R : add logical sparse matrix classes
1221 :    
1222 : maechler 687 2005-04-01 Martin Maechler <maechler@stat.math.ethz.ch>
1223 :    
1224 :     * R/dgTMatrix.R: add "[" method for triplet matrices
1225 :     * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
1226 :    
1227 : bates 835 2005-03-31 Douglas Bates <bates@wisc.edu>
1228 : maechler 687
1229 :     * DESCRIPTION (Version): release 0.95-5 to CRAN
1230 :    
1231 :     * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
1232 :     * R/sparseMatrix.R: %*%, crossprod()
1233 :     * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
1234 :     * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
1235 :     * src/lmer.c (lmer_fitted): fix thinko
1236 :    
1237 : maechler 676 2005-03-26 Martin Maechler <maechler@stat.math.ethz.ch>
1238 :    
1239 :     * R/AllClass.R: add two virtual sparse classes ``on top''
1240 :    
1241 :     2005-03-24 Martin Maechler <maechler@stat.math.ethz.ch>
1242 :    
1243 :     * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
1244 :     correspondingly fix examples and tests/ since new()
1245 :     doesn't work for virtual classes.
1246 :    
1247 : maechler 658 2005-03-17 Martin Maechler <maechler@stat.math.ethz.ch>
1248 :    
1249 :     * R/Matrix.R (as.matrix): method and one for unname()
1250 :     * tests/dpoMatrix.R: tests should now be less platform dependent;
1251 :     also run for R 2.1.0; using as.matrix()
1252 :    
1253 : bates 835 2005-03-15 Douglas Bates <bates@wisc.edu>
1254 : maechler 658
1255 :     * R/pMatrix.R: "pMatrix" class added
1256 :     * ....
1257 :    
1258 : bates 835 2005-03-14 Douglas Bates <bates@wisc.edu>
1259 : bates 645
1260 :     * R/dtpMatrix.R: Add unpack method and an example.
1261 :    
1262 :     * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
1263 :     of general symmetric matrices and associated S4 methods.
1264 :    
1265 : maechler 658 2005-03-10 Martin Maechler <maechler@stat.math.ethz.ch>
1266 :     +
1267 :     2005-03-05 Martin Maechler <maechler@stat.math.ethz.ch>
1268 :    
1269 :     * R/dgeMatrix.R (setAs): and many other files: more coercion,
1270 :     crossprod() and "%*%" methods added; tests, too.
1271 :     * tests/matprod.R: new, for testing these
1272 :    
1273 : bates 835 2005-03-03 Douglas Bates <bates@wisc.edu>
1274 : bates 599
1275 :     * src/lmer.c (lmer_fitted): Added.
1276 :    
1277 : bates 835 2005-03-02 Douglas Bates <bates@wisc.edu>
1278 : bates 596
1279 :     * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
1280 :    
1281 : bates 835 2005-02-28 Douglas Bates <bates@wisc.edu>
1282 : bates 582
1283 :     * src/*.c,po/,inst/po: Internationalization and localization of
1284 :     the package.
1285 :    
1286 :     * src/ldl.[ch]: Removed these as their contents are referenced in the
1287 :     R_ldl.c file.
1288 :    
1289 :     * src/flame.[ch]: Removed these source files.
1290 : maechler 658
1291 : bates 582 * src/dtrMatrix.c (make_array_triangular): Move to Mutils
1292 :    
1293 :     * src/LU.[ch],src/init.c: absorb in factorizations
1294 :    
1295 :     * src/Mutils.h: prepare for internationalization
1296 :    
1297 :     * src/cblas.h: move the enum definitions to Mutils.h and remove
1298 :     this file
1299 :    
1300 : maechler 578 2005-02-26 Martin Maechler <maechler@stat.math.ethz.ch>
1301 :    
1302 : maechler 579 * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
1303 :    
1304 :     * R/dtrMatrix.R: fix t() method
1305 :    
1306 : maechler 578 * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
1307 : maechler 658 * NAMESPACE: export them (and import generics from "methods")
1308 : maechler 578 * tests/group-methods.R : and test them.
1309 :    
1310 :     * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
1311 :     border case
1312 :    
1313 :     2005-02-24 Douglas Bates <bates@stat.wisc.edu>
1314 :    
1315 : maechler 658 * DESCRIPTION (Version): 0.95-2 released to CRAN
1316 : maechler 578
1317 :     * src/dgBCMatrix.c:
1318 :     * src/lmer.c: many changes
1319 :     * ...
1320 :    
1321 : maechler 512 2005-02-04 Martin Maechler <maechler@stat.math.ethz.ch>
1322 :    
1323 :     * R/Matrix.R: add more sophisticated show() method.
1324 :    
1325 : maechler 578 2005-02-02 Douglas Bates <bates@stat.wisc.edu>
1326 :    
1327 :     * */* : almost complete reorganization of classes.
1328 :    
1329 : bates 835 2005-01-26 Douglas Bates <bates@wisc.edu>
1330 : bates 460
1331 :     * R/AllGeneric.R: Added matrix exponential generic expm and a method
1332 :     for the geMatrix class.
1333 :    
1334 : bates 835 2005-01-24 Douglas Bates <bates@wisc.edu>
1335 : bates 460
1336 :     * src/Makefile (clean): Remove *.a and *.so
1337 :    
1338 :     * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
1339 :    
1340 : bates 835 2005-01-23 Douglas Bates <bates@wisc.edu>
1341 : bates 460
1342 : maechler 658 * src/lmer.c (Lind): Definition of Lind was backwards. This only
1343 : bates 460 had an effect in cases with more than 2 grouping factors.
1344 :    
1345 : bates 835 2005-01-03 Douglas Bates <bates@wisc.edu>
1346 : bates 415
1347 :     * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
1348 :    
1349 : bates 835 2004-12-23 Douglas Bates <bates@wisc.edu>
1350 : bates 410
1351 :     * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
1352 :     and R_useDynamicSymbols (suggested by B.D.Ripley).
1353 :    
1354 : bates 835 2004-12-14 Douglas Bates <bates@wisc.edu>
1355 : bates 392
1356 :     * R/sscMatrix.R: Add determinant methods
1357 :    
1358 :     * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
1359 :     for tripletMatrix to matrix.
1360 :    
1361 : bates 835 2004-12-13 Douglas Bates <bates@wisc.edu>
1362 : bates 388
1363 : bates 392 * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1364 :     no longer used.
1365 :    
1366 : bates 388 * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1367 :     with dynamic allocation of scratch arrays.
1368 :    
1369 :     * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1370 :     for multivariate random effects with multiple grouping factors.
1371 :     Fixes part but not all of #15.
1372 :    
1373 : bates 835 2004-12-03 Douglas Bates <bates@wisc.edu>
1374 : bates 375
1375 :     * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1376 :     scalar grouping factors corrected.
1377 :    
1378 : bates 835 2004-11-29 Douglas Bates <bates@wisc.edu>
1379 : bates 375
1380 :     * src/bCrosstab.c: remove diag_update which is no longer used
1381 :    
1382 : bates 835 2004-11-16 Douglas Bates <bates@wisc.edu>
1383 : bates 350
1384 :     * src/Metis_utils.c: Move metis.h include to C sources so that the
1385 :     .h file can be included.
1386 :    
1387 : bates 835 2004-11-12 Douglas Bates <bates@wisc.edu>
1388 : bates 342
1389 : bates 350 * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1390 : bates 342 Complete allocation of slots in NEW_OBJECT.
1391 :    
1392 :     * src/Mutils.h: Moved list of symbols to an include file
1393 :    
1394 : bates 835 2004-11-11 Douglas Bates <bates@wisc.edu>
1395 : bates 342
1396 :     * src/geMutils.c (Matrix_init): remove unused function
1397 :    
1398 : bates 835 2004-11-10 Douglas Bates <bates@wisc.edu>
1399 : bates 342
1400 :     * src/cscMatrix.c (csc_to_imagemat): removed unused function
1401 :    
1402 : bates 835 2004-11-05 Douglas Bates <bates@wisc.edu>
1403 : bates 327
1404 :     * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1405 :    
1406 : bates 835 2004-10-27 Douglas Bates <bates@wisc.edu>
1407 : bates 303
1408 :     * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1409 :    
1410 : bates 835 2004-10-04 Douglas Bates <bates@wisc.edu>
1411 : bates 296
1412 :     * src/init.c: Created R_init_Matrix and added registration of C
1413 :     routines.
1414 :    
1415 : bates 835 2004-10-02 Douglas Bates <bates@wisc.edu>
1416 : bates 283
1417 :     * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1418 :    
1419 : bates 835 2004-06-15 Douglas Bates <bates@wisc.edu>
1420 : bates 229
1421 :     * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1422 :    
1423 : bates 111 2004-04-20 Douglas Bates <bates@stat.wisc.edu>
1424 :    
1425 :     * src/Makefile.win ($(SHLIB)): Modifications per Uwe Ligges.
1426 :    
1427 : bates 109 2004-04-19 Douglas Bates <bates@stat.wisc.edu>
1428 :    
1429 :     * src/ssclme.c (ssclme_update_mm): fix logic error in
1430 :     ssclme_update_mm
1431 :    
1432 : bates 105 2004-04-18 Douglas Bates <bates@stat.wisc.edu>
1433 :    
1434 :     * src/ssclme.c (ssclme_coef, ssclme_coefGets): Create consistency
1435 :     in the order of unconstrained and constrained parameters.
1436 :     (ssclme_gradient): Added the gradients (not yet correct for
1437 :     multidimensional, unconstrained case).
1438 :    
1439 : bates 78 2004-04-14 Douglas Bates <bates@stat.wisc.edu>
1440 :    
1441 :     * src/ssclme.c (ssclme_EMsteps): Fix logic in REML update
1442 :    
1443 :     * src/Makefile.win: Remove unneeded ranlib call
1444 :    
1445 : bates 71 2004-04-12 Douglas Bates <bates@stat.wisc.edu>
1446 :    
1447 :     * DESCRIPTION (Version): New release
1448 :    
1449 :     * src/Makefile.win: Update Makefile.win to umfpack removal.
1450 :    
1451 : bates 49 2004-04-05 Douglas Bates <bates@bates2_home>
1452 :    
1453 :     * src/triplet_to_col.c: Create triplet_to_col as a native
1454 : maechler 658 function, not the version from umfpack. There were problems with
1455 : bates 49 the configuration of UMFPACK for 64-bit processors and there was
1456 :     only one umfpack routine being used so I moved it here.
1457 :    
1458 : bates 45 2004-04-04 Douglas Bates <bates@bates2_home>
1459 :    
1460 :     * src/ssclme.c (ssclme_variances): New function.
1461 :    
1462 : bates 28 2004-03-28 Douglas Bates <bates@bates2_home>
1463 :    
1464 :     * src/ssclme.c (ssclme_fitted): Added function.
1465 :    
1466 : bates 22 2004-03-27 Douglas Bates <bates@bates2_home>
1467 :    
1468 :     * src/ssclme.c (ssclme_transfer_dimnames): Add new function to
1469 :     store the dimnames in the XtX and bVar slots
1470 :     (ssclme_update_mm): Change the dimensions of the bVar slot
1471 :     components and the returned value from ssclme_ranef.
1472 :    
1473 : bates 10 2004-03-18 Douglas Bates <bates@stat.wisc.edu>
1474 :    
1475 :     * R/{pdMat.R,pdIdent.R,pdLogChol.R,pdMatrixLog.R,pdNatural.R},
1476 :     src/{pdMat.c,pdIdent.c,pdLogChol.c,pdNatural.c},
1477 :     tests/{pdCompSymm.R,pdDiag.R,pdIdent.R,pdLogChol.R,pdNatural.R},
1478 :     man/{pdMat-class.Rd,pdmatrix-class.Rd,corrmatrix-class.Rd,
1479 :     pdDiag-class.Rd,pdIdent-class.Rd,pdNatural-class.Rd,
1480 :     pdLogChol-class.Rd,coefGets.Rd,pdCompSymm-class.Rd,
1481 :     pdfactor-class.Rd,pdFactor.Rd,pdMatrix.Rd,
1482 :     pdBlocked-class.Rd},AllClass.R,AllGeneric.R:
1483 :     Moved the pdMat classes from the lme4 package.
1484 :    
1485 :     2004-03-02 Douglas Bates <bates@stat.wisc.edu>
1486 :    
1487 :     * man/ssclme-class.Rd: Update definition and documentation of the
1488 :     ssclme class to include the DIsqrt slot.
1489 :    
1490 :     * src/ssclme.c (ssclme_deviance): Modify order of computation
1491 :     (much faster using dsyrk, a level 3 BLAS routine).
1492 :    
1493 :     * src/Makefile (SUBLIBS): Change definition (K. Hornik)
1494 :    
1495 :     2004-02-28 Douglas Bates <bates@stat.wisc.edu>
1496 :    
1497 :     * tests/ssclme.R: Modify the test to account for the permutation
1498 :     of the levels of the grouping factors.
1499 :    
1500 :     2004-02-23 Douglas Bates <bates@stat.wisc.edu>
1501 :    
1502 :     * R/ssclme.R,src/ssclme.c (ssclme): Move slots of sscCrosstab slot
1503 :     directly into the ssclme class definition.
1504 :    
1505 :     2004-02-22 Douglas Bates <bates@stat.wisc.edu>
1506 :    
1507 :     * DESCRIPTION (Date): New release
1508 :    
1509 :     * man/ssclme-class.Rd: new file.
1510 :    
1511 :     * src/ssclme.c (ssclme_loglik): major revisions in design. It
1512 :     works and it's fast!
1513 :    
1514 :     2004-02-17 Douglas Bates <bates@stat.wisc.edu>
1515 :    
1516 :     * src/taucs/Makefile.win (lib): Change "ar" to "$(AR)" (B.Ripley)
1517 :    
1518 :     2004-02-16 Douglas Bates <bates@stat.wisc.edu>
1519 :    
1520 :     * DESCRIPTION (Date): New release
1521 :    
1522 :     * NAMESPACE: Don't export ssclme.
1523 :    
1524 :     * data/ScotsSec.rda, man/ScotsSec.Rd: Add Scottish secondary
1525 :     school data.
1526 :    
1527 :     2004-02-11 Douglas Bates <bates@stat.wisc.edu>
1528 :    
1529 :     * src/sscCrosstab.c (sscCrosstab): Added a row to the incidence to
1530 :     keep track of the fixed-effects and the response. Counts also
1531 :     gets an extra element, which is always one.
1532 :    
1533 :     * src/ldl.c: Include these routines from Tim Davis' LDL package.
1534 :    
1535 :     2004-02-10 Douglas Bates <bates@stat.wisc.edu>
1536 :    
1537 :     * src/cscMatrix.c (csc_transpose): new function
1538 :    
1539 :     * src/Mutils.c (csc_sort_columns): perm/iperm confusion corrected
1540 :     (csc_components_transpose): new function
1541 :    
1542 :     2004-02-06 Douglas Bates <bates@stat.wisc.edu>
1543 :    
1544 :     * src/triplet.c (triplet_validate): Fix Dim slot on generated
1545 :     triplets
1546 :    
1547 :     2004-01-30 Douglas Bates <bates@stat.wisc.edu>
1548 :    
1549 :     * R/sscCrosstab.R (sscCrosstab): Added sscCrosstab generator function.
1550 :    
1551 :     * src/LU.h (MATRIX_LU_H): Add #ifndef #define ... #endif to this
1552 :     and all other .h files in src.
1553 :    
1554 :     * src/Makefile.win: This and other Makefile.win files contributed
1555 :     by Brian Ripley.
1556 :    
1557 :     2004-01-27 Douglas Bates <bates@stat.wisc.edu>
1558 :    
1559 :     * R/syMatrix.R: Added methods for "%*%".
1560 :    
1561 :     * R/Hilbert.R (Hilbert): Changed Hilbert function to return a
1562 :     poMatrix object.
1563 :    
1564 :     2004-01-26 Douglas Bates <bates@stat.wisc.edu>
1565 :    
1566 :     * man/sscChol-class.Rd,man/mm.Rd,man/y.Rd: Added man pages.
1567 :    
1568 :     2004-01-25 Douglas Bates <bates@bates2_home>
1569 :    
1570 :     * inst/doc/Introduction.Rnw,Comparisons.Rnw: Added vignettes.
1571 :    
1572 :     * R/csc.R: Convert all cscMatrix classes to use Dim slot instead
1573 :     of nrow.
1574 :    
1575 :     2003-12-31 Douglas Bates <bates@stat.wisc.edu>
1576 :    
1577 :     * src/taucs/taucs.h: Moved taucs.h, amd.h, and umfpack.h into
1578 :     subdirectories.
1579 :    
1580 :     2003-12-08 Douglas Bates <bates@stat.wisc.edu>
1581 :    
1582 :     * src/taucs.h: Accidently referred to global header files
1583 :     instead of local files.
1584 :    
1585 :     2003-12-04 Douglas Bates <bates@stat.wisc.edu>
1586 :    
1587 :     * R/AllClass.R: Lots of changes. Removed all the lapack++ code
1588 :     and methods and replaced all classes with S4 classes.
1589 :    
1590 :     2003-04-19 Douglas Bates <bates@stat.wisc.edu>
1591 :    
1592 :     * R/det.R,man/det.Rd: Change name of det generic to determinant
1593 :    
1594 :     * src/R_LapackPP.cc: Change method of calculating determinants
1595 :    
1596 :     2003-02-03 Douglas Bates <bates@stat.wisc.edu>
1597 :    
1598 :     * DESCRIPTION (Version): removed empty data directory as requested
1599 :     by CRAN maintainers. Changed version number and date.
1600 :    
1601 :     2002-10-23 Douglas Bates <bates@stat.wisc.edu>
1602 :    
1603 :     * src/laindex.h: Applied patches from Brian Ripley for compilation
1604 :     under Windows.
1605 :    
1606 :     * Added configure.win and src/Makevars.win as requested by Brian
1607 :     Ripley.
1608 :    
1609 :     2002-05-03 Douglas Bates <bates@stat.wisc.edu>
1610 :    
1611 :     * src/lamatrix.h: Removing pre-1.2.0 compatibility code per Kurt
1612 :     Hornik.
1613 :    
1614 :     2002-04-24 Douglas Bates <bates@stat.wisc.edu>
1615 :    
1616 :     * configure.ac: Replaced configure.in with configure.ac
1617 :     contributed by Kurt Hornik.
1618 :    
1619 :     * aclocal.m4 (ac_clean_files): Replaced this with Kurt Hornik's
1620 :     version for R-1.5.0
1621 :    
1622 : maechler 512
1623 : bates 10 2001-12-10 Douglas Bates <bates@stat.wisc.edu>
1624 :    
1625 :     * man/eigen.Rd: Removed the .Alias in the example

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