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revision 1330, Fri Jul 21 08:28:18 2006 UTC revision 1577, Mon Sep 18 21:01:45 2006 UTC
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1    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
4            symmetric and y missing in R code using %*% (cholmod_aat doesn't
5            accept a symmetric matrix).
6            * tests/group-methods.R: Uncomment test of crossprod applied to
7            lsCMatrix objects.
8    
9    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/AllClass.R (symmetricMatrix): add validity method (available
12            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
13    
14            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
15    
16            * tests/indexing.Rout.save:
17            * tests/indexing.R: additions, mainly for 'lsparse'
18    
19            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
20            case.
21    
22            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
23    
24    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
27                    as 'N' (1-letter - Ok?)
28    
29            * tests/group-methods.R: add test for logical + NAs
30    
31            * R/dMatrix.R ("Compare"): fix to work with NA's
32    
33            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
34    
35            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
36                    which is implemented.
37    
38    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * src/chm_common.c: coerce logical <-> double instead of
41            typecasting;  needed for "l" matrix handling in cholmod.
42    
43            * tests/other-pkgs.R (graph): small extension in "graph" checks.
44    
45            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
46            (Tsp2grNEL): other fixes needed
47    
48    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
51                    Matrices, since "lMatrix", also "lsparseM" can have NA
52            * R/ndenseMatrix.R, etc: new source files
53            * man/nsparseMatrix-classes.Rd, etc: new help files
54            * tests/: adaptions
55            * src/chm_common.c (chm_dense_to_SEXP): and others:
56                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
57            * src/Csparse.c, etc: dito
58    
59    2006-09-11  Douglas Bates  <bates@R-project.org>
60    
61            * src/Mutils.[ch],init.c inst/include/*.h: Move the
62            alloc_d**Matrix functions to the lme4 package.
63    
64    2006-09-09  Douglas Bates  <bates@R-project.org>
65    
66            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
67            fixed
68    
69    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/lMatrix.R: new
72    
73            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
74    
75            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
76            * man/tcrossprod.Rd: dito
77    
78    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
79    
80            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
81            for exported functions
82            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
83            Remove partitioning algorithms for sparse matrix reordering.  The
84            copyright on the Metis code was problematic and the methods were
85            rarely used.
86            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
87            operations are now done entirely in CHOLMOD code.
88    
89    2006-09-06  Douglas Bates  <bates@R-project.org>
90    
91            * src/Mutils.h: Remove functions that are no longer used.
92    
93    2006-09-04  Douglas Bates  <bates@R-project.org>
94    
95            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
96            * src/DEPS.mkf: update
97    
98    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * created branches/Matrix-for-R-2.3.x;  on trunk: do
101            * DESCRIPTION (Version): 0.9975-0
102            (Depends): R (>= 2.4.0)
103    
104    2006-09-01  Douglas Bates  <bates@R-project.org>
105    
106            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
107    
108    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
111            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
112    
113            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
114    
115    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
118            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
119            * R/dsparseMatrix.R: dito
120            * R/Csparse.R: dito
121    
122    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/dMatrix.R (Compare): improve availability of "<", etc
125            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
126    
127    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
130            of a 0-index which was used as 1-index (..hmm)
131    
132            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
133    
134            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
135            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
136            (.is.diagonal): dito
137    
138            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
139    
140            * R/Matrix.R (Matrix): also work for NA data
141    
142    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
145            in all cases.
146    
147    2006-08-27  Douglas Bates  <bates@R-project.org>
148    
149            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
150            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
151    
152    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
155            subclasses of "ddenseMatrix"
156            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
157            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
158            instead of half dozen specialized ones.
159    
160    2006-08-25  Douglas Bates  <bates@R-project.org>
161    
162            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
163            <tillard@cirad.fr> - ordering standard errors to match effects.
164    
165    2006-08-24  Douglas Bates  <bates@R-project.org>
166    
167            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
168            on R_ldl.
169            * R/lCholCMatrix.R,
170            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
171            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
172            * many files in ./R and ./src: Use more general version of
173            dup_mMatrix_as_dgeMatrix to simplify method definitions.
174            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
175            dtpMatrix, dspMatrix and dppMatrix conversions.
176    
177    
178    2006-08-23  Douglas Bates  <bates@R-project.org>
179    
180            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
181            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
182            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
183            dgeMatrix_crossprod (may need to do this in other places).
184            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
185            generic and method for dsCMatrix.  Use CHOLMOD for chol().
186    
187    2006-08-22  Douglas Bates  <bates@R-project.org>
188    
189            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
190            types of classed Matrices, matrices or numeric or logical vectors.
191            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
192            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
193            to Mutils.h (as an inline) and change name to Matrix_check_class;
194            fixes in as_cholmod_factor and chm_factor_to_SEXP.
195            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
196            dsCMatrix_matrix_solve.  Comment out vestigial functions.
197            * src/Csparse.c: use diag_P and uplo_P macros.
198    
199    2006-08-21  Douglas Bates  <bates@R-project.org>
200    
201            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
202            valgrind.
203            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
204            inverses.
205            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
206            -Wall warnings.
207            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
208            Use dup_mMatrix_as_dgeMatrix.
209    
210    2006-08-20  Douglas Bates  <bates@R-project.org>
211    
212            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
213            * tests/sparseQR.R: Added
214            * man/sparseQR-class.Rd: Document methods for qr.* generics
215            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
216    
217    2006-08-19  Douglas Bates  <bates@R-project.org>
218    
219            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
220            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
221            and qr.fitted.
222            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
223            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
224    
225    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
228            the base version has no "..." argument.
229    
230            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
231    
232            * R/Matrix.R: define and
233            * NAMESPACE: export as.numeric() and as.logical() methods.
234                    Let's hope these do not badly slow down something...
235            Finally export the zapsmall() method.
236    
237    2006-08-17  Douglas Bates  <bates@R-project.org>
238    
239            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
240            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
241            * src/dtCMatrix.c :Remove code that is no longer used
242            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
243    
244    2006-08-14  Douglas Bates  <bates@R-project.org>
245    
246            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
247            Csparse_to_logical and Csparse_symmetric_to_general.
248            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
249            coercion methods between CsparseMatrix and TsparseMatrix.
250    
251    2006-08-14  Douglas Bates  <bates@R-project.org>
252    
253            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
254            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
255            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
256            possible.
257    
258    2006-08-12  Douglas Bates  <bates@R-project.org>
259    
260            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
261              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
262              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
263              generalize conversions between TsparseMatrix, CsparseMatrix,
264              denseMatrix and matrix.  Preserve triangularity property and
265              propagate Dimnames in the easy cases.
266    
267    2006-08-10  Douglas Bates  <bates@R-project.org>
268    
269            * src/lmer.c: adjust checks in glmer_init for S4SXP
270            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
271            before S4SXP but for the wrong reasons.
272    
273    2006-08-08  Douglas Bates  <bates@R-project.org>
274    
275            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
276            Later modified to return the upper triangle only.
277            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
278    
279    2006-08-07  Douglas Bates  <bates@R-project.org>
280    
281            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
282            R-level conversion to a sparse symmetric class.
283            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
284            Remove conversion to sparse symmetric classes (now done in C code).
285    
286    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
289            * man/band.Rd:  adapt the \dontshow{} unit test.
290    
291    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * DESCRIPTION (Version): 0.995-14  for CRAN
294    
295            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
296    
297            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
298            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
299    
300            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
301            * R/Tsparse.R (tril, triu, band): methods
302            * R/dgRMatrix.R (tril, ...):    ditto
303            * man/band.Rd:                  ditto
304    
305    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Matrix.R (head, tail): directly use utils:::head.matrix
308                    to be up-to-date automatically.
309    
310    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
313    
314            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
315            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
316            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
317            such that the S4 objects are always created by the current version
318            of R and 'Matrix' class definitions.
319    
320    2006-08-01  Douglas Bates  <bates@R-project.org>
321    
322            * R/lmer.R (LMEoptimize method), tests/lmer.R,
323            inst/external/test3comp.rda: Added warnings for convergence on
324            boundary and test cases.
325    
326            * src/lmer.c (mer_postVar): Modified to return the variances that
327            are marginal to the fixed effects, not conditional on them (which
328            is what the bVar slot contents represent).
329    
330    2006-07-31  Douglas Bates  <bates@R-project.org>
331    
332            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
333            function which calls the C function mer_hat_trace2.
334    
335            * man/ranef.Rd: Include description of "postVar" argument and
336            producing a caterpillar plot.
337    
338    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * NAMESPACE:    change  "correlation" to "corMatrix"
341            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
342            * R/dpoMatrix.R: ditto
343            * R/lmer.R:      ditto
344    
345    2006-07-28  Douglas Bates  <bates@R-project.org>
346    
347            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
348            RZXinv slot's contents into a separate internal function that can
349            be used in mer_hat_trace.
350    
351    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
354            via new smart
355            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
356            utility functions.
357    
358    
359  2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/Csparse.R (tril, triu, band): do return *triangular* classed
362            matrices when appropriate; band() even symmetric ones.
363            (replCmat): extend to potentially all "CsparseMatrix"
364            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
365            allow subassignment for special sparse matrices.
366    
367            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
368    
369          * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'          * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
370          argument; in glmer_*(): print only if(verbose).          argument; in glmer_*(): print only if(verbose).
371    
# Line 149  Line 515 
515    
516          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
517          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
518          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
519    
520    
521  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 272  Line 638 
638          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
639          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
640          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
641          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
642    
643  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
# Line 476  Line 842 
842  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
845          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
846          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
847    
848  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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