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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1455, Mon Aug 28 15:35:44 2006 UTC
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1    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
4            in all cases.
5    
6    2006-08-27  Douglas Bates  <bates@R-project.org>
7    
8            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
9            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
10    
11    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
14            subclasses of "ddenseMatrix"
15            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
16            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
17            instead of half dozen specialized ones.
18    
19    2006-08-25  Douglas Bates  <bates@R-project.org>
20    
21            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
22            <tillard@cirad.fr> - ordering standard errors to match effects.
23    
24    2006-08-24  Douglas Bates  <bates@R-project.org>
25    
26            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
27            on R_ldl.
28            * R/lCholCMatrix.R,
29            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
30            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
31            * many files in ./R and ./src: Use more general version of
32            dup_mMatrix_as_dgeMatrix to simplify method definitions.
33            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
34            dtpMatrix, dspMatrix and dppMatrix conversions.
35    
36    
37    2006-08-23  Douglas Bates  <bates@R-project.org>
38    
39            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
40            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
41            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
42            dgeMatrix_crossprod (may need to do this in other places).
43            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
44            generic and method for dsCMatrix.  Use CHOLMOD for chol().
45    
46    2006-08-22  Douglas Bates  <bates@R-project.org>
47    
48            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
49            types of classed Matrices, matrices or numeric or logical vectors.
50            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
51            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
52            to Mutils.h (as an inline) and change name to Matrix_check_class;
53            fixes in as_cholmod_factor and chm_factor_to_SEXP.
54            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
55            dsCMatrix_matrix_solve.  Comment out vestigial functions.
56            * src/Csparse.c: use diag_P and uplo_P macros.
57    
58    2006-08-21  Douglas Bates  <bates@R-project.org>
59    
60            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
61            valgrind.
62            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
63            inverses.
64            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
65            -Wall warnings.
66            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
67            Use dup_mMatrix_as_dgeMatrix.
68    
69    2006-08-20  Douglas Bates  <bates@R-project.org>
70    
71            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
72            * tests/sparseQR.R: Added
73            * man/sparseQR-class.Rd: Document methods for qr.* generics
74            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
75    
76    2006-08-19  Douglas Bates  <bates@R-project.org>
77    
78            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
79            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
80            and qr.fitted.
81            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
82            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
83    
84    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
87            the base version has no "..." argument.
88    
89            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
90    
91            * R/Matrix.R: define and
92            * NAMESPACE: export as.numeric() and as.logical() methods.
93                    Let's hope these do not badly slow down something...
94            Finally export the zapsmall() method.
95    
96    2006-08-17  Douglas Bates  <bates@R-project.org>
97    
98            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
99            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
100            * src/dtCMatrix.c :Remove code that is no longer used
101            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
102    
103    2006-08-14  Douglas Bates  <bates@R-project.org>
104    
105            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
106            Csparse_to_logical and Csparse_symmetric_to_general.
107            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
108            coercion methods between CsparseMatrix and TsparseMatrix.
109    
110    2006-08-14  Douglas Bates  <bates@R-project.org>
111    
112            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
113            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
114            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
115            possible.
116    
117    2006-08-12  Douglas Bates  <bates@R-project.org>
118    
119            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
120              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
121              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
122              generalize conversions between TsparseMatrix, CsparseMatrix,
123              denseMatrix and matrix.  Preserve triangularity property and
124              propagate Dimnames in the easy cases.
125    
126    2006-08-10  Douglas Bates  <bates@R-project.org>
127    
128            * src/lmer.c: adjust checks in glmer_init for S4SXP
129            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
130            before S4SXP but for the wrong reasons.
131    
132    2006-08-08  Douglas Bates  <bates@R-project.org>
133    
134            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
135            Later modified to return the upper triangle only.
136            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
137    
138    2006-08-07  Douglas Bates  <bates@R-project.org>
139    
140            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
141            R-level conversion to a sparse symmetric class.
142            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
143            Remove conversion to sparse symmetric classes (now done in C code).
144    
145    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
148            * man/band.Rd:  adapt the \dontshow{} unit test.
149    
150    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * DESCRIPTION (Version): 0.995-14  for CRAN
153    
154            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
155    
156            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
157            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
158    
159            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
160            * R/Tsparse.R (tril, triu, band): methods
161            * R/dgRMatrix.R (tril, ...):    ditto
162            * man/band.Rd:                  ditto
163    
164    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Matrix.R (head, tail): directly use utils:::head.matrix
167                    to be up-to-date automatically.
168    
169    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
172    
173            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
174            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
175            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
176            such that the S4 objects are always created by the current version
177            of R and 'Matrix' class definitions.
178    
179    2006-08-01  Douglas Bates  <bates@R-project.org>
180    
181            * R/lmer.R (LMEoptimize method), tests/lmer.R,
182            inst/external/test3comp.rda: Added warnings for convergence on
183            boundary and test cases.
184    
185            * src/lmer.c (mer_postVar): Modified to return the variances that
186            are marginal to the fixed effects, not conditional on them (which
187            is what the bVar slot contents represent).
188    
189    2006-07-31  Douglas Bates  <bates@R-project.org>
190    
191            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
192            function which calls the C function mer_hat_trace2.
193    
194            * man/ranef.Rd: Include description of "postVar" argument and
195            producing a caterpillar plot.
196    
197    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * NAMESPACE:    change  "correlation" to "corMatrix"
200            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
201            * R/dpoMatrix.R: ditto
202            * R/lmer.R:      ditto
203    
204    2006-07-28  Douglas Bates  <bates@R-project.org>
205    
206            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
207            RZXinv slot's contents into a separate internal function that can
208            be used in mer_hat_trace.
209    
210    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
213            via new smart
214            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
215            utility functions.
216    
217    
218    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Csparse.R (tril, triu, band): do return *triangular* classed
221            matrices when appropriate; band() even symmetric ones.
222            (replCmat): extend to potentially all "CsparseMatrix"
223            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
224            allow subassignment for special sparse matrices.
225    
226            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
227    
228            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
229            argument; in glmer_*(): print only if(verbose).
230    
231            speed-optimize a few places by moving REAL(.) out of loops.
232    
233            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
234    
235    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
238                    since that wrongly triggers also for M[ logi , ]
239    
240            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
241            a symmetric matrix that results in a non-symmetric one.
242            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
243    
244            * R/dMatrix.R: make round(M) work as round(M, 0)
245    
246            * R/dgTMatrix.R (image): coordinate system and axis now use
247            1-based indices, not 0-based ones.
248    
249            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
250            * tests/indexing.R: test it.
251    
252            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
253            * man/isSymmetric-methods.Rd: and document it.
254    
255            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
256            * man/SparseM-conv.Rd: docu them
257    
258            * tests/other-pkgs.R: renamed from tests/graph.R and add example
259                    for 'SparseM' conversions
260    
261    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
262    
263            * R/Matrix.R (head): added head() and tail() methods.
264    
265    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * DESCRIPTION (Version): 0.995-12 released to CRAN
268    
269    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * tests/simple.R: add check for correct dsT -> dgT coercion;
272                    add check for correct printing of symmetric sparse matrices.
273    
274            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
275            for sparse symmetric matrices.
276    
277            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
278            diagonal twice.
279    
280    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
281    
282            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
283            being applied to the x slot (detected by Brian Ripley).
284    
285    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
288    
289            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
290    
291    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * src/lgCMatrix.c (lgCMatrix_diag): new function
294            * R/lgCMatrix.R (diag): for new method
295    
296            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
297                 ==> construction of illegal "*gTMatrix" via new() should
298                 now be much less easy:
299            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
300    
301            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
302                    directly.
303            * man/Matrix.Rd: documents it.
304    
305    2006-07-06  Douglas Bates  <bates@R-project.org>
306    
307            * src/pedigree.c (pedigree_inbreeding): Correction in
308            initialization.  This function is not currently being used and is
309            not fully tested.
310    
311            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
312            Introduced the glmer class.  Added code for mcmcmsamp on glmer
313            objects.  Modified validity check on pedigree objects to account
314            for nonparallel patterns of missingness of parents.
315    
316            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
317            class.
318    
319    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/pMatrix.R: coercion pMatrix -> Tsparse
322    
323    2006-06-12  Douglas Bates  <bates@R-project.org>
324    
325            * DESCRIPTION (Version): 0.995-11 released to CRAN
326    
327            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
328            the output from mcmcsamp.
329    
330    2006-06-10  Douglas Bates  <bates@R-project.org>
331    
332            * R/lmer.R (simulestimate): added C code for calculating the trace
333            of the hat matrix.
334    
335    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
338            classes.
339            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
340    
341    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/dgTMatrix.R (colSums): etc. All four of
344            colSums(), rowSums(), colMeans(), rowMeans() now should work for
345            all "Matrices".
346    
347  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
348    
349          * R/lmer.R (panel.ci): Add a reference line at zero and a          * R/lmer.R (panel.ci): Add a reference line at zero and a
# Line 28  Line 374 
374    
375          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
376          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.
377          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
378    
379    
380  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 497 
497          * 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)
498          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
499          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
500          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
501    
502  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
# Line 355  Line 701 
701  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
704          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
705          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
706    
707  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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