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revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1439, Thu Aug 24 18:24:50 2006 UTC
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1    2006-08-24  Douglas Bates  <bates@R-project.org>
2    
3            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
4            on R_ldl.
5            * R/lCholCMatrix.R,
6            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
7            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
8            * many files in ./R and ./src: Use more general version of
9            dup_mMatrix_as_dgeMatrix to simplify method definitions.
10    
11    2006-08-23  Douglas Bates  <bates@R-project.org>
12    
13            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
14            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
15            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
16            dgeMatrix_crossprod (may need to do this in other places).
17            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
18            generic and method for dsCMatrix.  Use CHOLMOD for chol().
19    
20    2006-08-22  Douglas Bates  <bates@R-project.org>
21    
22            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
23            types of classed Matrices, matrices or numeric or logical vectors.
24            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
25            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
26            to Mutils.h (as an inline) and change name to Matrix_check_class;
27            fixes in as_cholmod_factor and chm_factor_to_SEXP.
28            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
29            dsCMatrix_matrix_solve.  Comment out vestigial functions.
30            * src/Csparse.c: use diag_P and uplo_P macros.
31    
32    2006-08-21  Douglas Bates  <bates@R-project.org>
33    
34            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
35            valgrind.
36            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
37            inverses.
38            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
39            -Wall warnings.
40            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
41            Use dup_mMatrix_as_dgeMatrix.
42    
43    2006-08-20  Douglas Bates  <bates@R-project.org>
44    
45            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
46            * tests/sparseQR.R: Added
47            * man/sparseQR-class.Rd: Document methods for qr.* generics
48            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
49    
50    2006-08-19  Douglas Bates  <bates@R-project.org>
51    
52            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
53            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
54            and qr.fitted.
55            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
56            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
57    
58    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
61            the base version has no "..." argument.
62    
63            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
64    
65            * R/Matrix.R: define and
66            * NAMESPACE: export as.numeric() and as.logical() methods.
67                    Let's hope these do not badly slow down something...
68            Finally export the zapsmall() method.
69    
70    2006-08-17  Douglas Bates  <bates@R-project.org>
71    
72            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
73            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
74            * src/dtCMatrix.c :Remove code that is no longer used
75            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
76    
77    2006-08-14  Douglas Bates  <bates@R-project.org>
78    
79            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
80            Csparse_to_logical and Csparse_symmetric_to_general.
81            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
82            coercion methods between CsparseMatrix and TsparseMatrix.
83    
84    2006-08-14  Douglas Bates  <bates@R-project.org>
85    
86            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
87            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
88            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
89            possible.
90    
91    2006-08-12  Douglas Bates  <bates@R-project.org>
92    
93            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
94              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
95              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
96              generalize conversions between TsparseMatrix, CsparseMatrix,
97              denseMatrix and matrix.  Preserve triangularity property and
98              propagate Dimnames in the easy cases.
99    
100    2006-08-10  Douglas Bates  <bates@R-project.org>
101    
102            * src/lmer.c: adjust checks in glmer_init for S4SXP
103            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
104            before S4SXP but for the wrong reasons.
105    
106    2006-08-08  Douglas Bates  <bates@R-project.org>
107    
108            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
109            Later modified to return the upper triangle only.
110            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
111    
112    2006-08-07  Douglas Bates  <bates@R-project.org>
113    
114            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
115            R-level conversion to a sparse symmetric class.
116            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
117            Remove conversion to sparse symmetric classes (now done in C code).
118    
119    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
122            * man/band.Rd:  adapt the \dontshow{} unit test.
123    
124    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * DESCRIPTION (Version): 0.995-14  for CRAN
127    
128            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
129    
130            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
131            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
132    
133            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
134            * R/Tsparse.R (tril, triu, band): methods
135            * R/dgRMatrix.R (tril, ...):    ditto
136            * man/band.Rd:                  ditto
137    
138    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Matrix.R (head, tail): directly use utils:::head.matrix
141                    to be up-to-date automatically.
142    
143    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
146    
147            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
148            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
149            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
150            such that the S4 objects are always created by the current version
151            of R and 'Matrix' class definitions.
152    
153    2006-08-01  Douglas Bates  <bates@R-project.org>
154    
155            * R/lmer.R (LMEoptimize method), tests/lmer.R,
156            inst/external/test3comp.rda: Added warnings for convergence on
157            boundary and test cases.
158    
159            * src/lmer.c (mer_postVar): Modified to return the variances that
160            are marginal to the fixed effects, not conditional on them (which
161            is what the bVar slot contents represent).
162    
163    2006-07-31  Douglas Bates  <bates@R-project.org>
164    
165            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
166            function which calls the C function mer_hat_trace2.
167    
168            * man/ranef.Rd: Include description of "postVar" argument and
169            producing a caterpillar plot.
170    
171    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * NAMESPACE:    change  "correlation" to "corMatrix"
174            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
175            * R/dpoMatrix.R: ditto
176            * R/lmer.R:      ditto
177    
178    2006-07-28  Douglas Bates  <bates@R-project.org>
179    
180            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
181            RZXinv slot's contents into a separate internal function that can
182            be used in mer_hat_trace.
183    
184    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
187            via new smart
188            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
189            utility functions.
190    
191    
192    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/Csparse.R (tril, triu, band): do return *triangular* classed
195            matrices when appropriate; band() even symmetric ones.
196            (replCmat): extend to potentially all "CsparseMatrix"
197            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
198            allow subassignment for special sparse matrices.
199    
200            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
201    
202            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
203            argument; in glmer_*(): print only if(verbose).
204    
205            speed-optimize a few places by moving REAL(.) out of loops.
206    
207            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
208    
209    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
212                    since that wrongly triggers also for M[ logi , ]
213    
214            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
215            a symmetric matrix that results in a non-symmetric one.
216            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
217    
218            * R/dMatrix.R: make round(M) work as round(M, 0)
219    
220            * R/dgTMatrix.R (image): coordinate system and axis now use
221            1-based indices, not 0-based ones.
222    
223            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
224            * tests/indexing.R: test it.
225    
226            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
227            * man/isSymmetric-methods.Rd: and document it.
228    
229            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
230            * man/SparseM-conv.Rd: docu them
231    
232            * tests/other-pkgs.R: renamed from tests/graph.R and add example
233                    for 'SparseM' conversions
234    
235    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
236    
237            * R/Matrix.R (head): added head() and tail() methods.
238    
239    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * DESCRIPTION (Version): 0.995-12 released to CRAN
242    
243    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * tests/simple.R: add check for correct dsT -> dgT coercion;
246                    add check for correct printing of symmetric sparse matrices.
247    
248            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
249            for sparse symmetric matrices.
250    
251            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
252            diagonal twice.
253    
254    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
255    
256            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
257            being applied to the x slot (detected by Brian Ripley).
258    
259    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
262    
263            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
264    
265    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * src/lgCMatrix.c (lgCMatrix_diag): new function
268            * R/lgCMatrix.R (diag): for new method
269    
270            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
271                 ==> construction of illegal "*gTMatrix" via new() should
272                 now be much less easy:
273            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
274    
275            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
276                    directly.
277            * man/Matrix.Rd: documents it.
278    
279    2006-07-06  Douglas Bates  <bates@R-project.org>
280    
281            * src/pedigree.c (pedigree_inbreeding): Correction in
282            initialization.  This function is not currently being used and is
283            not fully tested.
284    
285            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
286            Introduced the glmer class.  Added code for mcmcmsamp on glmer
287            objects.  Modified validity check on pedigree objects to account
288            for nonparallel patterns of missingness of parents.
289    
290            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
291            class.
292    
293    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/pMatrix.R: coercion pMatrix -> Tsparse
296    
297    2006-06-12  Douglas Bates  <bates@R-project.org>
298    
299            * DESCRIPTION (Version): 0.995-11 released to CRAN
300    
301            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
302            the output from mcmcsamp.
303    
304    2006-06-10  Douglas Bates  <bates@R-project.org>
305    
306            * R/lmer.R (simulestimate): added C code for calculating the trace
307            of the hat matrix.
308    
309    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
312            classes.
313            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
314    
315    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/dgTMatrix.R (colSums): etc. All four of
318            colSums(), rowSums(), colMeans(), rowMeans() now should work for
319            all "Matrices".
320    
321  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
322    
323          * 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 348 
348    
349          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
350          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.
351          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
352    
353    
354  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 471 
471          * 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)
472          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
473          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
474          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
475    
476  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
# Line 355  Line 675 
675  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
678          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
679          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
680    
681  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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