SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1288, Thu Jun 1 20:41:20 2006 UTC revision 1442, Thu Aug 24 22:08:11 2006 UTC
# Line 1  Line 1 
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            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
11            dtpMatrix, dspMatrix and dppMatrix conversions.
12    
13    
14    2006-08-23  Douglas Bates  <bates@R-project.org>
15    
16            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
17            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
18            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
19            dgeMatrix_crossprod (may need to do this in other places).
20            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
21            generic and method for dsCMatrix.  Use CHOLMOD for chol().
22    
23    2006-08-22  Douglas Bates  <bates@R-project.org>
24    
25            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
26            types of classed Matrices, matrices or numeric or logical vectors.
27            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
28            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
29            to Mutils.h (as an inline) and change name to Matrix_check_class;
30            fixes in as_cholmod_factor and chm_factor_to_SEXP.
31            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
32            dsCMatrix_matrix_solve.  Comment out vestigial functions.
33            * src/Csparse.c: use diag_P and uplo_P macros.
34    
35    2006-08-21  Douglas Bates  <bates@R-project.org>
36    
37            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
38            valgrind.
39            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
40            inverses.
41            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
42            -Wall warnings.
43            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
44            Use dup_mMatrix_as_dgeMatrix.
45    
46    2006-08-20  Douglas Bates  <bates@R-project.org>
47    
48            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
49            * tests/sparseQR.R: Added
50            * man/sparseQR-class.Rd: Document methods for qr.* generics
51            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
52    
53    2006-08-19  Douglas Bates  <bates@R-project.org>
54    
55            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
56            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
57            and qr.fitted.
58            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
59            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
60    
61    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
64            the base version has no "..." argument.
65    
66            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
67    
68            * R/Matrix.R: define and
69            * NAMESPACE: export as.numeric() and as.logical() methods.
70                    Let's hope these do not badly slow down something...
71            Finally export the zapsmall() method.
72    
73    2006-08-17  Douglas Bates  <bates@R-project.org>
74    
75            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
76            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
77            * src/dtCMatrix.c :Remove code that is no longer used
78            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
79    
80    2006-08-14  Douglas Bates  <bates@R-project.org>
81    
82            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
83            Csparse_to_logical and Csparse_symmetric_to_general.
84            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
85            coercion methods between CsparseMatrix and TsparseMatrix.
86    
87    2006-08-14  Douglas Bates  <bates@R-project.org>
88    
89            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
90            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
91            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
92            possible.
93    
94    2006-08-12  Douglas Bates  <bates@R-project.org>
95    
96            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
97              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
98              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
99              generalize conversions between TsparseMatrix, CsparseMatrix,
100              denseMatrix and matrix.  Preserve triangularity property and
101              propagate Dimnames in the easy cases.
102    
103    2006-08-10  Douglas Bates  <bates@R-project.org>
104    
105            * src/lmer.c: adjust checks in glmer_init for S4SXP
106            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
107            before S4SXP but for the wrong reasons.
108    
109    2006-08-08  Douglas Bates  <bates@R-project.org>
110    
111            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
112            Later modified to return the upper triangle only.
113            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
114    
115    2006-08-07  Douglas Bates  <bates@R-project.org>
116    
117            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
118            R-level conversion to a sparse symmetric class.
119            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
120            Remove conversion to sparse symmetric classes (now done in C code).
121    
122    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
125            * man/band.Rd:  adapt the \dontshow{} unit test.
126    
127    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * DESCRIPTION (Version): 0.995-14  for CRAN
130    
131            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
132    
133            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
134            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
135    
136            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
137            * R/Tsparse.R (tril, triu, band): methods
138            * R/dgRMatrix.R (tril, ...):    ditto
139            * man/band.Rd:                  ditto
140    
141    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/Matrix.R (head, tail): directly use utils:::head.matrix
144                    to be up-to-date automatically.
145    
146    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
149    
150            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
151            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
152            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
153            such that the S4 objects are always created by the current version
154            of R and 'Matrix' class definitions.
155    
156    2006-08-01  Douglas Bates  <bates@R-project.org>
157    
158            * R/lmer.R (LMEoptimize method), tests/lmer.R,
159            inst/external/test3comp.rda: Added warnings for convergence on
160            boundary and test cases.
161    
162            * src/lmer.c (mer_postVar): Modified to return the variances that
163            are marginal to the fixed effects, not conditional on them (which
164            is what the bVar slot contents represent).
165    
166    2006-07-31  Douglas Bates  <bates@R-project.org>
167    
168            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
169            function which calls the C function mer_hat_trace2.
170    
171            * man/ranef.Rd: Include description of "postVar" argument and
172            producing a caterpillar plot.
173    
174    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * NAMESPACE:    change  "correlation" to "corMatrix"
177            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
178            * R/dpoMatrix.R: ditto
179            * R/lmer.R:      ditto
180    
181    2006-07-28  Douglas Bates  <bates@R-project.org>
182    
183            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
184            RZXinv slot's contents into a separate internal function that can
185            be used in mer_hat_trace.
186    
187    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
190            via new smart
191            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
192            utility functions.
193    
194    
195    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/Csparse.R (tril, triu, band): do return *triangular* classed
198            matrices when appropriate; band() even symmetric ones.
199            (replCmat): extend to potentially all "CsparseMatrix"
200            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
201            allow subassignment for special sparse matrices.
202    
203            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
204    
205            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
206            argument; in glmer_*(): print only if(verbose).
207    
208            speed-optimize a few places by moving REAL(.) out of loops.
209    
210            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
211    
212    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
215                    since that wrongly triggers also for M[ logi , ]
216    
217            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
218            a symmetric matrix that results in a non-symmetric one.
219            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
220    
221            * R/dMatrix.R: make round(M) work as round(M, 0)
222    
223            * R/dgTMatrix.R (image): coordinate system and axis now use
224            1-based indices, not 0-based ones.
225    
226            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
227            * tests/indexing.R: test it.
228    
229            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
230            * man/isSymmetric-methods.Rd: and document it.
231    
232            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
233            * man/SparseM-conv.Rd: docu them
234    
235            * tests/other-pkgs.R: renamed from tests/graph.R and add example
236                    for 'SparseM' conversions
237    
238    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
239    
240            * R/Matrix.R (head): added head() and tail() methods.
241    
242    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * DESCRIPTION (Version): 0.995-12 released to CRAN
245    
246    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * tests/simple.R: add check for correct dsT -> dgT coercion;
249                    add check for correct printing of symmetric sparse matrices.
250    
251            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
252            for sparse symmetric matrices.
253    
254            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
255            diagonal twice.
256    
257    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
258    
259            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
260            being applied to the x slot (detected by Brian Ripley).
261    
262    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
265    
266            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
267    
268    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * src/lgCMatrix.c (lgCMatrix_diag): new function
271            * R/lgCMatrix.R (diag): for new method
272    
273            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
274                 ==> construction of illegal "*gTMatrix" via new() should
275                 now be much less easy:
276            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
277    
278            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
279                    directly.
280            * man/Matrix.Rd: documents it.
281    
282    2006-07-06  Douglas Bates  <bates@R-project.org>
283    
284            * src/pedigree.c (pedigree_inbreeding): Correction in
285            initialization.  This function is not currently being used and is
286            not fully tested.
287    
288            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
289            Introduced the glmer class.  Added code for mcmcmsamp on glmer
290            objects.  Modified validity check on pedigree objects to account
291            for nonparallel patterns of missingness of parents.
292    
293            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
294            class.
295    
296    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/pMatrix.R: coercion pMatrix -> Tsparse
299    
300    2006-06-12  Douglas Bates  <bates@R-project.org>
301    
302            * DESCRIPTION (Version): 0.995-11 released to CRAN
303    
304            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
305            the output from mcmcsamp.
306    
307    2006-06-10  Douglas Bates  <bates@R-project.org>
308    
309            * R/lmer.R (simulestimate): added C code for calculating the trace
310            of the hat matrix.
311    
312    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
315            classes.
316            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
317    
318    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/dgTMatrix.R (colSums): etc. All four of
321            colSums(), rowSums(), colMeans(), rowMeans() now should work for
322            all "Matrices".
323    
324  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>  2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
325    
326          * 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 351 
351    
352          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
353          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.
354          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
355    
356    
357  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 151  Line 474 
474          * 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)
475          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
476          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
477          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
478    
479  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
# Line 355  Line 678 
678  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
681          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
682          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
683    
684  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

Legend:
Removed from v.1288  
changed lines
  Added in v.1442

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge