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 1312, Thu Jul 6 15:29:56 2006 UTC revision 1405, Mon Aug 21 14:43:00 2006 UTC
# Line 1  Line 1 
1    2006-08-21  Douglas Bates  <bates@R-project.org>
2    
3            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
4            valgrind.
5    
6    2006-08-20  Douglas Bates  <bates@R-project.org>
7    
8            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
9            * tests/sparseQR.R: Added
10            * man/sparseQR-class.Rd: Document methods for qr.* generics
11            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
12    
13    2006-08-19  Douglas Bates  <bates@R-project.org>
14    
15            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
16            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
17            and qr.fitted.
18            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
19            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
20    
21    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
24            the base version has no "..." argument.
25    
26            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
27    
28            * R/Matrix.R: define and
29            * NAMESPACE: export as.numeric() and as.logical() methods.
30                    Let's hope these do not badly slow down something...
31            Finally export the zapsmall() method.
32    
33    2006-08-17  Douglas Bates  <bates@R-project.org>
34    
35            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
36            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
37            * src/dtCMatrix.c :Remove code that is no longer used
38            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
39    
40    2006-08-14  Douglas Bates  <bates@R-project.org>
41    
42            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
43            Csparse_to_logical and Csparse_symmetric_to_general.
44            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
45            coercion methods between CsparseMatrix and TsparseMatrix.
46    
47    2006-08-14  Douglas Bates  <bates@R-project.org>
48    
49            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
50            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
51            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
52            possible.
53    
54    2006-08-12  Douglas Bates  <bates@R-project.org>
55    
56            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
57              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
58              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
59              generalize conversions between TsparseMatrix, CsparseMatrix,
60              denseMatrix and matrix.  Preserve triangularity property and
61              propagate Dimnames in the easy cases.
62    
63    2006-08-10  Douglas Bates  <bates@R-project.org>
64    
65            * src/lmer.c: adjust checks in glmer_init for S4SXP
66            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
67            before S4SXP but for the wrong reasons.
68    
69    2006-08-08  Douglas Bates  <bates@R-project.org>
70    
71            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
72            Later modified to return the upper triangle only.
73            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
74    
75    2006-08-07  Douglas Bates  <bates@R-project.org>
76    
77            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
78            R-level conversion to a sparse symmetric class.
79            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
80            Remove conversion to sparse symmetric classes (now done in C code).
81    
82    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
85            * man/band.Rd:  adapt the \dontshow{} unit test.
86    
87    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * DESCRIPTION (Version): 0.995-14  for CRAN
90    
91            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
92    
93            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
94            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
95    
96            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
97            * R/Tsparse.R (tril, triu, band): methods
98            * R/dgRMatrix.R (tril, ...):    ditto
99            * man/band.Rd:                  ditto
100    
101    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Matrix.R (head, tail): directly use utils:::head.matrix
104                    to be up-to-date automatically.
105    
106    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
109    
110            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
111            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
112            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
113            such that the S4 objects are always created by the current version
114            of R and 'Matrix' class definitions.
115    
116    2006-08-01  Douglas Bates  <bates@R-project.org>
117    
118            * R/lmer.R (LMEoptimize method), tests/lmer.R,
119            inst/external/test3comp.rda: Added warnings for convergence on
120            boundary and test cases.
121    
122            * src/lmer.c (mer_postVar): Modified to return the variances that
123            are marginal to the fixed effects, not conditional on them (which
124            is what the bVar slot contents represent).
125    
126    2006-07-31  Douglas Bates  <bates@R-project.org>
127    
128            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
129            function which calls the C function mer_hat_trace2.
130    
131            * man/ranef.Rd: Include description of "postVar" argument and
132            producing a caterpillar plot.
133    
134    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * NAMESPACE:    change  "correlation" to "corMatrix"
137            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
138            * R/dpoMatrix.R: ditto
139            * R/lmer.R:      ditto
140    
141    2006-07-28  Douglas Bates  <bates@R-project.org>
142    
143            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
144            RZXinv slot's contents into a separate internal function that can
145            be used in mer_hat_trace.
146    
147    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
150            via new smart
151            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
152            utility functions.
153    
154    
155    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/Csparse.R (tril, triu, band): do return *triangular* classed
158            matrices when appropriate; band() even symmetric ones.
159            (replCmat): extend to potentially all "CsparseMatrix"
160            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
161            allow subassignment for special sparse matrices.
162    
163            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
164    
165            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
166            argument; in glmer_*(): print only if(verbose).
167    
168            speed-optimize a few places by moving REAL(.) out of loops.
169    
170            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
171    
172    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
175                    since that wrongly triggers also for M[ logi , ]
176    
177            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
178            a symmetric matrix that results in a non-symmetric one.
179            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
180    
181            * R/dMatrix.R: make round(M) work as round(M, 0)
182    
183            * R/dgTMatrix.R (image): coordinate system and axis now use
184            1-based indices, not 0-based ones.
185    
186            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
187            * tests/indexing.R: test it.
188    
189            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
190            * man/isSymmetric-methods.Rd: and document it.
191    
192            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
193            * man/SparseM-conv.Rd: docu them
194    
195            * tests/other-pkgs.R: renamed from tests/graph.R and add example
196                    for 'SparseM' conversions
197    
198    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
199    
200            * R/Matrix.R (head): added head() and tail() methods.
201    
202    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * DESCRIPTION (Version): 0.995-12 released to CRAN
205    
206    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * tests/simple.R: add check for correct dsT -> dgT coercion;
209                    add check for correct printing of symmetric sparse matrices.
210    
211            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
212            for sparse symmetric matrices.
213    
214            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
215            diagonal twice.
216    
217    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
218    
219            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
220            being applied to the x slot (detected by Brian Ripley).
221    
222    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
225    
226            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
227    
228    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * src/lgCMatrix.c (lgCMatrix_diag): new function
231            * R/lgCMatrix.R (diag): for new method
232    
233            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
234                 ==> construction of illegal "*gTMatrix" via new() should
235                 now be much less easy:
236            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
237    
238            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
239                    directly.
240            * man/Matrix.Rd: documents it.
241    
242  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
243    
244          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 250 
250          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
251          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
252    
253            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
254            class.
255    
256    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/pMatrix.R: coercion pMatrix -> Tsparse
259    
260  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
261    
262            * DESCRIPTION (Version): 0.995-11 released to CRAN
263    
264          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
265          the output from mcmcsamp.          the output from mcmcsamp.
266    
# Line 23  Line 273 
273    
274          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
275          classes.          classes.
276            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
277    
278  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
# Line 60  Line 311 
311    
312          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
313          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.
314          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
315    
316    
317  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 434 
434          * 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)
435          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
436          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
437          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
438    
439  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
# Line 387  Line 638 
638  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
639    
640          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
641          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
642          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
643    
644  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

Legend:
Removed from v.1312  
changed lines
  Added in v.1405

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