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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1398, Sun Aug 20 03:26:06 2006 UTC
# Line 1  Line 1 
1    2006-08-19  Douglas Bates  <bates@R-project.org>
2    
3            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
4            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
5            and qr.fitted.
6            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
7            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
8    
9    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
12            the base version has no "..." argument.
13    
14            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
15    
16            * R/Matrix.R: define and
17            * NAMESPACE: export as.numeric() and as.logical() methods.
18                    Let's hope these do not badly slow down something...
19            Finally export the zapsmall() method.
20    
21    2006-08-17  Douglas Bates  <bates@R-project.org>
22    
23            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
24            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
25            * src/dtCMatrix.c :Remove code that is no longer used
26            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
27    
28    2006-08-14  Douglas Bates  <bates@R-project.org>
29    
30            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
31            Csparse_to_logical and Csparse_symmetric_to_general.
32            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
33            coercion methods between CsparseMatrix and TsparseMatrix.
34    
35    2006-08-14  Douglas Bates  <bates@R-project.org>
36    
37            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
38            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
39            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
40            possible.
41    
42    2006-08-12  Douglas Bates  <bates@R-project.org>
43    
44            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
45              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
46              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
47              generalize conversions between TsparseMatrix, CsparseMatrix,
48              denseMatrix and matrix.  Preserve triangularity property and
49              propagate Dimnames in the easy cases.
50    
51    2006-08-10  Douglas Bates  <bates@R-project.org>
52    
53            * src/lmer.c: adjust checks in glmer_init for S4SXP
54            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
55            before S4SXP but for the wrong reasons.
56    
57    2006-08-08  Douglas Bates  <bates@R-project.org>
58    
59            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
60            Later modified to return the upper triangle only.
61            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
62    
63    2006-08-07  Douglas Bates  <bates@R-project.org>
64    
65            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
66            R-level conversion to a sparse symmetric class.
67            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
68            Remove conversion to sparse symmetric classes (now done in C code).
69    
70    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
73            * man/band.Rd:  adapt the \dontshow{} unit test.
74    
75    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * DESCRIPTION (Version): 0.995-14  for CRAN
78    
79            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
80    
81            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
82            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
83    
84            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
85            * R/Tsparse.R (tril, triu, band): methods
86            * R/dgRMatrix.R (tril, ...):    ditto
87            * man/band.Rd:                  ditto
88    
89    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/Matrix.R (head, tail): directly use utils:::head.matrix
92                    to be up-to-date automatically.
93    
94    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
97    
98            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
99            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
100            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
101            such that the S4 objects are always created by the current version
102            of R and 'Matrix' class definitions.
103    
104    2006-08-01  Douglas Bates  <bates@R-project.org>
105    
106            * R/lmer.R (LMEoptimize method), tests/lmer.R,
107            inst/external/test3comp.rda: Added warnings for convergence on
108            boundary and test cases.
109    
110            * src/lmer.c (mer_postVar): Modified to return the variances that
111            are marginal to the fixed effects, not conditional on them (which
112            is what the bVar slot contents represent).
113    
114    2006-07-31  Douglas Bates  <bates@R-project.org>
115    
116            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
117            function which calls the C function mer_hat_trace2.
118    
119            * man/ranef.Rd: Include description of "postVar" argument and
120            producing a caterpillar plot.
121    
122    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * NAMESPACE:    change  "correlation" to "corMatrix"
125            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
126            * R/dpoMatrix.R: ditto
127            * R/lmer.R:      ditto
128    
129    2006-07-28  Douglas Bates  <bates@R-project.org>
130    
131            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
132            RZXinv slot's contents into a separate internal function that can
133            be used in mer_hat_trace.
134    
135    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
138            via new smart
139            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
140            utility functions.
141    
142    
143    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/Csparse.R (tril, triu, band): do return *triangular* classed
146            matrices when appropriate; band() even symmetric ones.
147            (replCmat): extend to potentially all "CsparseMatrix"
148            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
149            allow subassignment for special sparse matrices.
150    
151            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
152    
153            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
154            argument; in glmer_*(): print only if(verbose).
155    
156            speed-optimize a few places by moving REAL(.) out of loops.
157    
158            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
159    
160    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
163                    since that wrongly triggers also for M[ logi , ]
164    
165            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
166            a symmetric matrix that results in a non-symmetric one.
167            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
168    
169            * R/dMatrix.R: make round(M) work as round(M, 0)
170    
171            * R/dgTMatrix.R (image): coordinate system and axis now use
172            1-based indices, not 0-based ones.
173    
174            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
175            * tests/indexing.R: test it.
176    
177            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
178            * man/isSymmetric-methods.Rd: and document it.
179    
180            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
181            * man/SparseM-conv.Rd: docu them
182    
183            * tests/other-pkgs.R: renamed from tests/graph.R and add example
184                    for 'SparseM' conversions
185    
186    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
187    
188            * R/Matrix.R (head): added head() and tail() methods.
189    
190    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * DESCRIPTION (Version): 0.995-12 released to CRAN
193    
194    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * tests/simple.R: add check for correct dsT -> dgT coercion;
197                    add check for correct printing of symmetric sparse matrices.
198    
199            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
200            for sparse symmetric matrices.
201    
202            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
203            diagonal twice.
204    
205    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
206    
207            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
208            being applied to the x slot (detected by Brian Ripley).
209    
210    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
213    
214            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
215    
216    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * src/lgCMatrix.c (lgCMatrix_diag): new function
219            * R/lgCMatrix.R (diag): for new method
220    
221            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
222                 ==> construction of illegal "*gTMatrix" via new() should
223                 now be much less easy:
224            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
225    
226            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
227                    directly.
228            * man/Matrix.Rd: documents it.
229    
230    2006-07-06  Douglas Bates  <bates@R-project.org>
231    
232            * src/pedigree.c (pedigree_inbreeding): Correction in
233            initialization.  This function is not currently being used and is
234            not fully tested.
235    
236            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
237            Introduced the glmer class.  Added code for mcmcmsamp on glmer
238            objects.  Modified validity check on pedigree objects to account
239            for nonparallel patterns of missingness of parents.
240    
241            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
242            class.
243    
244    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/pMatrix.R: coercion pMatrix -> Tsparse
247    
248    2006-06-12  Douglas Bates  <bates@R-project.org>
249    
250            * DESCRIPTION (Version): 0.995-11 released to CRAN
251    
252            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
253            the output from mcmcsamp.
254    
255  2006-06-10  Douglas Bates  <bates@R-project.org>  2006-06-10  Douglas Bates  <bates@R-project.org>
256    
257          * R/lmer.R (simulestimate): added          * R/lmer.R (simulestimate): added C code for calculating the trace
258            of the hat matrix.
259    
260  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
263          classes.          classes.
264            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
265    
266  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
# Line 43  Line 299 
299    
300          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
301          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.
302          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
303    
304    
305  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 422 
422          * 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)
423          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
424          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
425          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
426    
427  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
# Line 370  Line 626 
626  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
629          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
630          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
631    
632  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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