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revision 1313, Thu Jul 6 17:24:01 2006 UTC revision 1405, Mon Aug 21 14:43:00 2006 UTC
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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 12  Line 253 
253          * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer          * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
254          class.          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 26  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 63  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 186  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 390  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>

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