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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1414, Tue Aug 22 17:25:43 2006 UTC
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1    2006-08-22  Douglas Bates  <bates@R-project.org>
2    
3            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
4            types of classed Matrices, matrices or numeric or logical vectors.
5            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
6    
7    2006-08-21  Douglas Bates  <bates@R-project.org>
8    
9            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
10            valgrind.
11            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
12            inverses.
13            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
14            -Wall warnings.
15            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
16            Use dup_mMatrix_as_dgeMatrix.
17    
18    2006-08-20  Douglas Bates  <bates@R-project.org>
19    
20            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
21            * tests/sparseQR.R: Added
22            * man/sparseQR-class.Rd: Document methods for qr.* generics
23            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
24    
25    2006-08-19  Douglas Bates  <bates@R-project.org>
26    
27            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
28            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
29            and qr.fitted.
30            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
31            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
32    
33    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
36            the base version has no "..." argument.
37    
38            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
39    
40            * R/Matrix.R: define and
41            * NAMESPACE: export as.numeric() and as.logical() methods.
42                    Let's hope these do not badly slow down something...
43            Finally export the zapsmall() method.
44    
45    2006-08-17  Douglas Bates  <bates@R-project.org>
46    
47            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
48            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
49            * src/dtCMatrix.c :Remove code that is no longer used
50            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
51    
52    2006-08-14  Douglas Bates  <bates@R-project.org>
53    
54            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
55            Csparse_to_logical and Csparse_symmetric_to_general.
56            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
57            coercion methods between CsparseMatrix and TsparseMatrix.
58    
59    2006-08-14  Douglas Bates  <bates@R-project.org>
60    
61            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
62            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
63            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
64            possible.
65    
66    2006-08-12  Douglas Bates  <bates@R-project.org>
67    
68            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
69              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
70              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
71              generalize conversions between TsparseMatrix, CsparseMatrix,
72              denseMatrix and matrix.  Preserve triangularity property and
73              propagate Dimnames in the easy cases.
74    
75    2006-08-10  Douglas Bates  <bates@R-project.org>
76    
77            * src/lmer.c: adjust checks in glmer_init for S4SXP
78            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
79            before S4SXP but for the wrong reasons.
80    
81    2006-08-08  Douglas Bates  <bates@R-project.org>
82    
83            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
84            Later modified to return the upper triangle only.
85            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
86    
87    2006-08-07  Douglas Bates  <bates@R-project.org>
88    
89            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
90            R-level conversion to a sparse symmetric class.
91            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
92            Remove conversion to sparse symmetric classes (now done in C code).
93    
94    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
97            * man/band.Rd:  adapt the \dontshow{} unit test.
98    
99    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * DESCRIPTION (Version): 0.995-14  for CRAN
102    
103            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
104    
105            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
106            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
107    
108            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
109            * R/Tsparse.R (tril, triu, band): methods
110            * R/dgRMatrix.R (tril, ...):    ditto
111            * man/band.Rd:                  ditto
112    
113    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/Matrix.R (head, tail): directly use utils:::head.matrix
116                    to be up-to-date automatically.
117    
118    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
121    
122            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
123            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
124            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
125            such that the S4 objects are always created by the current version
126            of R and 'Matrix' class definitions.
127    
128    2006-08-01  Douglas Bates  <bates@R-project.org>
129    
130            * R/lmer.R (LMEoptimize method), tests/lmer.R,
131            inst/external/test3comp.rda: Added warnings for convergence on
132            boundary and test cases.
133    
134            * src/lmer.c (mer_postVar): Modified to return the variances that
135            are marginal to the fixed effects, not conditional on them (which
136            is what the bVar slot contents represent).
137    
138    2006-07-31  Douglas Bates  <bates@R-project.org>
139    
140            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
141            function which calls the C function mer_hat_trace2.
142    
143            * man/ranef.Rd: Include description of "postVar" argument and
144            producing a caterpillar plot.
145    
146    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * NAMESPACE:    change  "correlation" to "corMatrix"
149            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
150            * R/dpoMatrix.R: ditto
151            * R/lmer.R:      ditto
152    
153    2006-07-28  Douglas Bates  <bates@R-project.org>
154    
155            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
156            RZXinv slot's contents into a separate internal function that can
157            be used in mer_hat_trace.
158    
159    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
162            via new smart
163            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
164            utility functions.
165    
166    
167    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/Csparse.R (tril, triu, band): do return *triangular* classed
170            matrices when appropriate; band() even symmetric ones.
171            (replCmat): extend to potentially all "CsparseMatrix"
172            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
173            allow subassignment for special sparse matrices.
174    
175            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
176    
177            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
178            argument; in glmer_*(): print only if(verbose).
179    
180            speed-optimize a few places by moving REAL(.) out of loops.
181    
182            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
183    
184    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
187                    since that wrongly triggers also for M[ logi , ]
188    
189            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
190            a symmetric matrix that results in a non-symmetric one.
191            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
192    
193            * R/dMatrix.R: make round(M) work as round(M, 0)
194    
195            * R/dgTMatrix.R (image): coordinate system and axis now use
196            1-based indices, not 0-based ones.
197    
198            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
199            * tests/indexing.R: test it.
200    
201            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
202            * man/isSymmetric-methods.Rd: and document it.
203    
204            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
205            * man/SparseM-conv.Rd: docu them
206    
207            * tests/other-pkgs.R: renamed from tests/graph.R and add example
208                    for 'SparseM' conversions
209    
210    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
211    
212            * R/Matrix.R (head): added head() and tail() methods.
213    
214    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * DESCRIPTION (Version): 0.995-12 released to CRAN
217    
218    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * tests/simple.R: add check for correct dsT -> dgT coercion;
221                    add check for correct printing of symmetric sparse matrices.
222    
223            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
224            for sparse symmetric matrices.
225    
226            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
227            diagonal twice.
228    
229    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
230    
231            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
232            being applied to the x slot (detected by Brian Ripley).
233    
234    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
237    
238            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
239    
240    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * src/lgCMatrix.c (lgCMatrix_diag): new function
243            * R/lgCMatrix.R (diag): for new method
244    
245            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
246                 ==> construction of illegal "*gTMatrix" via new() should
247                 now be much less easy:
248            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
249    
250            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
251                    directly.
252            * man/Matrix.Rd: documents it.
253    
254  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
255    
256          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 262 
262          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
263          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
264    
265            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
266            class.
267    
268    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/pMatrix.R: coercion pMatrix -> Tsparse
271    
272  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
273    
274            * DESCRIPTION (Version): 0.995-11 released to CRAN
275    
276          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
277          the output from mcmcsamp.          the output from mcmcsamp.
278    
# Line 23  Line 285 
285    
286          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
287          classes.          classes.
288            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
289    
290  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
# Line 60  Line 323 
323    
324          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
325          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.
326          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
327    
328    
329  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 446 
446          * 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)
447          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
448          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
449          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
450    
451  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
# Line 387  Line 650 
650  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
653          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
654          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
655    
656  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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