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revision 1351, Mon Aug 7 16:51:14 2006 UTC revision 1455, Mon Aug 28 15:35:44 2006 UTC
# Line 1  Line 1 
1    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
4            in all cases.
5    
6    2006-08-27  Douglas Bates  <bates@R-project.org>
7    
8            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
9            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
10    
11    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
14            subclasses of "ddenseMatrix"
15            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
16            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
17            instead of half dozen specialized ones.
18    
19    2006-08-25  Douglas Bates  <bates@R-project.org>
20    
21            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
22            <tillard@cirad.fr> - ordering standard errors to match effects.
23    
24    2006-08-24  Douglas Bates  <bates@R-project.org>
25    
26            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
27            on R_ldl.
28            * R/lCholCMatrix.R,
29            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
30            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
31            * many files in ./R and ./src: Use more general version of
32            dup_mMatrix_as_dgeMatrix to simplify method definitions.
33            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
34            dtpMatrix, dspMatrix and dppMatrix conversions.
35    
36    
37    2006-08-23  Douglas Bates  <bates@R-project.org>
38    
39            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
40            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
41            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
42            dgeMatrix_crossprod (may need to do this in other places).
43            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
44            generic and method for dsCMatrix.  Use CHOLMOD for chol().
45    
46    2006-08-22  Douglas Bates  <bates@R-project.org>
47    
48            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
49            types of classed Matrices, matrices or numeric or logical vectors.
50            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
51            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
52            to Mutils.h (as an inline) and change name to Matrix_check_class;
53            fixes in as_cholmod_factor and chm_factor_to_SEXP.
54            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
55            dsCMatrix_matrix_solve.  Comment out vestigial functions.
56            * src/Csparse.c: use diag_P and uplo_P macros.
57    
58    2006-08-21  Douglas Bates  <bates@R-project.org>
59    
60            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
61            valgrind.
62            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
63            inverses.
64            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
65            -Wall warnings.
66            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
67            Use dup_mMatrix_as_dgeMatrix.
68    
69    2006-08-20  Douglas Bates  <bates@R-project.org>
70    
71            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
72            * tests/sparseQR.R: Added
73            * man/sparseQR-class.Rd: Document methods for qr.* generics
74            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
75    
76    2006-08-19  Douglas Bates  <bates@R-project.org>
77    
78            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
79            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
80            and qr.fitted.
81            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
82            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
83    
84    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
87            the base version has no "..." argument.
88    
89            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
90    
91            * R/Matrix.R: define and
92            * NAMESPACE: export as.numeric() and as.logical() methods.
93                    Let's hope these do not badly slow down something...
94            Finally export the zapsmall() method.
95    
96    2006-08-17  Douglas Bates  <bates@R-project.org>
97    
98            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
99            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
100            * src/dtCMatrix.c :Remove code that is no longer used
101            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
102    
103    2006-08-14  Douglas Bates  <bates@R-project.org>
104    
105            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
106            Csparse_to_logical and Csparse_symmetric_to_general.
107            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
108            coercion methods between CsparseMatrix and TsparseMatrix.
109    
110    2006-08-14  Douglas Bates  <bates@R-project.org>
111    
112            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
113            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
114            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
115            possible.
116    
117    2006-08-12  Douglas Bates  <bates@R-project.org>
118    
119            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
120              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
121              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
122              generalize conversions between TsparseMatrix, CsparseMatrix,
123              denseMatrix and matrix.  Preserve triangularity property and
124              propagate Dimnames in the easy cases.
125    
126    2006-08-10  Douglas Bates  <bates@R-project.org>
127    
128            * src/lmer.c: adjust checks in glmer_init for S4SXP
129            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
130            before S4SXP but for the wrong reasons.
131    
132    2006-08-08  Douglas Bates  <bates@R-project.org>
133    
134            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
135            Later modified to return the upper triangle only.
136            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
137    
138    2006-08-07  Douglas Bates  <bates@R-project.org>
139    
140            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
141            R-level conversion to a sparse symmetric class.
142            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
143            Remove conversion to sparse symmetric classes (now done in C code).
144    
145  2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147          * R/dgCMatrix.R: disable old crossprod and tcrossprod methods          * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
# Line 14  Line 158 
158    
159          * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new          * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
160          * R/Tsparse.R (tril, triu, band): methods          * R/Tsparse.R (tril, triu, band): methods
161          * R/dgRMatrix.R (tril, ...):    dito          * R/dgRMatrix.R (tril, ...):    ditto
162          * man/band.Rd:                  dito          * man/band.Rd:                  ditto
163    
164  2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
# Line 54  Line 198 
198    
199          * NAMESPACE:    change  "correlation" to "corMatrix"          * NAMESPACE:    change  "correlation" to "corMatrix"
200          * R/AllClass.R: to avoid clash with S3 class in 'nlme'.          * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
201          * R/dpoMatrix.R: dito          * R/dpoMatrix.R: ditto
202          * R/lmer.R:      dito          * R/lmer.R:      ditto
203    
204  2006-07-28  Douglas Bates  <bates@R-project.org>  2006-07-28  Douglas Bates  <bates@R-project.org>
205    
# Line 230  Line 374 
374    
375          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
376          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.
377          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
378    
379    
380  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 353  Line 497 
497          * 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)
498          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
499          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
500          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
501    
502  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
# Line 557  Line 701 
701  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
704          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
705          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
706    
707  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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