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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1577, Mon Sep 18 21:01:45 2006 UTC
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1    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
4            symmetric and y missing in R code using %*% (cholmod_aat doesn't
5            accept a symmetric matrix).
6            * tests/group-methods.R: Uncomment test of crossprod applied to
7            lsCMatrix objects.
8    
9    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/AllClass.R (symmetricMatrix): add validity method (available
12            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
13    
14            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
15    
16            * tests/indexing.Rout.save:
17            * tests/indexing.R: additions, mainly for 'lsparse'
18    
19            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
20            case.
21    
22            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
23    
24    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
27                    as 'N' (1-letter - Ok?)
28    
29            * tests/group-methods.R: add test for logical + NAs
30    
31            * R/dMatrix.R ("Compare"): fix to work with NA's
32    
33            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
34    
35            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
36                    which is implemented.
37    
38    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * src/chm_common.c: coerce logical <-> double instead of
41            typecasting;  needed for "l" matrix handling in cholmod.
42    
43            * tests/other-pkgs.R (graph): small extension in "graph" checks.
44    
45            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
46            (Tsp2grNEL): other fixes needed
47    
48    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
51                    Matrices, since "lMatrix", also "lsparseM" can have NA
52            * R/ndenseMatrix.R, etc: new source files
53            * man/nsparseMatrix-classes.Rd, etc: new help files
54            * tests/: adaptions
55            * src/chm_common.c (chm_dense_to_SEXP): and others:
56                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
57            * src/Csparse.c, etc: dito
58    
59    2006-09-11  Douglas Bates  <bates@R-project.org>
60    
61            * src/Mutils.[ch],init.c inst/include/*.h: Move the
62            alloc_d**Matrix functions to the lme4 package.
63    
64    2006-09-09  Douglas Bates  <bates@R-project.org>
65    
66            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
67            fixed
68    
69    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/lMatrix.R: new
72    
73            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
74    
75            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
76            * man/tcrossprod.Rd: dito
77    
78    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
79    
80            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
81            for exported functions
82            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
83            Remove partitioning algorithms for sparse matrix reordering.  The
84            copyright on the Metis code was problematic and the methods were
85            rarely used.
86            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
87            operations are now done entirely in CHOLMOD code.
88    
89    2006-09-06  Douglas Bates  <bates@R-project.org>
90    
91            * src/Mutils.h: Remove functions that are no longer used.
92    
93    2006-09-04  Douglas Bates  <bates@R-project.org>
94    
95            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
96            * src/DEPS.mkf: update
97    
98    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * created branches/Matrix-for-R-2.3.x;  on trunk: do
101            * DESCRIPTION (Version): 0.9975-0
102            (Depends): R (>= 2.4.0)
103    
104    2006-09-01  Douglas Bates  <bates@R-project.org>
105    
106            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
107    
108    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
111            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
112    
113            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
114    
115    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
118            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
119            * R/dsparseMatrix.R: dito
120            * R/Csparse.R: dito
121    
122    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/dMatrix.R (Compare): improve availability of "<", etc
125            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
126    
127    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
130            of a 0-index which was used as 1-index (..hmm)
131    
132            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
133    
134            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
135            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
136            (.is.diagonal): dito
137    
138            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
139    
140            * R/Matrix.R (Matrix): also work for NA data
141    
142    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
145            in all cases.
146    
147    2006-08-27  Douglas Bates  <bates@R-project.org>
148    
149            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
150            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
151    
152    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
155            subclasses of "ddenseMatrix"
156            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
157            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
158            instead of half dozen specialized ones.
159    
160    2006-08-25  Douglas Bates  <bates@R-project.org>
161    
162            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
163            <tillard@cirad.fr> - ordering standard errors to match effects.
164    
165    2006-08-24  Douglas Bates  <bates@R-project.org>
166    
167            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
168            on R_ldl.
169            * R/lCholCMatrix.R,
170            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
171            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
172            * many files in ./R and ./src: Use more general version of
173            dup_mMatrix_as_dgeMatrix to simplify method definitions.
174            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
175            dtpMatrix, dspMatrix and dppMatrix conversions.
176    
177    
178    2006-08-23  Douglas Bates  <bates@R-project.org>
179    
180            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
181            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
182            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
183            dgeMatrix_crossprod (may need to do this in other places).
184            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
185            generic and method for dsCMatrix.  Use CHOLMOD for chol().
186    
187    2006-08-22  Douglas Bates  <bates@R-project.org>
188    
189            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
190            types of classed Matrices, matrices or numeric or logical vectors.
191            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
192            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
193            to Mutils.h (as an inline) and change name to Matrix_check_class;
194            fixes in as_cholmod_factor and chm_factor_to_SEXP.
195            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
196            dsCMatrix_matrix_solve.  Comment out vestigial functions.
197            * src/Csparse.c: use diag_P and uplo_P macros.
198    
199  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
200    
201          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
202          valgrind.          valgrind.
203            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
204            inverses.
205            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
206            -Wall warnings.
207            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
208            Use dup_mMatrix_as_dgeMatrix.
209    
210  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
211    

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