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revision 1312, Thu Jul 6 15:29:56 2006 UTC revision 1352, Mon Aug 7 18:31:12 2006 UTC
# Line 1  Line 1 
1    2006-08-07  Douglas Bates  <bates@R-project.org>
2    
3            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
4            R-level conversion to a sparse symmetric class.
5            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
6            Remove conversion to sparse symmetric classes (now done in C code).
7    
8    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
11            * man/band.Rd:  adapt the \dontshow{} unit test.
12    
13    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * DESCRIPTION (Version): 0.995-14  for CRAN
16    
17            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
18    
19            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
20            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
21    
22            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
23            * R/Tsparse.R (tril, triu, band): methods
24            * R/dgRMatrix.R (tril, ...):    ditto
25            * man/band.Rd:                  ditto
26    
27    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Matrix.R (head, tail): directly use utils:::head.matrix
30                    to be up-to-date automatically.
31    
32    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
35    
36            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
37            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
38            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
39            such that the S4 objects are always created by the current version
40            of R and 'Matrix' class definitions.
41    
42    2006-08-01  Douglas Bates  <bates@R-project.org>
43    
44            * R/lmer.R (LMEoptimize method), tests/lmer.R,
45            inst/external/test3comp.rda: Added warnings for convergence on
46            boundary and test cases.
47    
48            * src/lmer.c (mer_postVar): Modified to return the variances that
49            are marginal to the fixed effects, not conditional on them (which
50            is what the bVar slot contents represent).
51    
52    2006-07-31  Douglas Bates  <bates@R-project.org>
53    
54            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
55            function which calls the C function mer_hat_trace2.
56    
57            * man/ranef.Rd: Include description of "postVar" argument and
58            producing a caterpillar plot.
59    
60    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * NAMESPACE:    change  "correlation" to "corMatrix"
63            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
64            * R/dpoMatrix.R: ditto
65            * R/lmer.R:      ditto
66    
67    2006-07-28  Douglas Bates  <bates@R-project.org>
68    
69            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
70            RZXinv slot's contents into a separate internal function that can
71            be used in mer_hat_trace.
72    
73    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
76            via new smart
77            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
78            utility functions.
79    
80    
81    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/Csparse.R (tril, triu, band): do return *triangular* classed
84            matrices when appropriate; band() even symmetric ones.
85            (replCmat): extend to potentially all "CsparseMatrix"
86            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
87            allow subassignment for special sparse matrices.
88    
89            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
90    
91            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
92            argument; in glmer_*(): print only if(verbose).
93    
94            speed-optimize a few places by moving REAL(.) out of loops.
95    
96            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
97    
98    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
101                    since that wrongly triggers also for M[ logi , ]
102    
103            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
104            a symmetric matrix that results in a non-symmetric one.
105            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
106    
107            * R/dMatrix.R: make round(M) work as round(M, 0)
108    
109            * R/dgTMatrix.R (image): coordinate system and axis now use
110            1-based indices, not 0-based ones.
111    
112            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
113            * tests/indexing.R: test it.
114    
115            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
116            * man/isSymmetric-methods.Rd: and document it.
117    
118            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
119            * man/SparseM-conv.Rd: docu them
120    
121            * tests/other-pkgs.R: renamed from tests/graph.R and add example
122                    for 'SparseM' conversions
123    
124    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
125    
126            * R/Matrix.R (head): added head() and tail() methods.
127    
128    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * DESCRIPTION (Version): 0.995-12 released to CRAN
131    
132    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * tests/simple.R: add check for correct dsT -> dgT coercion;
135                    add check for correct printing of symmetric sparse matrices.
136    
137            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
138            for sparse symmetric matrices.
139    
140            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
141            diagonal twice.
142    
143    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
144    
145            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
146            being applied to the x slot (detected by Brian Ripley).
147    
148    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
151    
152            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
153    
154    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * src/lgCMatrix.c (lgCMatrix_diag): new function
157            * R/lgCMatrix.R (diag): for new method
158    
159            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
160                 ==> construction of illegal "*gTMatrix" via new() should
161                 now be much less easy:
162            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
163    
164            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
165                    directly.
166            * man/Matrix.Rd: documents it.
167    
168  2006-07-06  Douglas Bates  <bates@R-project.org>  2006-07-06  Douglas Bates  <bates@R-project.org>
169    
170          * src/pedigree.c (pedigree_inbreeding): Correction in          * src/pedigree.c (pedigree_inbreeding): Correction in
# Line 9  Line 176 
176          objects.  Modified validity check on pedigree objects to account          objects.  Modified validity check on pedigree objects to account
177          for nonparallel patterns of missingness of parents.          for nonparallel patterns of missingness of parents.
178    
179            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
180            class.
181    
182    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/pMatrix.R: coercion pMatrix -> Tsparse
185    
186  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
187    
188            * DESCRIPTION (Version): 0.995-11 released to CRAN
189    
190          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
191          the output from mcmcsamp.          the output from mcmcsamp.
192    
# Line 23  Line 199 
199    
200          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
201          classes.          classes.
202            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
203    
204  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
# Line 60  Line 237 
237    
238          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
239          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.
240          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
241    
242    
243  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 183  Line 360 
360          * 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)
361          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
362          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
363          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
364    
365  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
# Line 387  Line 564 
564  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
567          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
568          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
569    
570  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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