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revision 1316, Tue Jul 11 22:00:41 2006 UTC revision 1368, Sat Aug 12 17:34:00 2006 UTC
# Line 1  Line 1 
1    2006-08-12  Douglas Bates  <bates@R-project.org>
2    
3            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
4              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
5              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
6              generalize conversions between TsparseMatrix, CsparseMatrix,
7              denseMatrix and matrix.  Preserve triangularity property and
8              propagate Dimnames in the easy cases.
9    
10    2006-08-10  Douglas Bates  <bates@R-project.org>
11    
12            * src/lmer.c: adjust checks in glmer_init for S4SXP
13            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
14            before S4SXP but for the wrong reasons.
15    
16    2006-08-08  Douglas Bates  <bates@R-project.org>
17    
18            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
19            Later modified to return the upper triangle only.
20            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
21    
22    2006-08-07  Douglas Bates  <bates@R-project.org>
23    
24            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
25            R-level conversion to a sparse symmetric class.
26            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
27            Remove conversion to sparse symmetric classes (now done in C code).
28    
29    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
32            * man/band.Rd:  adapt the \dontshow{} unit test.
33    
34    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Version): 0.995-14  for CRAN
37    
38            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
39    
40            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
41            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
42    
43            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
44            * R/Tsparse.R (tril, triu, band): methods
45            * R/dgRMatrix.R (tril, ...):    ditto
46            * man/band.Rd:                  ditto
47    
48    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/Matrix.R (head, tail): directly use utils:::head.matrix
51                    to be up-to-date automatically.
52    
53    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
56    
57            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
58            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
59            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
60            such that the S4 objects are always created by the current version
61            of R and 'Matrix' class definitions.
62    
63    2006-08-01  Douglas Bates  <bates@R-project.org>
64    
65            * R/lmer.R (LMEoptimize method), tests/lmer.R,
66            inst/external/test3comp.rda: Added warnings for convergence on
67            boundary and test cases.
68    
69            * src/lmer.c (mer_postVar): Modified to return the variances that
70            are marginal to the fixed effects, not conditional on them (which
71            is what the bVar slot contents represent).
72    
73    2006-07-31  Douglas Bates  <bates@R-project.org>
74    
75            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
76            function which calls the C function mer_hat_trace2.
77    
78            * man/ranef.Rd: Include description of "postVar" argument and
79            producing a caterpillar plot.
80    
81    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * NAMESPACE:    change  "correlation" to "corMatrix"
84            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
85            * R/dpoMatrix.R: ditto
86            * R/lmer.R:      ditto
87    
88    2006-07-28  Douglas Bates  <bates@R-project.org>
89    
90            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
91            RZXinv slot's contents into a separate internal function that can
92            be used in mer_hat_trace.
93    
94    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
97            via new smart
98            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
99            utility functions.
100    
101    
102    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * R/Csparse.R (tril, triu, band): do return *triangular* classed
105            matrices when appropriate; band() even symmetric ones.
106            (replCmat): extend to potentially all "CsparseMatrix"
107            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
108            allow subassignment for special sparse matrices.
109    
110            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
111    
112            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
113            argument; in glmer_*(): print only if(verbose).
114    
115            speed-optimize a few places by moving REAL(.) out of loops.
116    
117            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
118    
119    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
122                    since that wrongly triggers also for M[ logi , ]
123    
124            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
125            a symmetric matrix that results in a non-symmetric one.
126            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
127    
128            * R/dMatrix.R: make round(M) work as round(M, 0)
129    
130            * R/dgTMatrix.R (image): coordinate system and axis now use
131            1-based indices, not 0-based ones.
132    
133            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
134            * tests/indexing.R: test it.
135    
136            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
137            * man/isSymmetric-methods.Rd: and document it.
138    
139            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
140            * man/SparseM-conv.Rd: docu them
141    
142            * tests/other-pkgs.R: renamed from tests/graph.R and add example
143                    for 'SparseM' conversions
144    
145    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
146    
147            * R/Matrix.R (head): added head() and tail() methods.
148    
149    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * DESCRIPTION (Version): 0.995-12 released to CRAN
152    
153    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * tests/simple.R: add check for correct dsT -> dgT coercion;
156                    add check for correct printing of symmetric sparse matrices.
157    
158            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
159            for sparse symmetric matrices.
160    
161            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
162            diagonal twice.
163    
164  2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>  2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
165    
166          * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER          * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
167          being applied to the x slot (detected by Brian Ripley).  Possible          being applied to the x slot (detected by Brian Ripley).
         problem with copying the diagonal elements twice?  
168    
169  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
# Line 44  Line 206 
206    
207  2006-06-12  Douglas Bates  <bates@R-project.org>  2006-06-12  Douglas Bates  <bates@R-project.org>
208    
209            * DESCRIPTION (Version): 0.995-11 released to CRAN
210    
211          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on          * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
212          the output from mcmcsamp.          the output from mcmcsamp.
213    
# Line 94  Line 258 
258    
259          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
260          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.
261          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
262    
263    
264  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 217  Line 381 
381          * 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)
382          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
383          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
384          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
385    
386  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
# Line 421  Line 585 
585  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
588          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
589          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
590    
591  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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