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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1370, Mon Aug 14 19:00:02 2006 UTC
# Line 1  Line 1 
1    2006-08-14  Douglas Bates  <bates@R-project.org>
2    
3            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
4            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
5            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
6            possible.
7    
8    2006-08-12  Douglas Bates  <bates@R-project.org>
9    
10            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
11              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
12              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
13              generalize conversions between TsparseMatrix, CsparseMatrix,
14              denseMatrix and matrix.  Preserve triangularity property and
15              propagate Dimnames in the easy cases.
16    
17    2006-08-10  Douglas Bates  <bates@R-project.org>
18    
19            * src/lmer.c: adjust checks in glmer_init for S4SXP
20            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
21            before S4SXP but for the wrong reasons.
22    
23    2006-08-08  Douglas Bates  <bates@R-project.org>
24    
25            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
26            Later modified to return the upper triangle only.
27            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
28    
29    2006-08-07  Douglas Bates  <bates@R-project.org>
30    
31            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
32            R-level conversion to a sparse symmetric class.
33            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
34            Remove conversion to sparse symmetric classes (now done in C code).
35    
36    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
39            * man/band.Rd:  adapt the \dontshow{} unit test.
40    
41    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * DESCRIPTION (Version): 0.995-14  for CRAN
44    
45            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
46    
47            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
48            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
49    
50            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
51            * R/Tsparse.R (tril, triu, band): methods
52            * R/dgRMatrix.R (tril, ...):    ditto
53            * man/band.Rd:                  ditto
54    
55    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Matrix.R (head, tail): directly use utils:::head.matrix
58                    to be up-to-date automatically.
59    
60    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
63    
64            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
65            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
66            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
67            such that the S4 objects are always created by the current version
68            of R and 'Matrix' class definitions.
69    
70    2006-08-01  Douglas Bates  <bates@R-project.org>
71    
72            * R/lmer.R (LMEoptimize method), tests/lmer.R,
73            inst/external/test3comp.rda: Added warnings for convergence on
74            boundary and test cases.
75    
76            * src/lmer.c (mer_postVar): Modified to return the variances that
77            are marginal to the fixed effects, not conditional on them (which
78            is what the bVar slot contents represent).
79    
80    2006-07-31  Douglas Bates  <bates@R-project.org>
81    
82            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
83            function which calls the C function mer_hat_trace2.
84    
85            * man/ranef.Rd: Include description of "postVar" argument and
86            producing a caterpillar plot.
87    
88    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * NAMESPACE:    change  "correlation" to "corMatrix"
91            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
92            * R/dpoMatrix.R: ditto
93            * R/lmer.R:      ditto
94    
95    2006-07-28  Douglas Bates  <bates@R-project.org>
96    
97            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
98            RZXinv slot's contents into a separate internal function that can
99            be used in mer_hat_trace.
100    
101    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
104            via new smart
105            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
106            utility functions.
107    
108    
109    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/Csparse.R (tril, triu, band): do return *triangular* classed
112            matrices when appropriate; band() even symmetric ones.
113            (replCmat): extend to potentially all "CsparseMatrix"
114            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
115            allow subassignment for special sparse matrices.
116    
117            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
118    
119            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
120            argument; in glmer_*(): print only if(verbose).
121    
122            speed-optimize a few places by moving REAL(.) out of loops.
123    
124            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
125    
126    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
129                    since that wrongly triggers also for M[ logi , ]
130    
131            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
132            a symmetric matrix that results in a non-symmetric one.
133            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
134    
135            * R/dMatrix.R: make round(M) work as round(M, 0)
136    
137            * R/dgTMatrix.R (image): coordinate system and axis now use
138            1-based indices, not 0-based ones.
139    
140            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
141            * tests/indexing.R: test it.
142    
143            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
144            * man/isSymmetric-methods.Rd: and document it.
145    
146            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
147            * man/SparseM-conv.Rd: docu them
148    
149            * tests/other-pkgs.R: renamed from tests/graph.R and add example
150                    for 'SparseM' conversions
151    
152    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
153    
154            * R/Matrix.R (head): added head() and tail() methods.
155    
156    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * DESCRIPTION (Version): 0.995-12 released to CRAN
159    
160    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * tests/simple.R: add check for correct dsT -> dgT coercion;
163                    add check for correct printing of symmetric sparse matrices.
164    
165            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
166            for sparse symmetric matrices.
167    
168            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
169            diagonal twice.
170    
171    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
172    
173            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
174            being applied to the x slot (detected by Brian Ripley).
175    
176    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
179    
180            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
181    
182    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * src/lgCMatrix.c (lgCMatrix_diag): new function
185            * R/lgCMatrix.R (diag): for new method
186    
187            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
188                 ==> construction of illegal "*gTMatrix" via new() should
189                 now be much less easy:
190            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
191    
192            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
193                    directly.
194            * man/Matrix.Rd: documents it.
195    
196    2006-07-06  Douglas Bates  <bates@R-project.org>
197    
198            * src/pedigree.c (pedigree_inbreeding): Correction in
199            initialization.  This function is not currently being used and is
200            not fully tested.
201    
202            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
203            Introduced the glmer class.  Added code for mcmcmsamp on glmer
204            objects.  Modified validity check on pedigree objects to account
205            for nonparallel patterns of missingness of parents.
206    
207            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
208            class.
209    
210    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/pMatrix.R: coercion pMatrix -> Tsparse
213    
214    2006-06-12  Douglas Bates  <bates@R-project.org>
215    
216            * DESCRIPTION (Version): 0.995-11 released to CRAN
217    
218            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
219            the output from mcmcsamp.
220    
221    2006-06-10  Douglas Bates  <bates@R-project.org>
222    
223            * R/lmer.R (simulestimate): added C code for calculating the trace
224            of the hat matrix.
225    
226    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
229            classes.
230            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
231    
232    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/dgTMatrix.R (colSums): etc. All four of
235            colSums(), rowSums(), colMeans(), rowMeans() now should work for
236            all "Matrices".
237    
238    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
239    
240            * R/lmer.R (panel.ci): Add a reference line at zero and a
241            background grid to the qqmath plot of ranef.lmer.
242    
243    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
244    
245            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
246            grouping factors to be specified in the formula as (1|foo/bar).
247    
248    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
249    
250            * R/lmer.R (findbars and others): Change check of is.numeric to
251            !is.language to resolve the bug reported by Jacob Wegelin.
252    
253            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
254            code to evaluate inbreeding coefficients without calculating T,
255            based on code in Sargolzaei and Iwaisaki's paper.
256    
257    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
258    
259            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
260            generic and mer methods for isNested and denomDF. This denomDF was
261            an attempt to emulate that in lme but I don't think that makes
262            sense.  Use the trace of the hat matrix instead.
263    
264  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
267          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.
268          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
269    
270    
271  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 388 
388          * 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)
389          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
390          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
391          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
392    
393  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
# Line 329  Line 592 
592  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
595          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
596          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
597    
598  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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