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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1403, Sun Aug 20 16:15:59 2006 UTC
# Line 1  Line 1 
1    2006-08-20  Douglas Bates  <bates@R-project.org>
2    
3            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
4            * tests/sparseQR.R: Added
5            * man/sparseQR-class.Rd: Document methods for qr.* generics
6            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
7    
8    2006-08-19  Douglas Bates  <bates@R-project.org>
9    
10            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
11            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
12            and qr.fitted.
13            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
14            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
15    
16    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
19            the base version has no "..." argument.
20    
21            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
22    
23            * R/Matrix.R: define and
24            * NAMESPACE: export as.numeric() and as.logical() methods.
25                    Let's hope these do not badly slow down something...
26            Finally export the zapsmall() method.
27    
28    2006-08-17  Douglas Bates  <bates@R-project.org>
29    
30            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
31            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
32            * src/dtCMatrix.c :Remove code that is no longer used
33            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
34    
35    2006-08-14  Douglas Bates  <bates@R-project.org>
36    
37            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
38            Csparse_to_logical and Csparse_symmetric_to_general.
39            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
40            coercion methods between CsparseMatrix and TsparseMatrix.
41    
42    2006-08-14  Douglas Bates  <bates@R-project.org>
43    
44            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
45            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
46            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
47            possible.
48    
49    2006-08-12  Douglas Bates  <bates@R-project.org>
50    
51            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
52              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
53              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
54              generalize conversions between TsparseMatrix, CsparseMatrix,
55              denseMatrix and matrix.  Preserve triangularity property and
56              propagate Dimnames in the easy cases.
57    
58    2006-08-10  Douglas Bates  <bates@R-project.org>
59    
60            * src/lmer.c: adjust checks in glmer_init for S4SXP
61            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
62            before S4SXP but for the wrong reasons.
63    
64    2006-08-08  Douglas Bates  <bates@R-project.org>
65    
66            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
67            Later modified to return the upper triangle only.
68            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
69    
70    2006-08-07  Douglas Bates  <bates@R-project.org>
71    
72            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
73            R-level conversion to a sparse symmetric class.
74            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
75            Remove conversion to sparse symmetric classes (now done in C code).
76    
77    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
80            * man/band.Rd:  adapt the \dontshow{} unit test.
81    
82    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * DESCRIPTION (Version): 0.995-14  for CRAN
85    
86            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
87    
88            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
89            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
90    
91            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
92            * R/Tsparse.R (tril, triu, band): methods
93            * R/dgRMatrix.R (tril, ...):    ditto
94            * man/band.Rd:                  ditto
95    
96    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/Matrix.R (head, tail): directly use utils:::head.matrix
99                    to be up-to-date automatically.
100    
101    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
104    
105            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
106            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
107            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
108            such that the S4 objects are always created by the current version
109            of R and 'Matrix' class definitions.
110    
111    2006-08-01  Douglas Bates  <bates@R-project.org>
112    
113            * R/lmer.R (LMEoptimize method), tests/lmer.R,
114            inst/external/test3comp.rda: Added warnings for convergence on
115            boundary and test cases.
116    
117            * src/lmer.c (mer_postVar): Modified to return the variances that
118            are marginal to the fixed effects, not conditional on them (which
119            is what the bVar slot contents represent).
120    
121    2006-07-31  Douglas Bates  <bates@R-project.org>
122    
123            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
124            function which calls the C function mer_hat_trace2.
125    
126            * man/ranef.Rd: Include description of "postVar" argument and
127            producing a caterpillar plot.
128    
129    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * NAMESPACE:    change  "correlation" to "corMatrix"
132            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
133            * R/dpoMatrix.R: ditto
134            * R/lmer.R:      ditto
135    
136    2006-07-28  Douglas Bates  <bates@R-project.org>
137    
138            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
139            RZXinv slot's contents into a separate internal function that can
140            be used in mer_hat_trace.
141    
142    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
145            via new smart
146            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
147            utility functions.
148    
149    
150    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/Csparse.R (tril, triu, band): do return *triangular* classed
153            matrices when appropriate; band() even symmetric ones.
154            (replCmat): extend to potentially all "CsparseMatrix"
155            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
156            allow subassignment for special sparse matrices.
157    
158            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
159    
160            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
161            argument; in glmer_*(): print only if(verbose).
162    
163            speed-optimize a few places by moving REAL(.) out of loops.
164    
165            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
166    
167    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
170                    since that wrongly triggers also for M[ logi , ]
171    
172            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
173            a symmetric matrix that results in a non-symmetric one.
174            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
175    
176            * R/dMatrix.R: make round(M) work as round(M, 0)
177    
178            * R/dgTMatrix.R (image): coordinate system and axis now use
179            1-based indices, not 0-based ones.
180    
181            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
182            * tests/indexing.R: test it.
183    
184            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
185            * man/isSymmetric-methods.Rd: and document it.
186    
187            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
188            * man/SparseM-conv.Rd: docu them
189    
190            * tests/other-pkgs.R: renamed from tests/graph.R and add example
191                    for 'SparseM' conversions
192    
193    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
194    
195            * R/Matrix.R (head): added head() and tail() methods.
196    
197    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Version): 0.995-12 released to CRAN
200    
201    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * tests/simple.R: add check for correct dsT -> dgT coercion;
204                    add check for correct printing of symmetric sparse matrices.
205    
206            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
207            for sparse symmetric matrices.
208    
209            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
210            diagonal twice.
211    
212    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
213    
214            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
215            being applied to the x slot (detected by Brian Ripley).
216    
217    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
220    
221            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
222    
223    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * src/lgCMatrix.c (lgCMatrix_diag): new function
226            * R/lgCMatrix.R (diag): for new method
227    
228            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
229                 ==> construction of illegal "*gTMatrix" via new() should
230                 now be much less easy:
231            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
232    
233            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
234                    directly.
235            * man/Matrix.Rd: documents it.
236    
237    2006-07-06  Douglas Bates  <bates@R-project.org>
238    
239            * src/pedigree.c (pedigree_inbreeding): Correction in
240            initialization.  This function is not currently being used and is
241            not fully tested.
242    
243            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
244            Introduced the glmer class.  Added code for mcmcmsamp on glmer
245            objects.  Modified validity check on pedigree objects to account
246            for nonparallel patterns of missingness of parents.
247    
248            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
249            class.
250    
251    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/pMatrix.R: coercion pMatrix -> Tsparse
254    
255    2006-06-12  Douglas Bates  <bates@R-project.org>
256    
257            * DESCRIPTION (Version): 0.995-11 released to CRAN
258    
259            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
260            the output from mcmcsamp.
261    
262    2006-06-10  Douglas Bates  <bates@R-project.org>
263    
264            * R/lmer.R (simulestimate): added C code for calculating the trace
265            of the hat matrix.
266    
267    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
270            classes.
271            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
272    
273    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/dgTMatrix.R (colSums): etc. All four of
276            colSums(), rowSums(), colMeans(), rowMeans() now should work for
277            all "Matrices".
278    
279    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
280    
281            * R/lmer.R (panel.ci): Add a reference line at zero and a
282            background grid to the qqmath plot of ranef.lmer.
283    
284    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
285    
286            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
287            grouping factors to be specified in the formula as (1|foo/bar).
288    
289    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
290    
291            * R/lmer.R (findbars and others): Change check of is.numeric to
292            !is.language to resolve the bug reported by Jacob Wegelin.
293    
294            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
295            code to evaluate inbreeding coefficients without calculating T,
296            based on code in Sargolzaei and Iwaisaki's paper.
297    
298    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
299    
300            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
301            generic and mer methods for isNested and denomDF. This denomDF was
302            an attempt to emulate that in lme but I don't think that makes
303            sense.  Use the trace of the hat matrix instead.
304    
305  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
308          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.
309          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
310    
311    
312  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 429 
429          * 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)
430          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
431          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
432          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
433    
434  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
# Line 329  Line 633 
633  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
636          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
637          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
638    
639  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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