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revision 1271, Thu May 18 06:47:09 2006 UTC revision 1445, Fri Aug 25 14:54:54 2006 UTC
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1    2006-08-25  Douglas Bates  <bates@R-project.org>
2    
3            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
4            <tillard@cirad.fr> - ordering standard errors to match effects.
5    
6    2006-08-24  Douglas Bates  <bates@R-project.org>
7    
8            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
9            on R_ldl.
10            * R/lCholCMatrix.R,
11            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
12            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
13            * many files in ./R and ./src: Use more general version of
14            dup_mMatrix_as_dgeMatrix to simplify method definitions.
15            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
16            dtpMatrix, dspMatrix and dppMatrix conversions.
17    
18    
19    2006-08-23  Douglas Bates  <bates@R-project.org>
20    
21            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
22            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
23            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
24            dgeMatrix_crossprod (may need to do this in other places).
25            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
26            generic and method for dsCMatrix.  Use CHOLMOD for chol().
27    
28    2006-08-22  Douglas Bates  <bates@R-project.org>
29    
30            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
31            types of classed Matrices, matrices or numeric or logical vectors.
32            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
33            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
34            to Mutils.h (as an inline) and change name to Matrix_check_class;
35            fixes in as_cholmod_factor and chm_factor_to_SEXP.
36            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
37            dsCMatrix_matrix_solve.  Comment out vestigial functions.
38            * src/Csparse.c: use diag_P and uplo_P macros.
39    
40    2006-08-21  Douglas Bates  <bates@R-project.org>
41    
42            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
43            valgrind.
44            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
45            inverses.
46            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
47            -Wall warnings.
48            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
49            Use dup_mMatrix_as_dgeMatrix.
50    
51    2006-08-20  Douglas Bates  <bates@R-project.org>
52    
53            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
54            * tests/sparseQR.R: Added
55            * man/sparseQR-class.Rd: Document methods for qr.* generics
56            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
57    
58    2006-08-19  Douglas Bates  <bates@R-project.org>
59    
60            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
61            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
62            and qr.fitted.
63            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
64            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
65    
66    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
69            the base version has no "..." argument.
70    
71            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
72    
73            * R/Matrix.R: define and
74            * NAMESPACE: export as.numeric() and as.logical() methods.
75                    Let's hope these do not badly slow down something...
76            Finally export the zapsmall() method.
77    
78    2006-08-17  Douglas Bates  <bates@R-project.org>
79    
80            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
81            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
82            * src/dtCMatrix.c :Remove code that is no longer used
83            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
84    
85    2006-08-14  Douglas Bates  <bates@R-project.org>
86    
87            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
88            Csparse_to_logical and Csparse_symmetric_to_general.
89            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
90            coercion methods between CsparseMatrix and TsparseMatrix.
91    
92    2006-08-14  Douglas Bates  <bates@R-project.org>
93    
94            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
95            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
96            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
97            possible.
98    
99    2006-08-12  Douglas Bates  <bates@R-project.org>
100    
101            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
102              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
103              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
104              generalize conversions between TsparseMatrix, CsparseMatrix,
105              denseMatrix and matrix.  Preserve triangularity property and
106              propagate Dimnames in the easy cases.
107    
108    2006-08-10  Douglas Bates  <bates@R-project.org>
109    
110            * src/lmer.c: adjust checks in glmer_init for S4SXP
111            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
112            before S4SXP but for the wrong reasons.
113    
114    2006-08-08  Douglas Bates  <bates@R-project.org>
115    
116            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
117            Later modified to return the upper triangle only.
118            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
119    
120    2006-08-07  Douglas Bates  <bates@R-project.org>
121    
122            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
123            R-level conversion to a sparse symmetric class.
124            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
125            Remove conversion to sparse symmetric classes (now done in C code).
126    
127    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
130            * man/band.Rd:  adapt the \dontshow{} unit test.
131    
132    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * DESCRIPTION (Version): 0.995-14  for CRAN
135    
136            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
137    
138            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
139            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
140    
141            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
142            * R/Tsparse.R (tril, triu, band): methods
143            * R/dgRMatrix.R (tril, ...):    ditto
144            * man/band.Rd:                  ditto
145    
146    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Matrix.R (head, tail): directly use utils:::head.matrix
149                    to be up-to-date automatically.
150    
151    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
154    
155            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
156            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
157            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
158            such that the S4 objects are always created by the current version
159            of R and 'Matrix' class definitions.
160    
161    2006-08-01  Douglas Bates  <bates@R-project.org>
162    
163            * R/lmer.R (LMEoptimize method), tests/lmer.R,
164            inst/external/test3comp.rda: Added warnings for convergence on
165            boundary and test cases.
166    
167            * src/lmer.c (mer_postVar): Modified to return the variances that
168            are marginal to the fixed effects, not conditional on them (which
169            is what the bVar slot contents represent).
170    
171    2006-07-31  Douglas Bates  <bates@R-project.org>
172    
173            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
174            function which calls the C function mer_hat_trace2.
175    
176            * man/ranef.Rd: Include description of "postVar" argument and
177            producing a caterpillar plot.
178    
179    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * NAMESPACE:    change  "correlation" to "corMatrix"
182            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
183            * R/dpoMatrix.R: ditto
184            * R/lmer.R:      ditto
185    
186    2006-07-28  Douglas Bates  <bates@R-project.org>
187    
188            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
189            RZXinv slot's contents into a separate internal function that can
190            be used in mer_hat_trace.
191    
192    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
195            via new smart
196            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
197            utility functions.
198    
199    
200    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Csparse.R (tril, triu, band): do return *triangular* classed
203            matrices when appropriate; band() even symmetric ones.
204            (replCmat): extend to potentially all "CsparseMatrix"
205            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
206            allow subassignment for special sparse matrices.
207    
208            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
209    
210            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
211            argument; in glmer_*(): print only if(verbose).
212    
213            speed-optimize a few places by moving REAL(.) out of loops.
214    
215            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
216    
217    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
220                    since that wrongly triggers also for M[ logi , ]
221    
222            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
223            a symmetric matrix that results in a non-symmetric one.
224            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
225    
226            * R/dMatrix.R: make round(M) work as round(M, 0)
227    
228            * R/dgTMatrix.R (image): coordinate system and axis now use
229            1-based indices, not 0-based ones.
230    
231            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
232            * tests/indexing.R: test it.
233    
234            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
235            * man/isSymmetric-methods.Rd: and document it.
236    
237            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
238            * man/SparseM-conv.Rd: docu them
239    
240            * tests/other-pkgs.R: renamed from tests/graph.R and add example
241                    for 'SparseM' conversions
242    
243    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
244    
245            * R/Matrix.R (head): added head() and tail() methods.
246    
247    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * DESCRIPTION (Version): 0.995-12 released to CRAN
250    
251    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * tests/simple.R: add check for correct dsT -> dgT coercion;
254                    add check for correct printing of symmetric sparse matrices.
255    
256            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
257            for sparse symmetric matrices.
258    
259            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
260            diagonal twice.
261    
262    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
263    
264            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
265            being applied to the x slot (detected by Brian Ripley).
266    
267    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
270    
271            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
272    
273    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * src/lgCMatrix.c (lgCMatrix_diag): new function
276            * R/lgCMatrix.R (diag): for new method
277    
278            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
279                 ==> construction of illegal "*gTMatrix" via new() should
280                 now be much less easy:
281            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
282    
283            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
284                    directly.
285            * man/Matrix.Rd: documents it.
286    
287    2006-07-06  Douglas Bates  <bates@R-project.org>
288    
289            * src/pedigree.c (pedigree_inbreeding): Correction in
290            initialization.  This function is not currently being used and is
291            not fully tested.
292    
293            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
294            Introduced the glmer class.  Added code for mcmcmsamp on glmer
295            objects.  Modified validity check on pedigree objects to account
296            for nonparallel patterns of missingness of parents.
297    
298            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
299            class.
300    
301    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/pMatrix.R: coercion pMatrix -> Tsparse
304    
305    2006-06-12  Douglas Bates  <bates@R-project.org>
306    
307            * DESCRIPTION (Version): 0.995-11 released to CRAN
308    
309            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
310            the output from mcmcsamp.
311    
312    2006-06-10  Douglas Bates  <bates@R-project.org>
313    
314            * R/lmer.R (simulestimate): added C code for calculating the trace
315            of the hat matrix.
316    
317    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
320            classes.
321            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
322    
323    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/dgTMatrix.R (colSums): etc. All four of
326            colSums(), rowSums(), colMeans(), rowMeans() now should work for
327            all "Matrices".
328    
329    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * R/lmer.R (panel.ci): Add a reference line at zero and a
332            background grid to the qqmath plot of ranef.lmer.
333    
334    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
335    
336            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
337            grouping factors to be specified in the formula as (1|foo/bar).
338    
339    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * R/lmer.R (findbars and others): Change check of is.numeric to
342            !is.language to resolve the bug reported by Jacob Wegelin.
343    
344            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
345            code to evaluate inbreeding coefficients without calculating T,
346            based on code in Sargolzaei and Iwaisaki's paper.
347    
348    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
349    
350            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
351            generic and mer methods for isNested and denomDF. This denomDF was
352            an attempt to emulate that in lme but I don't think that makes
353            sense.  Use the trace of the hat matrix instead.
354    
355  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
358          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.
359          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
360    
361    
362  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 125  Line 479 
479          * 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)
480          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
481          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
482          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
483    
484  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
# Line 329  Line 683 
683  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
686          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
687          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
688    
689  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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