SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1222, Tue Mar 7 11:05:08 2006 UTC revision 1577, Mon Sep 18 21:01:45 2006 UTC
# Line 1  Line 1 
1    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
4            symmetric and y missing in R code using %*% (cholmod_aat doesn't
5            accept a symmetric matrix).
6            * tests/group-methods.R: Uncomment test of crossprod applied to
7            lsCMatrix objects.
8    
9    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/AllClass.R (symmetricMatrix): add validity method (available
12            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
13    
14            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
15    
16            * tests/indexing.Rout.save:
17            * tests/indexing.R: additions, mainly for 'lsparse'
18    
19            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
20            case.
21    
22            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
23    
24    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
27                    as 'N' (1-letter - Ok?)
28    
29            * tests/group-methods.R: add test for logical + NAs
30    
31            * R/dMatrix.R ("Compare"): fix to work with NA's
32    
33            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
34    
35            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
36                    which is implemented.
37    
38    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * src/chm_common.c: coerce logical <-> double instead of
41            typecasting;  needed for "l" matrix handling in cholmod.
42    
43            * tests/other-pkgs.R (graph): small extension in "graph" checks.
44    
45            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
46            (Tsp2grNEL): other fixes needed
47    
48    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
51                    Matrices, since "lMatrix", also "lsparseM" can have NA
52            * R/ndenseMatrix.R, etc: new source files
53            * man/nsparseMatrix-classes.Rd, etc: new help files
54            * tests/: adaptions
55            * src/chm_common.c (chm_dense_to_SEXP): and others:
56                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
57            * src/Csparse.c, etc: dito
58    
59    2006-09-11  Douglas Bates  <bates@R-project.org>
60    
61            * src/Mutils.[ch],init.c inst/include/*.h: Move the
62            alloc_d**Matrix functions to the lme4 package.
63    
64    2006-09-09  Douglas Bates  <bates@R-project.org>
65    
66            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
67            fixed
68    
69    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/lMatrix.R: new
72    
73            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
74    
75            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
76            * man/tcrossprod.Rd: dito
77    
78    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
79    
80            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
81            for exported functions
82            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
83            Remove partitioning algorithms for sparse matrix reordering.  The
84            copyright on the Metis code was problematic and the methods were
85            rarely used.
86            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
87            operations are now done entirely in CHOLMOD code.
88    
89    2006-09-06  Douglas Bates  <bates@R-project.org>
90    
91            * src/Mutils.h: Remove functions that are no longer used.
92    
93    2006-09-04  Douglas Bates  <bates@R-project.org>
94    
95            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
96            * src/DEPS.mkf: update
97    
98    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * created branches/Matrix-for-R-2.3.x;  on trunk: do
101            * DESCRIPTION (Version): 0.9975-0
102            (Depends): R (>= 2.4.0)
103    
104    2006-09-01  Douglas Bates  <bates@R-project.org>
105    
106            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
107    
108    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
111            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
112    
113            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
114    
115    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
118            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
119            * R/dsparseMatrix.R: dito
120            * R/Csparse.R: dito
121    
122    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/dMatrix.R (Compare): improve availability of "<", etc
125            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
126    
127    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
130            of a 0-index which was used as 1-index (..hmm)
131    
132            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
133    
134            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
135            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
136            (.is.diagonal): dito
137    
138            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
139    
140            * R/Matrix.R (Matrix): also work for NA data
141    
142    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
145            in all cases.
146    
147    2006-08-27  Douglas Bates  <bates@R-project.org>
148    
149            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
150            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
151    
152    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
155            subclasses of "ddenseMatrix"
156            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
157            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
158            instead of half dozen specialized ones.
159    
160    2006-08-25  Douglas Bates  <bates@R-project.org>
161    
162            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
163            <tillard@cirad.fr> - ordering standard errors to match effects.
164    
165    2006-08-24  Douglas Bates  <bates@R-project.org>
166    
167            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
168            on R_ldl.
169            * R/lCholCMatrix.R,
170            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
171            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
172            * many files in ./R and ./src: Use more general version of
173            dup_mMatrix_as_dgeMatrix to simplify method definitions.
174            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
175            dtpMatrix, dspMatrix and dppMatrix conversions.
176    
177    
178    2006-08-23  Douglas Bates  <bates@R-project.org>
179    
180            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
181            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
182            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
183            dgeMatrix_crossprod (may need to do this in other places).
184            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
185            generic and method for dsCMatrix.  Use CHOLMOD for chol().
186    
187    2006-08-22  Douglas Bates  <bates@R-project.org>
188    
189            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
190            types of classed Matrices, matrices or numeric or logical vectors.
191            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
192            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
193            to Mutils.h (as an inline) and change name to Matrix_check_class;
194            fixes in as_cholmod_factor and chm_factor_to_SEXP.
195            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
196            dsCMatrix_matrix_solve.  Comment out vestigial functions.
197            * src/Csparse.c: use diag_P and uplo_P macros.
198    
199    2006-08-21  Douglas Bates  <bates@R-project.org>
200    
201            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
202            valgrind.
203            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
204            inverses.
205            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
206            -Wall warnings.
207            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
208            Use dup_mMatrix_as_dgeMatrix.
209    
210    2006-08-20  Douglas Bates  <bates@R-project.org>
211    
212            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
213            * tests/sparseQR.R: Added
214            * man/sparseQR-class.Rd: Document methods for qr.* generics
215            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
216    
217    2006-08-19  Douglas Bates  <bates@R-project.org>
218    
219            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
220            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
221            and qr.fitted.
222            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
223            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
224    
225    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
228            the base version has no "..." argument.
229    
230            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
231    
232            * R/Matrix.R: define and
233            * NAMESPACE: export as.numeric() and as.logical() methods.
234                    Let's hope these do not badly slow down something...
235            Finally export the zapsmall() method.
236    
237    2006-08-17  Douglas Bates  <bates@R-project.org>
238    
239            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
240            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
241            * src/dtCMatrix.c :Remove code that is no longer used
242            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
243    
244    2006-08-14  Douglas Bates  <bates@R-project.org>
245    
246            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
247            Csparse_to_logical and Csparse_symmetric_to_general.
248            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
249            coercion methods between CsparseMatrix and TsparseMatrix.
250    
251    2006-08-14  Douglas Bates  <bates@R-project.org>
252    
253            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
254            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
255            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
256            possible.
257    
258    2006-08-12  Douglas Bates  <bates@R-project.org>
259    
260            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
261              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
262              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
263              generalize conversions between TsparseMatrix, CsparseMatrix,
264              denseMatrix and matrix.  Preserve triangularity property and
265              propagate Dimnames in the easy cases.
266    
267    2006-08-10  Douglas Bates  <bates@R-project.org>
268    
269            * src/lmer.c: adjust checks in glmer_init for S4SXP
270            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
271            before S4SXP but for the wrong reasons.
272    
273    2006-08-08  Douglas Bates  <bates@R-project.org>
274    
275            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
276            Later modified to return the upper triangle only.
277            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
278    
279    2006-08-07  Douglas Bates  <bates@R-project.org>
280    
281            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
282            R-level conversion to a sparse symmetric class.
283            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
284            Remove conversion to sparse symmetric classes (now done in C code).
285    
286    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
289            * man/band.Rd:  adapt the \dontshow{} unit test.
290    
291    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * DESCRIPTION (Version): 0.995-14  for CRAN
294    
295            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
296    
297            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
298            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
299    
300            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
301            * R/Tsparse.R (tril, triu, band): methods
302            * R/dgRMatrix.R (tril, ...):    ditto
303            * man/band.Rd:                  ditto
304    
305    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Matrix.R (head, tail): directly use utils:::head.matrix
308                    to be up-to-date automatically.
309    
310    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
313    
314            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
315            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
316            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
317            such that the S4 objects are always created by the current version
318            of R and 'Matrix' class definitions.
319    
320    2006-08-01  Douglas Bates  <bates@R-project.org>
321    
322            * R/lmer.R (LMEoptimize method), tests/lmer.R,
323            inst/external/test3comp.rda: Added warnings for convergence on
324            boundary and test cases.
325    
326            * src/lmer.c (mer_postVar): Modified to return the variances that
327            are marginal to the fixed effects, not conditional on them (which
328            is what the bVar slot contents represent).
329    
330    2006-07-31  Douglas Bates  <bates@R-project.org>
331    
332            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
333            function which calls the C function mer_hat_trace2.
334    
335            * man/ranef.Rd: Include description of "postVar" argument and
336            producing a caterpillar plot.
337    
338    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * NAMESPACE:    change  "correlation" to "corMatrix"
341            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
342            * R/dpoMatrix.R: ditto
343            * R/lmer.R:      ditto
344    
345    2006-07-28  Douglas Bates  <bates@R-project.org>
346    
347            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
348            RZXinv slot's contents into a separate internal function that can
349            be used in mer_hat_trace.
350    
351    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
354            via new smart
355            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
356            utility functions.
357    
358    
359    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/Csparse.R (tril, triu, band): do return *triangular* classed
362            matrices when appropriate; band() even symmetric ones.
363            (replCmat): extend to potentially all "CsparseMatrix"
364            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
365            allow subassignment for special sparse matrices.
366    
367            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
368    
369            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
370            argument; in glmer_*(): print only if(verbose).
371    
372            speed-optimize a few places by moving REAL(.) out of loops.
373    
374            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
375    
376    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
379                    since that wrongly triggers also for M[ logi , ]
380    
381            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
382            a symmetric matrix that results in a non-symmetric one.
383            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
384    
385            * R/dMatrix.R: make round(M) work as round(M, 0)
386    
387            * R/dgTMatrix.R (image): coordinate system and axis now use
388            1-based indices, not 0-based ones.
389    
390            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
391            * tests/indexing.R: test it.
392    
393            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
394            * man/isSymmetric-methods.Rd: and document it.
395    
396            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
397            * man/SparseM-conv.Rd: docu them
398    
399            * tests/other-pkgs.R: renamed from tests/graph.R and add example
400                    for 'SparseM' conversions
401    
402    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
403    
404            * R/Matrix.R (head): added head() and tail() methods.
405    
406    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * DESCRIPTION (Version): 0.995-12 released to CRAN
409    
410    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * tests/simple.R: add check for correct dsT -> dgT coercion;
413                    add check for correct printing of symmetric sparse matrices.
414    
415            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
416            for sparse symmetric matrices.
417    
418            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
419            diagonal twice.
420    
421    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
422    
423            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
424            being applied to the x slot (detected by Brian Ripley).
425    
426    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
429    
430            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
431    
432    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * src/lgCMatrix.c (lgCMatrix_diag): new function
435            * R/lgCMatrix.R (diag): for new method
436    
437            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
438                 ==> construction of illegal "*gTMatrix" via new() should
439                 now be much less easy:
440            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
441    
442            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
443                    directly.
444            * man/Matrix.Rd: documents it.
445    
446    2006-07-06  Douglas Bates  <bates@R-project.org>
447    
448            * src/pedigree.c (pedigree_inbreeding): Correction in
449            initialization.  This function is not currently being used and is
450            not fully tested.
451    
452            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
453            Introduced the glmer class.  Added code for mcmcmsamp on glmer
454            objects.  Modified validity check on pedigree objects to account
455            for nonparallel patterns of missingness of parents.
456    
457            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
458            class.
459    
460    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/pMatrix.R: coercion pMatrix -> Tsparse
463    
464    2006-06-12  Douglas Bates  <bates@R-project.org>
465    
466            * DESCRIPTION (Version): 0.995-11 released to CRAN
467    
468            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
469            the output from mcmcsamp.
470    
471    2006-06-10  Douglas Bates  <bates@R-project.org>
472    
473            * R/lmer.R (simulestimate): added C code for calculating the trace
474            of the hat matrix.
475    
476    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
479            classes.
480            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
481    
482    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/dgTMatrix.R (colSums): etc. All four of
485            colSums(), rowSums(), colMeans(), rowMeans() now should work for
486            all "Matrices".
487    
488    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
489    
490            * R/lmer.R (panel.ci): Add a reference line at zero and a
491            background grid to the qqmath plot of ranef.lmer.
492    
493    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
494    
495            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
496            grouping factors to be specified in the formula as (1|foo/bar).
497    
498    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
499    
500            * R/lmer.R (findbars and others): Change check of is.numeric to
501            !is.language to resolve the bug reported by Jacob Wegelin.
502    
503            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
504            code to evaluate inbreeding coefficients without calculating T,
505            based on code in Sargolzaei and Iwaisaki's paper.
506    
507    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
508    
509            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
510            generic and mer methods for isNested and denomDF. This denomDF was
511            an attempt to emulate that in lme but I don't think that makes
512            sense.  Use the trace of the hat matrix instead.
513    
514    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
517            the C code depending on a slot structure that's no longer valid.
518            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
519    
520    
521    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
522    
523            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
524            of lowerTriMatrix generic and methods to tril (also upper to triu)
525            and added a general band extractor.
526    
527    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
528    
529            * R/pedigree.R (pedigree): Replace sire and dam values outside the
530            allowable range with NAs. Added a corresponding check in the
531            validity check for the pedigree class.
532    
533            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
534            crossprod methods now inherits from symmetricMatrix.
535    
536    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
537    
538            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
539            generics lowerTriMatrix and upperTriMatrix along with methods for
540            the Csparse virtual class.  Also added a C function Csparse_band
541            that implements these methods by calling cholmod_band.
542    
543    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
546            erased when it was NULL.  This led to invalid subselections!
547    
548    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
549    
550            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
551            in method for "t" so as not to lose the unit diagonal property.
552    
553    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
554    
555            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
556            and methods.  This is now an option to the ranef method for the
557            mer class.
558    
559            * src/cs_utils.c: Ensure that the nz component is -1 for a
560            compressed column-oriented matrix.  Minor formatting cleanup.
561    
562            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
563            objects.
564    
565    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
568            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
569    
570    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
571    
572            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
573            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
574    
575            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
576            for the dtCMatrix class.
577    
578    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
579    
580            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
581            and methods for it.
582    
583    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
586            arguments, such that M %*% 1:6 now works
587            * Tests/matprod.R: test the above
588    
589    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
590    
591            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
592            the ranef.lmer class.
593    
594            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
595            methods to extract the posterior variances from the bVar slot.
596    
597    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
600            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
601    
602            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
603            * tests/simple: (extended)
604    
605            * R/sparseMatrix.R (isTriangular): now using much improved
606            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
607    
608    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
609    
610            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
611            (problem report from Franklin Parlamis).  This should be done
612            generally.
613    
614    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
615    
616            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
617            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
618            update the plot methods.
619    
620    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
621    
622            * R/lmer.R (resid and ranef methods):  Added methods for the
623            "residuals" and "resid" generic but only for linear mixed model
624            fits.  Changed the ranef method to return a list of data frames so
625            that the plot methods now work.
626    
627    2006-03-16  Douglas Bates  <bates@bates2>
628    
629            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
630            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
631    
632            * DESCRIPTION (Date): New release
633    
634    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
637    
638            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
639            * man/KNex.Rd: and other help files
640            * tests/*.R: several ones needed adaption
641            * inst/doc/Comparisons.Rnw: ditto
642    
643    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
646    
647            * tests/indexing.R: tests for new [<- methods for sparse matrices.
648    
649    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
652    
653            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
654    
655    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/dMatrix.R: enable things like  M [ M < 10 ]
658            * R/dgeMatrix.R: implement it
659    
660  2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662          * R/AllClass.R: define "summary.mer" and "*.lmer"          * R/AllClass.R: define "summary.mer" and "*.lmer"
# Line 183  Line 842 
842  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
845          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
846          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
847    
848  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

Legend:
Removed from v.1222  
changed lines
  Added in v.1577

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge