-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathChangeLog
946 lines (583 loc) · 28.8 KB
/
ChangeLog
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
2013-07-02 Brian Ripley
* DESCRIPTION: version is 3.1-110,
* R/{gls,gnls,lme}.R: Replace as.name() calls by quote(stats::nls) etc.
* inst/LICENCE: remove.
2013-03-21 Brian Ripley
* inst/CITATION: modernize.
2013-03-11 Brian Ripley
* LICENCE: remove (it was not a licence file).
2013-01-26 Brian Ripley
* DESCRIPTION: version is 3.1-109,
depends on R (>= 3.0.0).
2013-01-26 Brian Ripley
* DESCRIPTION: version is 3.1-108,
depends on R (< 3.0.0) and has chol.f and rs.f in .Rbuildignore.
2013-01-23 Brian Ripley
* man/[n]lme.Rd: add a note about the need to scale the response.
* man/lmeControl.Rd: correct description of 'msTol' argument.
* man/[n]lmeControl.Rd: correct description of 'opt' argument (it is
a character string).
* man/*.Rd: s/Jose/José/
* R/[n]lme.R, man/[n]lmeControl.Rd: allow '...' for further
control arguments to be based though to nlminb() and optim().
2013-01-13 Brian Ripley
* DESCRIPTION: add accent on JCP's first name (and declare
UTF-8 encoding). Add EISPACK authors.
* src/rs.f: minimal version of eigen.f containing just RS and
ancillaries (replacing eigen.f).
2013-01-12 Brian Ripley
* DESCRIPTION: version is 3.1-107
* src/{chol,eigen}.f: port files from R (where they are
deprecated/defunct).
2012-12-06 Kurt Hornik
* DESCRIPTION: version is 3.1-106, add roles to Authors@R.
2012-11-28 Brian Ripley <[email protected]>
* NAMESPACE: import selectively from lattice and stats.
2012-09-24 Brian Ripley <[email protected]>
* DESCRIPTION: version is 3.1-105
* R: improve messages for translation.
2012-09-01 Brian Ripley <[email protected]>
* po: add Polish translations.
2012-08-30 Brian Ripley <[email protected]>
* src/init.c: force use of registered symbols in R >= 2.16.0
2012-05-23 Brian Ripley <[email protected]>
* DESCRIPTION: version is 3.1-104
* src/gnls.c, src/nlme.c, src/nlmefit.[ch]:
type mismatches shown by clang's -Wconversion
2012-04-25 Brian Ripley <[email protected]>
* src/nlmefit.c: type mismatch shown by clang's -Wconversion
2012-03-29 Brian Ripley <[email protected]>
* src/nlOptimizer.c: increase PROTECTion (reported by Andrew Runnalls).
2012-02-15 Brian Ripley <[email protected]>
* inst/CITATION: protect against TRE bug in UTF-8 locales.
2012-01-14 Brian Ripley <[email protected]>
* DESCRIPTION: version is 3.1-103
2011-12-25 Brian Ripley <[email protected]>
* DESCRIPTION: needs Suggests: MASS for data(package=)
2011-07-19 Brian Ripley <[email protected]>
* DESCRIPTION: version is 3.1-102
* R/newMethods.R: getData.nls (aka getData.lme) used the na.action
of the call on the whole data and not on the model frame: should
have used the na.action component of the result.
* tests/{lme.R,lme.Rout.save,ss2.rda}: test for above.
* man/simulate.lme: document as method.
2011-07-11 Brian Ripley <[email protected]>
* COPYING: rename to GPL-2
* LICENCE, inst/LICENCE: adjust wording accordingly
2011-05-30 Brian Ripley <[email protected]>
* R/newFunc.R: name arguments to lapply() when ... is present.
2011-05-06 Brian Ripley <[email protected]>
* DESCRIPTION: version is 3.1-101
2011-04-23 Martin Maechler <[email protected]>
2011-04-14 Martin Maechler <[email protected]>
* man/augPred.Rd, R/groupedData.R, R/gls.R, R/lme.R, R/simulate.R
Changes he failed to document.
2011-03-26 Brian Ripley <[email protected]>
* src/{nlmefit,pdMat}.c: remove unused variables detected by
-Wunused-but-set-variable
2011-03-11 Brian Ripley <[email protected]>
* Release 3.1-100 for R 2.13.0
* NAMESPACE: no longer re-export BIC
* man/BIC.Rd: removed.
2011-02-23 Brian Ripley <[email protected]>
* DESCRIPTION: version is 3.1-100, require R >= 2.13
* man/BIC.Rd: make a stub referring to stats::BIC()
* Everywhere: remove obsolete email addresses of former authors
2011-02-23 Brian Ripley <[email protected]>
* DESCRIPTION: version is 3.1-99 (unreleased, used for R-devel),
remove email addresses of former authors (and JCP has moved).
* R/{new,zz}Methods.R:
Put all BIC() methods in one place, as the default method.
* man/BIC.Rd: remove aliases to methods (not all of which actually
existed)
* man/BIC.logLik.Rd: merge into BIC.Rd
* tests/lme.Rout.save: update for R 2.13.0.
* NAMESPACE, R/newMethods.R: prepare for migration of BIC() to stats.
* R/{gls,gnls,lme}.R, NAMESPACE: add nobs() methods.
2011-02-10 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-98
2011-02-04 Brian Ripley <[email protected]>
* data/{MathAchieve,bdf}.rda: resave with xz compression.
* DESCRIPTION: depend on R (>= 2.10).
2010-10-01 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-97
2010-09-22 Brian Ripley <[email protected]>
* man/residuals.gls.Rd: incorrect default, see
https://stat.ethz.ch/pipermail/r-devel/2010-September/058487.html
2009-12-22 Brian Ripley <[email protected]>
* man/ACF.gls.Rd: has \seealso to itself: seems ACF.lme was meant.
2009-12-18 Brian Ripley <[email protected]>
* DESCRIPTION: add BugReports field.
2009-10-12,16 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-96
* po/R-de.po, po/de.po: update
2009-09-16 Martin Maechler <[email protected]>
* DESCRIPTION (Version, Date): 3.1-95
* R/nlme.R (nonlinModel): use unname() instead of clearNames()
2009-09-02 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-94
* man/*.Rd: remove unnecessarily anchored links, including several
incorrect ones.
2009-08-16 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-93
* R/lmList.R, tests/lmList.R: bug fix for predict.lmList (PR#13788)
* R/gls.R, tests/anova.gls.R: bug fix for anova.gls (PR#13567)
2009-05-30 Brian Ripley <[email protected]>
* R/gnls.R, R/corStruct.Rd: minor message wording changes from
Debian 'bug' report.
* R/R-de.po: add
[ Missing entries for 3.1-9[12] which were concerned with German
translations. ]
2009-01-16 Brian Ripley <[email protected]>
* man/*.Rd: expand tabs
2008-12-30 Brian Ripley <[email protected]>
* man/summary.pdMat.Rd: avoid embedded newlines in \code strings.
2008-12-27 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-90
* R/gls.R: call dist correctly (PR#13418)
2008-12-19 Brian Ripley <[email protected]>
* man/*.Rd: clean up some reference formats and misuse of $...$.
2008-12-11 Brian Ripley <[email protected]>
* man/*.Rd: spelling
* src/nlOptimizer.c: missing PROTECT
2008-06-07 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-89
* R/lme.R: fitted.lme() always dropped, when it should drop for
one column but not for one row.
* tests/lme.R, lme.Rout.save: add regression test for
single-row predictions.
2008-04-10 Brian Ripley <[email protected]>
* R/zzMethods.R: add .onUnload() to unload the DLL.
2008-03-30 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-88
2008-02-19 Brian Ripley <[email protected]>
* man/logLik.lme.Rd, man/logLik.gnls.Rd: correct description of
'REML' argument.
2008-02-19 Brian Ripley <[email protected]>
* inst/CITATION: add file (essentially what citation() would
produce, without the warning).
2008-02-18 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-87
* R/gnls.R, tests/gls.R: fix for PR#10364, missing row names
on predict.gnls.
2008-02-11 Duncan Murdoch <[email protected]>
* R/*.R: Return invisible(x) from numerous print methods.
2007-12-30 Douglas Bates <[email protected]>
* [r4884] man/plot.nffGroupedData.Rd: Correct malformed link reported
by Yihui Xie <[email protected]>. Remove reference to nonexistent
URL.
* [r4885] Initialize.reStruct.Rd, collapse.groupedData.Rd,
fitted.lmeStruct.Rd, lme.Rd, lme.groupedData.Rd, lme.lmList.Rd,
logLik.reStruct.Rd, nlme.nlsList.Rd, plot.nfnGroupedData.Rd,
plot.nmGroupedData.Rd, recalc.reStruct.Rd, residuals.lme.Rd,
residuals.lmeStruct.Rd: Remove reference to nonexistent URL
2007-10-04 Kurt Hornik
* DESCRIPTION (Version, Date): 3.1-86
2007-10-04 Brian Ripley <[email protected]>
* R/corStruct.R: check for uninitialized corARMA structures.
2007-09-17 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-85
Also, use approved form of GPL (>=2).
* R/varFunc.R: fix for PR#9831.
* tests/coef.R: test for the above.
* tests/lme.Rout.save: update format for R >= 2.6.0.
* man/corRatio.Rd: wrong formula, reported to R-devel by
Ben Bolker on 2007-09-03.
2007-07-26 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-84
* LICENCE, inst/LICENCE: clarify this is licensed under GPL >= 2.
* README, R/*.R, src/*.[ch]: Update source for GPL.
* man/*.Rd: add header with licence conditions
2007-07-02 Brian Ripley <[email protected]>
* R/varFunc.R: varIdent did not look at its 'fixed' arg, PR#9765
* tests/varIndent.R: test for the above.
2007-06-13 Brian Ripley <[email protected]>
* R/VarCov.R: correct getVarCov.gls, PR#9752
2007-06-13 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-83
Also, update authors and email addresses where known.
* R/lme.R: called quantile on potentially missing values.
* tests/missing.{R,Rout.save}: test summary methods
2007-06-12 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-82
Also, R >= 2.4.0 because of seq_along.
* tests/lme.Rout.save: back to 2.5.1 layout.
2007-05-29 Brian Ripley <[email protected]>
* R/{gls,lme,pdMat}.R: qualify uses of nchar() by 'type'.
* R/lme.R: layout of over-long error message.
* tests/lme.Rout.save: update for above and for 2.6.0 layout.
* R/{gls,gnls,lme,nlme}.R: copy row names to fitted values and
residuals.
* R/{gls,gnls,lme}.R: support naresid and napredict.
* man/{residuals,fitted}.lme.Rd: document this.
* tests/missing.{R,Rout.save}: tests of missing-value support.
2007-05-20,24 Brian Ripley <[email protected]>
* R/*.R: partial matching issues, switch to seq_along.
2007-05-15 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-81
* NAMESPACE, R/zzMethods.R: migrate vcov methods from stats to here.
2007-05-04 Brian Ripley <[email protected]>
* man/{Extracr.pdMat,getdata.*,summary.varFunc}.Rd: remove
surplus }.
2007-03-30 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-80
* R/nlme.R (contrMat): Allow for expressions in 'fixed'.
* tests/contrMat.R: regression test for above.
* R/gls.R: bug fix for the case of y ~ 0.
* tests/gls.R: regression test for above.
* R/{lme,lmList,newMethods}.R: patch for lattice 0.15-x.
2007-01-30 Brian Ripley <[email protected]>
* DESCRIPTION (Title): Capitalize for consistency.
2006-12-29 Brian Ripley <[email protected]>
* DESCRIPTION (Version, Date): 3.1-79
* R/corStruct.R, R/pdMat.R, R/reStruct.R, man/corStruct.Rd,
man/pdMat.Rd, man/reStruct.Rd: add '...' argument to as.matrix()
methods. (Needed for 2.5.0, but works in earier versions.)
2006-12-10 Douglas Bates <[email protected]>
* DESCRIPTION (Version, Date): 3.1-78
2006-12-06 Douglas Bates <[email protected]>
* R/nlme.R (contrMat): Ensure that the contrasts component is a
list of matrices by expanding function names if necessary.
2006-11-29 Douglas Bates <[email protected]>
* DESCRIPTION: Prepare for new version.
* R/newMethods.R (getData.nls): getData.nls for R's nls objects
* inst/scripts/ch*.R: update Pinheiro and Bates (2000) scripts
2006-11-29 Brian Ripley <[email protected]>
* R/reStruct.R: fix PR#9262, multiple-line deparse.
* R/gls.R, groupedData.R, lme.R, lmList.R, newMethods,R, nlme.R:
more deparse width issues.
2006-09-28 Douglas Bates <[email protected]>
* R/nlme.R (getParsNlme): backed out change that caused failure
reported by Christian Ritz.
2006-09-18 Douglas Bates <[email protected]>
* R/VarCorr.R (VarCorr): Clean up problems in this file and
several others detected by codetools.
2006-09-11 Douglas Bates <[email protected]>
* R/nlme.R (getParsNlme): '[[' not '[' in case start$fixed is a list
* R/gls.R,gnls.R,newMethods.R,nlme.R,pdMat,Rsimulate.R: fix
problems exposed by codetools.
2006-07-31 Douglas Bates <[email protected]>
* man/ranef.lme.Rd: Modified the description of the `standard'
argument to more clearly describe its effect.
2006-07-24 Douglas Bates <[email protected]>
* R/lme.R: Patch by Andrew Robinson <[email protected]>
and Berwin Turlach <[email protected]> to set maximum number
of function calls in nlminb.
2006-07-03 Douglas Bates <[email protected]>
* DESCRIPTION: Version is 3.1-75
* man/{many files}: Documentation changes contributed by Spencer
Graves <[email protected]>. Most of the changes add Pinheiro
and Bates (2000) as a reference or add additional \seealso{}
entries. Some examples from Pinheiro and Bates (2000) have also
been added.
* R/nlme.R: reformat the code, typo.
2006-07-03 Martin Maechler <[email protected]>
* R/lme.R (lme.formula): when control()$returnObject is TRUE, only
warn instead of stop() in the case of non-convergence.
* tests/lme.R: test the above
* tests/lme.Rout.save:
2006-06-02 Brian Ripley <[email protected]>
* DESCRIPTION: Version is 3.1-74
2006-05-31 Brian Ripley <[email protected]>
* R/lme.R: Keep terms and optional model frame in lme.formula.
Use terms for prediction (get safe prediction that way).
Add keep.data argument to lme and methods.
* man/lme*.Rd: update for keep.data argument.
* R/newMethods.R: make use of saved data in getData methods.
* tests/getData.R, tests/predict.lme.R: new tests.
2006-05-24 Brian Ripley <[email protected]>
* R/gls.R, man/comparePred.Rd: 'minimum' and 'maximum' were
evaluated on a formula in the comparePred methods. Instead,
evaluate 'primary' in the 'data' used to fit object1, and document
what is done. (Reported by Mark Difford.)
2006-05-22 Brian Ripley <[email protected]>
* DESCRIPTION: Version is 3.1-73
2006-05-21 Brian Ripley <[email protected]>
* LICENCE, inst/LICENCE: add and install a licence file.
2006-05-18 Brian Ripley <[email protected]>
* R/groupedData.R: adjust method of as.data.frame.
* R/newFunc.R: fix bug in gsummary with objects that have
classes, e.g. Hmisc labels. (Reported by Mark Difford, in a
private followup to
https://stat.ethz.ch/pipermail/r-help/2006-May/094549.html.)
* tests/augPred_lab.R: tests for the above fix.
2006-05-12 Brian Ripley <[email protected]>
* R/gls.R, R/gnls.R, R/nlme.R: missing data=data in terms calls,
needed to resolve '.' on rhs of formulae.
* DESCRIPTION: Version is 3.1-72
2006-03-29 Brian Ripley <[email protected]>
* R/newMethods.R: as.list() did not work on symbols in R.
2006-03-14 Brian Ripley <[email protected]>
* R/lme.R, man/Variogram.Rd: make example work (na.omit in
the wrong place).
2006-03-10 Brian Ripley <[email protected]>
* DESCRIPTION: Version is 3.1-71
2006-02-17 Brian Ripley <[email protected]>
* R/nlsList.R: need to allow for multi-line deparse.
* tests/deparse.R: add regression test
2006-01-05 Brian Ripley <[email protected]>
* DESCRIPTION: Version is 3.1-70
* src/init.c, src/Makevars: make use of gcc4 visibility where supported
* inst/mlbook/ch0[45].R: remove unnecessary use of data()
* inst/scripts/ch0[58].R: all allowed versions of R have nlminb
* R/gls.R: element 'optimMethod' in the return value for
glsControl was unnamed.
* R/{gls,ngls,lme,nlme}.R, man/{gls,ngls,lme,nlme}Control.Rd:
let the user (rather than the version of R) choose the optimizer
to be used.
2006-01-05 Brian Ripley <[email protected]>
* src/init.c: missing registration for ARMA_constCoef
* inst/scripts/ch02.R: correct argument names in simulate.lme call
2005-12-31 Brian Ripley <[email protected]>
* DESCRIPTION: Version is 3.1-69, require 2.3.0.
* NAMESPACE: use registration.
* R/*.R: use registered symbols.
2005-12-31 Brian Ripley <[email protected]>
* DESCRIPTION: Version is 3.1-68.
* src/init.c: new file to register symbols
* R/corStruct.R: corrected one use of PACKAGE="base"
* R/lmList.R: remove attempted use of 'frame = 1'
2005-12-09 Deepayan Sarkar <[email protected]>
* R/newMethods.R, R/groupedData.R: fix for problem described in
https://stat.ethz.ch/pipermail/r-help/2005-December/082890.html
(superpose.line/symbol components were being truncated to length
of an arbitrary component).
2005-12-09 Brian Ripley <[email protected]>
* DESCRIPTION: Version is 3.1-67.
* R/gls.R: Replace do.call by eval.parent on massaged call.
* po/fr.R, po/R-fr.R, inst/po: add French translation by
Philippe Grosjean and automated en@quot translation.
2005-08-25 Douglas Bates <[email protected]>
* R/gls.R: Added option "optimMethod" to gls, gnls, and lme.
2005-08-24 Douglas Bates <[email protected]>
* R/lme.R (print.intervals.lme): Replace calls to print.matrix by
print(as.matrix()).
2005-07-25 Douglas Bates <bates@bates1-home>
* inst/scripts/ch08.R: Cleaned up examples in ch04, ch06, ch08.
* src/matrix.h: Include R_Ext/Linpack.h in addition to R_Ext/Applic.h
2005-07-19 Douglas Bates <[email protected]>
* R/gnls.R: Added definition of convIter when using nlminb or when
using optim. Reindented this and other R source files.
2005-07-12 Douglas Bates <bates@bates1-home>
* inst/scripts/ch01.R: Clean up and check these scripts
* src/nlmefit.c (gls_loglik): re-write contributed by ?? (I
accidently deleted the email message).
* R/lme.R (lme.formula): Use nlminb if available.
2005-06-08 Douglas Bates <bates@bates1-home>
* R/lme.R (predict.lme): Fixed bug when using a name for a formula
in original fit. (Reported by [email protected])
2005-05-20 Douglas Bates <bates@bates1-home>
* man/contr.SAS.Rd: Removed
2005-04-04 Douglas Bates <bates@bates1-home>
* R/newFunc.R: Removed contr.SAS definition as it has been revised
and moved into the stats package for R-2.1.0
2005-03-02 Douglas Bates <bates@bates1-home>
* src/nlmefit.c (gls_loglik): Replaced rnkm1 by p.
* po/,inst/po/: Added localization support.
2004-11-04 Douglas Bates <bates@bates1-home>
* src/nlmefit.c (dimFree): Fix memory leak reported by Brian Ripley.
2004-11-03 Douglas Bates <bates@bates1-home>
* man/varWeights.Rd: Remove all calls to data()
* man/corExp.Rd: Remove all references to the mva package
2004-08-10 Douglas Bates <bates@bates1-home>
* man/pairs.compareFits.Rd: fix syntax errors (new check available
in R CMD check)
2004-01-14 Douglas Bates <[email protected]>
* man/getCovariate.varFunc.Rd: Syntax correction from Kurt.
2003-12-16 Douglas Bates <[email protected]>
* install.R: Create stored image
2003-08-29 Douglas Bates <[email protected]>
* tests/lme.Rout.save (Coefficients): Now consistent with
i386-linux result.
* src/base.h: Replace R_ext/Mathlib.h by Rmath.h
2003-08-09 Douglas Bates <[email protected]>
* man/Covariate.varFunc.Rd, man/Matrix.pdMat.Rd, man/Matrix.reStruct.Rd, man/Names.pdMat.Rd, man/Names.reStruct.Rd, man/coef.corStruct.Rd, man/coef.modelStruct.Rd, man/coef.pdMat.Rd, man/coef.reStruct.Rd, man/coef.varFunc.Rd, man/getData.lmList.Rd, man/gnls.Rd:
Use \method for replacement method documentation as per Rd changes
* R/lme.R:
Changed check for intercept-like column in getFixDF (PR#2418)
2003-06-12 Douglas Bates <[email protected]>
* DESCRIPTION: New release
* man/ranef.lmList.Rd, man/nlme.Rd: Overdocumented arguments
2003-06-10 Douglas Bates <[email protected]>
* man/MathAchSchool.Rd, man/MathAchieve.Rd, ChangeLog, DESCRIPTION, R/groupedData.R, inst/scripts/ch03.R, inst/scripts/ch04.R:
Release 3.1-42
* inst/scripts/ch01.R: Protecting power in formula
2003-06-10 Douglas Bates <[email protected]>
* R/groupedData.R: Fixed bug in groupedData constructor when outer
is not missing.
2003-05-16 Douglas Bates <[email protected]>
* src/nlmefit.c (internal_EM): Fix by Peter Dalgaard for compound
symmetry EM calculations (PR#2985)
2003-05-05 Douglas Bates <[email protected]>
* R/lmList.R (update.lmList): Changed this and several other
update methods.
* R/groupedData.R: Use eval instead of do.call (Dieter Menne)
2003-04-17 Douglas Bates <[email protected]>
* NAMESPACE: contributed by Brian Ripley
* man/print.corStruct.Rd: Removed this and many other redundant
documentation files for S3 methods.
* R/<many files> Remove redundant GPL notices.
2003-03-25 Douglas Bates <[email protected]>
* R/nlme.R (nonlinModel): Moved definition from AAA.R to here
* man/summary.nlsList.Rd: Remove references to summary.nls
* R/newMethods.R: Remove vestigial definitions of AIC.lm
* R/zzMethods.R: Remove references to AIC.lm
2003-02-08 Douglas Bates <[email protected]>
* R/lme.R (lme.formula): Removed hessian=TRUE in calls to optim as
suggested by Brian Ripley.
2003-01-30 Douglas Bates <[email protected]>
* R/lme.R:
Incorporate change from Brian Ripley in response to Dieter Menne
* man/lme.lmList.Rd, man/lme.groupedData.Rd, man/lme.Rd:
Documentation of the contrasts argument added (Greg Warnes).
2003-01-30 Douglas Bates <[email protected]>
* R/lme.R (lme.formula): Incorporate Greg Warnes' changes for
the contrasts argument.
* R/nlsList.R: Correct check for is.null(class(FUN))
2002-12-27 Douglas Bates <[email protected]>
* R/newFunc.R (gsummary): Fix comparison in check for varying
columns (PR#1775 - bug report with fix provided by Dieter Menne.
2002-12-11 Douglas Bates <[email protected]>
* R/lme.R (print.lme): Removed one more as.vector()
* R/varFunc.R (print.summary.varFixed): changed instances of
deparse(as.vector(x)) to deparse(x) here and in many other places.
2002-09-10 Saikat DebRoy
* nlsList.R (nlsList.formula): Use "try" instead of "restart".
2002-08-09 Douglas Bates <[email protected]>
* R/groupedData.R: Fixed creation of grouped data from a formula
only
* R/newGenerics.R: Renamed the initialize generic and all methods
and calls to Initialize so as not to conflict with the methods
package.
2002-07-23 Douglas Bates <[email protected]>
* R/lme.R (update.lme): Fix formula handling in update methods
(Brian Ripley).
2002-04-20 Douglas Bates <[email protected]>
* R/nlme.R: Bug fix by SDR - convergence criterion was being
calculated incorrectly.
2002-04-04 Douglas Bates <[email protected]>
* man/getVarCov.Rd: Added an example of the type="marginal"
Corrected misplaced brace.
* R/VarCov.R (getVarCov.lme): Added the getVarCov functions
contributed by Mary Lindstrom <[email protected]>
2002-03-27 Douglas Bates <[email protected]>
* R/lme.R (anova.lme): Change strvar != "NA" to !is.na(strvar)
2002-03-05 Douglas Bates <[email protected]>
* man/ACF.gls.Rd: Changed Jose's email address on this and all the
other man pages.
* R/varFunc.R: Incorporate fix from Thomas Lumley and from Setzer
Woodrow for the logic where ifelse(length(el) == 1, is used
instead of if(length(el) == 1)
* R/pdMat.R: Change all vestigial instances of T and F to TRUE and
FALSE.
2001-12-18 Douglas Bates <[email protected]>
* R/corStruct.R: Finally resolved the print.summary.corSymm
controversy so it prints and it prints the correct value.
2001-12-10 Douglas Bates <[email protected]>
* R/lme.R: unclassed the logLik component of an lme summary before
trying to put it into a data frame for printing.
2001-12-01 Douglas Bates <[email protected]>
* R/zzMethods.R: Removed the .Alias calls.
2001-10-30 Douglas Bates <[email protected]>
* man/pairs.lme.Rd: Modified many documentation files to pass the
codoc checks.
2001-10-23 Douglas Bates <[email protected]>
* man/ACF.lme.Rd: Modified many, many method definitions and
documentation files to get them to pass the R-1.4.0 (in
development) package checking process.
2001-10-08 Douglas Bates <[email protected]>
* R/lmList.R: Fixed definition of logLik.lmList to work with R
(but it is still rather ugly).
* R/varFunc.R: Changed definition of logLik.varComb to return a
logLik object.
2001-10-05 Douglas Bates <[email protected]>
* R/lmList.R: Fixed selection of id[subscripts] in the panel
function of pairs.lmList (and several other functions) so it does
not produce a warning from evaluating is.na(NULL).
2001-09-17 Douglas Bates <[email protected]>
* R/nlme.R: Incorporated a change from
[email protected] for using nested grouping factors
in nlme.
2001-06-20 Douglas Bates <[email protected]>
* R/varFunc.R: Changes in calling sequences and in documentation
so the package passes codoc() checks. These affect many files in
both the R and the man directory. No changes of substance.
2001-05-29 Martin Maechler <[email protected]>
* R/zzMethods.R: Use .Alias()
* R/newGenerics.R: Generic AIC()
* R/newMethods.R: logLik.lm() moved to "base R"
* man/AIC.Rd,
* man/AIC.logLik.Rd: AIC.logLik() and AIC.lm() as well
* man/logLik.lm.Rd:
2001-03-28 Douglas Bates <[email protected]>
* R/simulate.R: Modified simulate.lme for default pdMat class of
pdLogChol.
2001-02-24 Douglas Bates <[email protected]>
* R/newFunc.R: Removed the old fake xyplot function. The new work
by Murrell and Sarkar will make this superfluous.
* man/MEestimate.Rd: Added manual pages for MEEM, MEdecomp,
MEestimate.
* R/newMethods.R: Revised assignments in plotting methods to be
compatible with the Murrell/Sarkar preliminary trellis package.
* src/nlmefit.c (internal_decomp): Corrected an error reported by
Kathryn Chaloner where Srows >= ZXrows.
2001-01-10 Douglas Bates <[email protected]>
* DESCRIPTION (Maintainer): Added Maintainer entry to
DESCRIPTION.
2000-12-09 Douglas Bates <[email protected]>
* R/lme.R: (Variogram.lme) Coerced n.pairs to numeric and
corrected calls to dist.
2000-12-08 Douglas Bates <[email protected]>
* R/lme.R: Changed all calls to dist in lme.R, gls.R and
corStruct.R to use the argument "method" rather than "metric".
* R/pdMat.R: Replaced calls to .Fortran("dbksl", ...) with calls
to the R function solve() for R-1.2.0 where the S_compat.c file
has been removed.
* inst/scripts/ch01.R: Added the chapter scripts from
"Mixed-Effects Models in S and S-PLUS" to the inst directory.
* man/formula.nlme.Rd: Modified the examples in this and many
other .Rd files to use the Loblolly data and the SSasymp
self-starting function. There were many occasions where the
Soybean data was being fit to a default formulation of an nlme
model just to get things like a formula. This fit of the Soybean
data is difficult and time consuming and not very illuminating.
2000-11-30 Douglas Bates <[email protected]>
* src/matrix.c: Removed dependency on S_compat.h by replacing
calls to dqrdca with the equivalent call to dqrdc2.
2000-07-24 Saikat DebRoy
* Changed various uses of do.call to eval. The reason for doing
this is to allow calls to the function calling eval from within
another function. It's the old scoping problem again.
2000-07-07 Saikat DebRoy
* src/nlme.c, src/nlmefit.c: Added mixed_grad in calls to optif9.
* src/nlmefit.c : Added handling of pdLogChol objects (pdClass =
4) in various functions.
* src/nlmefit.c (mixed_grad): New function giving analytic
gradient for mixed-effects log-likelihood.
* R/nlme.R (nlme.formula): Added updating of the pdFactor in the
PNLS step.
* R/reStruct.R: Made pdLogChol the default representation for
reStruct objects.
* src/pdMat.c (logChol_pd): new function.
* R/pdMat.R: Added back the pdLogChol class and associated
methods.
2000-07-03 Douglas Bates <[email protected]>
* man/corFactor.corStruct.Rd: Added an alias for
corFactor.corNatural
* src/nlmefit.c (internal_loglik): Changed the return value on
error from R_NegInf to -DOUBLE_XMAX so the optif[09] optimizers
will work properly.
* src/corStruct.c (corStruct_factList): Provided a correct call to
the R version of F77_CALL(chol) here and everywhere else in this
source file.
* R/zzz.R: Removed the deprecated call to provide
2000-03-17 Douglas Bates <[email protected]>
* added many data sets
* incorporated patches from Brian Ripley to use optim for the
optimization rather than nlm
* src/nlmefit.c (internal_loglik): Returned R_NegInf instead of
generating a error on a singular precision matrix.
* DESCRIPTION (Depends): Changed Depends to R version 1.0.1
because of problem with assigning components of lists.
1999-12-23 Douglas Bates <[email protected]>
* TITLE: Changed the title to nlme