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revision 350, Tue Nov 23 15:39:45 2004 UTC revision 1442, Thu Aug 24 22:08:11 2006 UTC
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1  2004-11-16  Douglas Bates  <bates@bates1-home>  2006-08-24  Douglas Bates  <bates@R-project.org>
2    
3            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
4            on R_ldl.
5            * R/lCholCMatrix.R,
6            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
7            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
8            * many files in ./R and ./src: Use more general version of
9            dup_mMatrix_as_dgeMatrix to simplify method definitions.
10            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
11            dtpMatrix, dspMatrix and dppMatrix conversions.
12    
13    
14    2006-08-23  Douglas Bates  <bates@R-project.org>
15    
16            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
17            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
18            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
19            dgeMatrix_crossprod (may need to do this in other places).
20            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
21            generic and method for dsCMatrix.  Use CHOLMOD for chol().
22    
23    2006-08-22  Douglas Bates  <bates@R-project.org>
24    
25            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
26            types of classed Matrices, matrices or numeric or logical vectors.
27            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
28            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
29            to Mutils.h (as an inline) and change name to Matrix_check_class;
30            fixes in as_cholmod_factor and chm_factor_to_SEXP.
31            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
32            dsCMatrix_matrix_solve.  Comment out vestigial functions.
33            * src/Csparse.c: use diag_P and uplo_P macros.
34    
35    2006-08-21  Douglas Bates  <bates@R-project.org>
36    
37            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
38            valgrind.
39            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
40            inverses.
41            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
42            -Wall warnings.
43            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
44            Use dup_mMatrix_as_dgeMatrix.
45    
46    2006-08-20  Douglas Bates  <bates@R-project.org>
47    
48            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
49            * tests/sparseQR.R: Added
50            * man/sparseQR-class.Rd: Document methods for qr.* generics
51            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
52    
53    2006-08-19  Douglas Bates  <bates@R-project.org>
54    
55            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
56            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
57            and qr.fitted.
58            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
59            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
60    
61    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
64            the base version has no "..." argument.
65    
66            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
67    
68            * R/Matrix.R: define and
69            * NAMESPACE: export as.numeric() and as.logical() methods.
70                    Let's hope these do not badly slow down something...
71            Finally export the zapsmall() method.
72    
73    2006-08-17  Douglas Bates  <bates@R-project.org>
74    
75            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
76            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
77            * src/dtCMatrix.c :Remove code that is no longer used
78            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
79    
80    2006-08-14  Douglas Bates  <bates@R-project.org>
81    
82            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
83            Csparse_to_logical and Csparse_symmetric_to_general.
84            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
85            coercion methods between CsparseMatrix and TsparseMatrix.
86    
87    2006-08-14  Douglas Bates  <bates@R-project.org>
88    
89            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
90            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
91            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
92            possible.
93    
94    2006-08-12  Douglas Bates  <bates@R-project.org>
95    
96            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
97              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
98              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
99              generalize conversions between TsparseMatrix, CsparseMatrix,
100              denseMatrix and matrix.  Preserve triangularity property and
101              propagate Dimnames in the easy cases.
102    
103    2006-08-10  Douglas Bates  <bates@R-project.org>
104    
105            * src/lmer.c: adjust checks in glmer_init for S4SXP
106            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
107            before S4SXP but for the wrong reasons.
108    
109    2006-08-08  Douglas Bates  <bates@R-project.org>
110    
111            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
112            Later modified to return the upper triangle only.
113            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
114    
115    2006-08-07  Douglas Bates  <bates@R-project.org>
116    
117            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
118            R-level conversion to a sparse symmetric class.
119            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
120            Remove conversion to sparse symmetric classes (now done in C code).
121    
122    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
125            * man/band.Rd:  adapt the \dontshow{} unit test.
126    
127    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * DESCRIPTION (Version): 0.995-14  for CRAN
130    
131            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
132    
133            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
134            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
135    
136            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
137            * R/Tsparse.R (tril, triu, band): methods
138            * R/dgRMatrix.R (tril, ...):    ditto
139            * man/band.Rd:                  ditto
140    
141    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/Matrix.R (head, tail): directly use utils:::head.matrix
144                    to be up-to-date automatically.
145    
146    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
149    
150            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
151            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
152            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
153            such that the S4 objects are always created by the current version
154            of R and 'Matrix' class definitions.
155    
156    2006-08-01  Douglas Bates  <bates@R-project.org>
157    
158            * R/lmer.R (LMEoptimize method), tests/lmer.R,
159            inst/external/test3comp.rda: Added warnings for convergence on
160            boundary and test cases.
161    
162            * src/lmer.c (mer_postVar): Modified to return the variances that
163            are marginal to the fixed effects, not conditional on them (which
164            is what the bVar slot contents represent).
165    
166    2006-07-31  Douglas Bates  <bates@R-project.org>
167    
168            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
169            function which calls the C function mer_hat_trace2.
170    
171            * man/ranef.Rd: Include description of "postVar" argument and
172            producing a caterpillar plot.
173    
174    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * NAMESPACE:    change  "correlation" to "corMatrix"
177            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
178            * R/dpoMatrix.R: ditto
179            * R/lmer.R:      ditto
180    
181    2006-07-28  Douglas Bates  <bates@R-project.org>
182    
183            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
184            RZXinv slot's contents into a separate internal function that can
185            be used in mer_hat_trace.
186    
187    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
190            via new smart
191            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
192            utility functions.
193    
194    
195    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/Csparse.R (tril, triu, band): do return *triangular* classed
198            matrices when appropriate; band() even symmetric ones.
199            (replCmat): extend to potentially all "CsparseMatrix"
200            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
201            allow subassignment for special sparse matrices.
202    
203            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
204    
205            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
206            argument; in glmer_*(): print only if(verbose).
207    
208            speed-optimize a few places by moving REAL(.) out of loops.
209    
210            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
211    
212    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
215                    since that wrongly triggers also for M[ logi , ]
216    
217            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
218            a symmetric matrix that results in a non-symmetric one.
219            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
220    
221            * R/dMatrix.R: make round(M) work as round(M, 0)
222    
223            * R/dgTMatrix.R (image): coordinate system and axis now use
224            1-based indices, not 0-based ones.
225    
226            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
227            * tests/indexing.R: test it.
228    
229            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
230            * man/isSymmetric-methods.Rd: and document it.
231    
232            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
233            * man/SparseM-conv.Rd: docu them
234    
235            * tests/other-pkgs.R: renamed from tests/graph.R and add example
236                    for 'SparseM' conversions
237    
238    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
239    
240            * R/Matrix.R (head): added head() and tail() methods.
241    
242    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * DESCRIPTION (Version): 0.995-12 released to CRAN
245    
246    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * tests/simple.R: add check for correct dsT -> dgT coercion;
249                    add check for correct printing of symmetric sparse matrices.
250    
251            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
252            for sparse symmetric matrices.
253    
254            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
255            diagonal twice.
256    
257    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
258    
259            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
260            being applied to the x slot (detected by Brian Ripley).
261    
262    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
265    
266            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
267    
268    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * src/lgCMatrix.c (lgCMatrix_diag): new function
271            * R/lgCMatrix.R (diag): for new method
272    
273            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
274                 ==> construction of illegal "*gTMatrix" via new() should
275                 now be much less easy:
276            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
277    
278            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
279                    directly.
280            * man/Matrix.Rd: documents it.
281    
282    2006-07-06  Douglas Bates  <bates@R-project.org>
283    
284            * src/pedigree.c (pedigree_inbreeding): Correction in
285            initialization.  This function is not currently being used and is
286            not fully tested.
287    
288            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
289            Introduced the glmer class.  Added code for mcmcmsamp on glmer
290            objects.  Modified validity check on pedigree objects to account
291            for nonparallel patterns of missingness of parents.
292    
293            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
294            class.
295    
296    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/pMatrix.R: coercion pMatrix -> Tsparse
299    
300    2006-06-12  Douglas Bates  <bates@R-project.org>
301    
302            * DESCRIPTION (Version): 0.995-11 released to CRAN
303    
304            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
305            the output from mcmcsamp.
306    
307    2006-06-10  Douglas Bates  <bates@R-project.org>
308    
309            * R/lmer.R (simulestimate): added C code for calculating the trace
310            of the hat matrix.
311    
312    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
315            classes.
316            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
317    
318    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/dgTMatrix.R (colSums): etc. All four of
321            colSums(), rowSums(), colMeans(), rowMeans() now should work for
322            all "Matrices".
323    
324    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
325    
326            * R/lmer.R (panel.ci): Add a reference line at zero and a
327            background grid to the qqmath plot of ranef.lmer.
328    
329    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
330    
331            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
332            grouping factors to be specified in the formula as (1|foo/bar).
333    
334    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
335    
336            * R/lmer.R (findbars and others): Change check of is.numeric to
337            !is.language to resolve the bug reported by Jacob Wegelin.
338    
339            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
340            code to evaluate inbreeding coefficients without calculating T,
341            based on code in Sargolzaei and Iwaisaki's paper.
342    
343    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
344    
345            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
346            generic and mer methods for isNested and denomDF. This denomDF was
347            an attempt to emulate that in lme but I don't think that makes
348            sense.  Use the trace of the hat matrix instead.
349    
350    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
353            the C code depending on a slot structure that's no longer valid.
354            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
355    
356    
357    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
358    
359            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
360            of lowerTriMatrix generic and methods to tril (also upper to triu)
361            and added a general band extractor.
362    
363    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
364    
365            * R/pedigree.R (pedigree): Replace sire and dam values outside the
366            allowable range with NAs. Added a corresponding check in the
367            validity check for the pedigree class.
368    
369            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
370            crossprod methods now inherits from symmetricMatrix.
371    
372    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
375            generics lowerTriMatrix and upperTriMatrix along with methods for
376            the Csparse virtual class.  Also added a C function Csparse_band
377            that implements these methods by calling cholmod_band.
378    
379    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
382            erased when it was NULL.  This led to invalid subselections!
383    
384    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
385    
386            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
387            in method for "t" so as not to lose the unit diagonal property.
388    
389    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
390    
391            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
392            and methods.  This is now an option to the ranef method for the
393            mer class.
394    
395            * src/cs_utils.c: Ensure that the nz component is -1 for a
396            compressed column-oriented matrix.  Minor formatting cleanup.
397    
398            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
399            objects.
400    
401    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
404            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
405    
406    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
407    
408            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
409            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
410    
411            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
412            for the dtCMatrix class.
413    
414    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
415    
416            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
417            and methods for it.
418    
419    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
422            arguments, such that M %*% 1:6 now works
423            * Tests/matprod.R: test the above
424    
425    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
426    
427            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
428            the ranef.lmer class.
429    
430            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
431            methods to extract the posterior variances from the bVar slot.
432    
433    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
436            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
437    
438            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
439            * tests/simple: (extended)
440    
441            * R/sparseMatrix.R (isTriangular): now using much improved
442            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
443    
444    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
445    
446            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
447            (problem report from Franklin Parlamis).  This should be done
448            generally.
449    
450    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
451    
452            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
453            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
454            update the plot methods.
455    
456    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
457    
458            * R/lmer.R (resid and ranef methods):  Added methods for the
459            "residuals" and "resid" generic but only for linear mixed model
460            fits.  Changed the ranef method to return a list of data frames so
461            that the plot methods now work.
462    
463    2006-03-16  Douglas Bates  <bates@bates2>
464    
465            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
466            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
467    
468            * DESCRIPTION (Date): New release
469    
470    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
473    
474            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
475            * man/KNex.Rd: and other help files
476            * tests/*.R: several ones needed adaption
477            * inst/doc/Comparisons.Rnw: ditto
478    
479    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
482    
483            * tests/indexing.R: tests for new [<- methods for sparse matrices.
484    
485    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
488    
489            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
490    
491    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/dMatrix.R: enable things like  M [ M < 10 ]
494            * R/dgeMatrix.R: implement it
495    
496    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/AllClass.R: define "summary.mer" and "*.lmer"
499            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
500            * R/lmer.R (show): now works with summary()
501    
502    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
505            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
506                    support the above
507    
508    2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
509    
510            * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
511            Use glmFit$prior.weights for weights in a glmm.
512            Allow an option usePQL = FALSE to skip the PQL steps for the
513            Laplace method (and, in time, the AGQ method).
514    
515            * src/lmer.c (mer_factor): Move downdating and factoring of XtX
516            into a separate function internal_mer_Xfactor to be able to call
517            it from internal_bhat.
518    
519    2006-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * tests/Class+Meth.R (tstMatrixClass): function for much better
522            testing; now again of all actual classes.
523    
524            * src/Mutils.c (MAKE_TRIANGULAR_BODY, MAKE_SYMMETRIC_BODY):
525                    use macros and define make_d_matrix_* and make_i_matrix_*
526                    where _i_ is for the ldense routines:
527    
528            * src/ldense.c (ltrMatrix_as_lgeMatrix): provide functions
529            * src/ldense.c (lsyMatrix_as_lgeMatrix):
530    
531            * R/ldenseMatrix.R: use the above in setAs(*,"lgeMatrix")
532    
533    
534    2006-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * R/Matrix.R (Matrix): has become much "smarter" now auto-producing
537                    many different kinds of matrices.
538            * R/*.R: quite a few new methods were needed for R CMD check with
539                    new Matrix().  Very good for users playing around.
540    
541    
542    2006-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * src/dgeMatrix.c (dMatrix_validate): new
545            * src/Mutils.c (dense_nonpacked_validate): new
546    
547            * src/dtrMatrix.c (dtrMatrix_validate): improved/fixed
548    
549    
550    2006-01-14  Douglas Bates  <bates@stat.wisc.edu>
551    
552            * R/AllClass.R (compMatrix), (generalMatrix): new virtual classes
553    
554    2006-01-07  Douglas Bates  <bates@stat.wisc.edu>
555    
556            * DESCRIPTION (Version): 0.99-6 released to CRAN
557    
558            * src/dgBCMatrix.c (cscb_trcbsm): Fix due to Peter Dalgaard for
559            segfault in cases with multiple non-nested grouping factors.
560    
561    2006-01-03  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * DESCRIPTION (Version): 0.99-4 to be released to CRAN
564                    (Depends): also on 'utils'
565    
566            * R/AllClass.R (diagonalMatrix): new class with "ddi*" and "ldi*"
567            * R/diagMatrix.R (Diagonal): constructor and methods for
568            diagonal matrices
569    
570            * R/ltTMatrix.R: new "minimal methods"
571    
572    2005-12-12  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/AllGeneric.R (tcrossprod): 2-argument version; here, and for
575            all methods (and help files).
576    
577    2005-12-09  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * R/Auxiliaries.R (dimNamesCheck): fixed thinko -> bug
580                    for case (dimn.  op  no_dimn.)
581    
582    2005-11-14  Douglas Bates  <bates@stat.wisc.edu>
583    
584            * DESCRIPTION (Version): 0.99-2  released to CRAN
585    
586    2005-10-21  Douglas Bates  <bates@stat.wisc.edu>
587    
588            * R/lmer.R (simulate method): Fixed a drop=FALSE problem reported
589            by Julian Faraway.
590    
591    2005-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/Auxiliaries.R (try_as): new utility
594            * R/sparseMatrix.R: use try_as() in coercion to original class
595    
596    2005-09-30  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * src/dgCMatrix.c (double_to_csc): and dgeMatrix_to_csc()
599    
600    2005-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/Auxiliaries.R (dimNamesCheck): added
603    
604            * R/Matrix.R (as.array), (as.vector): new
605    
606    2005-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/Matrix.R (Matrix): get logical argument 'sparse' with a smart
609                    default.
610            * R/AllClass.R: move 'factors' slot toplevel "Matrix";
611                    "pMatrix" now contains "sparseMatrix"
612    
613    2005-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * tests/Class+Meth.R: new tests; t(t(m)) == m
616    
617            * src/dtCMatrix.c (tsc_transpose): add forgotten "diag" slot
618    
619            * src/dsTMatrix.c (dsTMatrix_as_dsCMatrix): bad typo (segfault!)
620            * src/dtTMatrix.c (dtTMatrix_as_dtCMatrix): new
621    
622            * R/dspMatrix.R: typo in "t" method
623    
624    2005-09-18  Douglas Bates  <bates@wisc.edu>
625    
626            * R/AllClass.R (TsparseMatrix), CsparseM* and RsparseM*
627            * R/Tsparse.R: instead of R/gTMatrix.R
628            * R/Csparse.R: new
629            * src/Tsparse.c (Tsparse_to_Csparse): new; -> cholmod_()
630            * src/Tsparse.c: new; many trivial methods calling cholmod_()
631            * src/Csparse.c (Csparse_to_Tsparse), transpose, (mat|cross)prod:
632                            via cholmod
633    
634    2005-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/Auxiliaries.R (non0ind): new function using new C code
637            * src/dgCMatrix.c (compressed_non_0_ij): new utility
638    
639    2005-09-15  Douglas Bates  <bates@localhost.localdomain>
640    
641            * src/chm_common.h: header file required by all C sources that
642            call CHOLMOD functions.  It defines a cholmod_common structure
643            called 'c' whose address is passed as the last argument to
644            (virtually) every CHOLMOD function.
645    
646            * src/Pattern.c: Simple example of the use of CHOLMOD.
647    
648            * src/init.c: initialize and finalize the cholmod_common structure.
649    
650            * src/Makefile: Added source packages CHOLMOD UMFPACK AMD COLAMD
651            LDL and CCOLAMD from the U. of Florida sparse matrix library.
652    
653    2005-09-08  Martin Maechler  <maechler@stat.math.ethz.ch>
654    
655            * inst/test-tools.R: new file collecting the utility functions used
656                    in ./tests/*.R
657    
658            * R/ddenseMatrix.R (cbind2): new methods for "numeric" and "matrix"
659            * R/Matrix.R (cbind2): methods for NULL and missing
660    
661    2005-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * R/AllClass.R: new "index" class for "[" and "[<-":
664                    First cut at "symmetricMatrix" and "triangularMatrix"
665            * R/gTMatrix.R (.ind.prep): new function;
666                    Logical and character indexing now work too.
667            * R/Matrix.R: cheap "[<-" methods for denseMatrix now work
668            * tests/indexing.R: new, including *.Rout.save
669            * tests/dgTMatrix.R: new
670    
671    2005-08-29  Douglas Bates  <bates@wisc.edu>
672    
673            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): Corrected the position
674            indicator pos not being updated.  Also enforced upper triangular
675            for symmetric case.  Need to coerce edges component of elements of
676            edge list - grr! (Why don't they define their classes cleanly?)
677    
678    2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Matrix.R:  added first "[<-" methods; not yet functional
681            * R/denseMatrix.R: ditto
682            * man/Subassign-methods.Rd: new help file for these
683    
684    2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * DESCRIPTION (Version): 0.98-6
687    
688            * R/denseMatrix.R: new file for "[" fallback methods for all dense
689            matrices.
690    
691    2005-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * src/lgCMatrix.c (lcsc_to_matrix): new; need for
694                    as( <logical>, "matrix")
695    
696            * R/pMatrix.R: coercion to "lgTMatrix"
697    
698            * R/gTMatrix.R: new virtual class to define "[" methods for.
699            * man/gTMatrix-class.Rd:
700            * General slight re-organization of where "[" methods are defined.
701              more to come.
702    
703    2005-08-18  Douglas Bates  <bates@wisc.edu>
704    
705            * DESCRIPTION (Version): 0.98-5  released to CRAN
706    
707            * src/dgTMatrix.c (graphNEL_as_dgTMatrix): add first graphNEL methods
708            * .....
709    
710    2005-08-18  Douglas Bates  <bates@localhost.localdomain>
711    
712            * R/lmer.R: Corrected naming scheme in mcmcsamp to work with lmer
713            or glmer objects.
714    
715    2005-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * DESCRIPTION (Version): 0.98-4 : upload to CRAN
718    
719    2005-08-16  Douglas Bates  <bates@localhost.localdomain>
720    
721            * R/HBMM.R: finish re-writing R-only code.
722    
723    2005-08-15  Douglas Bates  <bates@localhost.localdomain>
724    
725            * man/externalFormats.Rd: move documentation for writeHB and
726            writeMM here.
727    
728            * src/mmio.c: replace inclusion of <malloc.h> by <stdlib.h>
729            (suggested by Paul Roecker).
730    
731            * tests/validObj.R (assertError): Comment out test that is failing
732            after recent changes in r-devel.
733    
734    
735    2005-08-11  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/AllClass.R: intermediate virtual class "denseMatrix"
738            * man/denseMatrix-class.Rd
739            * NAMESPACE: export it, and also export
740            * man/unused-classes.Rd: "iMatrix", "zMatrix" and "ldenseMatrix"
741    
742    2005-08-10  Douglas Bates  <bates@wisc.edu>
743    
744            * DESCRIPTION (Version): 0.98-3 to CRAN
745    
746            * src/dtrMatrix.c (dtrMatrix_validate): fixed up validation and
747            matrix_solve code (which was really, really wrong).
748    
749    2005-08-07  Douglas Bates  <bates@wisc.edu>
750    
751            * DESCRIPTION (Version): 0.98-2
752    
753            * R/HBMM.R (readHB), (readMM): read Matrix Market formats
754    
755            * R/lmer.R (abbrvNms): new
756            * R/lmer.R (mcmcsamp): allow transformed parameters
757            * src/HBMM.c (Matrix_writeMatrixMarket): Added read/write routines
758            for the Harwell-Boeing and the MatrixMarket formats.
759    
760    2005-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
761    
762            * man/dtrMatrix-class.Rd: add examples
763            * man/dtpMatrix-class.Rd: ditto; plus note about PROBLEM
764    
765            * TODO: note the dtpMatrix (docu) bug
766    
767            * R/zzz.R (.onLoad): assignInNamespace("as.matrix", *, "base")
768            in order to ensure that new as.matrix() is used by old functions,
769            e.g., svd(), qr(), eigen(), dist(),..;
770                  apply(), also matplot() or pairs().
771    
772    
773    2005-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/lmer.R: add 'fixme' comments and move the linear vs glm check;
776              add comments about 'control' / lmerControl() arguments
777    
778    2005-07-27  Douglas Bates  <bates@wisc.edu>
779    
780            * man/sleepstudy.Rd: Added the sleep data set.
781            * DESCRIPTION (Version): 0.98-1  released to CRAN
782    
783    2005-07-12  Douglas Bates  <bates@wisc.edu>
784            * man/sleepstudy.Rd: Added the sleep data set.
785    
786            * R/lmer.R (glmmMCMC): Added PACKAGE = "Matrix" in a couple of
787            .Call calls that were producing spurious output.
788    
789    2005-07-05  Douglas Bates  <bates@wisc.edu>
790    
791            * R/lmer.R (lmer): stored updated variance component estimates in
792            mer object for the generalized model.  (Bug reported by Renaud
793            Lancelot).
794    
795    2005-07-03  Douglas Bates  <bates@wisc.edu>
796    
797            * src/lmer.c (glmer_devAGQ): Added AGQ for single grouping factor,
798            unidimensional case.
799    
800    2005-06-08  Douglas Bates  <bates@wisc.edu>
801    
802            * DESCRIPTION (Version): 0.96-1
803    
804            * moved  lmer-class' R and C code moved from lme4 to here
805    
806    2005-06-04  Douglas Bates  <bates@wisc.edu>
807    
808            * R/dgCMatrix.R: Call to csc_matrix_mm used undefined arguments
809            (reported by Guissepe Ragusa <gragusa@ucsd.edu>)
810    
811    2005-06-02  Douglas Bates  <bates@wisc.edu>
812    
813            * src/Makefile.win: Forgot to update this when Makefile changed.
814    
815    2005-05-11  Douglas Bates  <bates@wisc.edu>
816    
817            * src/dgCMatrix.c (csc_transpose): Simplified function fixing a
818            bug reported by Kurt Hornik and Michael Hahsler.
819    
820    2005-05-10  Douglas Bates  <bates@wisc.edu>
821    
822            * src/lgCMatrix.c (Matrix_lgClgCmm): Implementation of methods for
823            logical sparse matrices.  These will also be used in the symbolic
824            analysis for lmer objects.
825    
826            * src/dsCMatrix.c (dsCMatrix_matrix_solve): Copied the dimensions
827            of b to the result.  Fixes bug reported by Jean.Coursol@math.u-psud.fr
828    
829    2005-05-06  Douglas Bates  <bates@wisc.edu>
830    
831            * src/dgeMatrix.c (dgeMatrix_colsums): Added an implementation of
832            colMeans, colSums, rowMeans and rowSums.
833    
834    2005-04-18  Douglas Bates  <bates@wisc.edu>
835    
836            * src/lgCMatrix.[ch]: code for _validate method and stub for
837            multiplication operation.
838    
839            * src/dgeMatrix.c (dgeMatrix_matrix_solve): Passing wrong argument
840            to dgetrs.
841    
842            * src/init.c: Fix cut-and-paste error in definition of
843            dgeMatrix_matrix_solve
844    
845            * src/{many files}: Tighten code by using ALLOC_SLOT.
846    
847    2005-04-15  Douglas Bates  <bates@wisc.edu>
848    
849            * R/AllClass.R: Add lgTMatrix and lgCMatrix classes
850    
851            * DESCRIPTION: Eliminate import of stats.
852    
853    
854    2005-04-06  Douglas Bates  <bates@wisc.edu>
855    
856            * R/AllClass.R : add logical sparse matrix classes
857    
858    2005-04-01  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
860            * R/dgTMatrix.R: add "[" method for triplet matrices
861            * R/sparseMatrix.R: and other sparse ones; --> add show() for sparse
862    
863    2005-03-31  Douglas Bates  <bates@wisc.edu>
864    
865            * DESCRIPTION (Version): release 0.95-5 to CRAN
866    
867            * R/dMatrix.R: add %*%, crossprod and solve "fallback" methods
868            * R/sparseMatrix.R: %*%, crossprod()
869            * R/dgeMatrix.R: more "fallback" methods for numeric/dense matrices
870            * man/*.Rd: move method definitions to 'Matrix' and 'dMatrix'
871            * src/lmer.c (lmer_fitted): fix thinko
872    
873    2005-03-26  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/AllClass.R: add two virtual sparse classes ``on top''
876    
877    2005-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
878    
879            * R/AllClass.R (setClass): use "VIRTUAL" for the virtual classes;
880                    correspondingly fix examples and tests/ since new()
881                    doesn't work for virtual classes.
882    
883    2005-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
884    
885            * R/Matrix.R (as.matrix): method and one for unname()
886            * tests/dpoMatrix.R: tests should now be less platform dependent;
887              also run for R 2.1.0; using as.matrix()
888    
889    2005-03-15  Douglas Bates  <bates@wisc.edu>
890    
891            * R/pMatrix.R: "pMatrix" class added
892            * ....
893    
894    2005-03-14  Douglas Bates  <bates@wisc.edu>
895    
896            * R/dtpMatrix.R: Add unpack method and an example.
897    
898            * src/dsyMatrix.c (dsyMatrix_trf): Add BunchKaufman factorization
899            of general symmetric matrices and associated S4 methods.
900    
901    2005-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
902            +
903    2005-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * R/dgeMatrix.R (setAs): and many other files: more coercion,
906              crossprod() and "%*%" methods added; tests, too.
907            * tests/matprod.R: new, for testing these
908    
909    2005-03-03  Douglas Bates  <bates@wisc.edu>
910    
911            * src/lmer.c (lmer_fitted): Added.
912    
913    2005-03-02  Douglas Bates  <bates@wisc.edu>
914    
915            * R/dsTMatrix.R: Conversion from dsTMatrix to dsCMatrix
916    
917    2005-02-28  Douglas Bates  <bates@wisc.edu>
918    
919            * src/*.c,po/,inst/po: Internationalization and localization of
920            the package.
921    
922            * src/ldl.[ch]: Removed these as their contents are referenced in the
923            R_ldl.c file.
924    
925            * src/flame.[ch]: Removed these source files.
926    
927            * src/dtrMatrix.c (make_array_triangular): Move to Mutils
928    
929            * src/LU.[ch],src/init.c: absorb in factorizations
930    
931            * src/Mutils.h: prepare for internationalization
932    
933            * src/cblas.h: move the enum definitions to Mutils.h and remove
934            this file
935    
936    2005-02-26  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * R/dgeMatrix.R: provide "dimnames" and "dimnames<-" methods
939    
940            * R/dtrMatrix.R: fix t() method
941    
942            * R/dgeMatrix.R: define group methods "Arith", "Math", "Math2"
943            * NAMESPACE: export them (and import generics from "methods")
944            * tests/group-methods.R : and test them.
945    
946            * src/dtrMatrix.c (dtrMatrix_as_dgeMatrix): prevent seg.fault in
947            border case
948    
949    2005-02-24  Douglas Bates  <bates@stat.wisc.edu>
950    
951            * DESCRIPTION (Version): 0.95-2  released to CRAN
952    
953            * src/dgBCMatrix.c:
954            * src/lmer.c: many changes
955            * ...
956    
957    2005-02-04  Martin Maechler  <maechler@stat.math.ethz.ch>
958    
959            * R/Matrix.R: add more sophisticated show() method.
960    
961    2005-02-02  Douglas Bates  <bates@stat.wisc.edu>
962    
963            * */* : almost complete reorganization of classes.
964    
965    2005-01-26  Douglas Bates  <bates@wisc.edu>
966    
967            * R/AllGeneric.R: Added matrix exponential generic expm and a method
968            for the geMatrix class.
969    
970    2005-01-24  Douglas Bates  <bates@wisc.edu>
971    
972            * src/Makefile (clean): Remove *.a and *.so
973    
974            * man/cscBlocked-class.Rd: Remove reference to the lmer-class.
975    
976    2005-01-23  Douglas Bates  <bates@wisc.edu>
977    
978            * src/lmer.c (Lind): Definition of Lind was backwards.  This only
979            had an effect in cases with more than 2 grouping factors.
980    
981    2005-01-03  Douglas Bates  <bates@wisc.edu>
982    
983            * src/lmeRep.c (lmer_variances): change from lmeRep to lmer
984    
985    2004-12-23  Douglas Bates  <bates@wisc.edu>
986    
987            * src/init.c (R_init_Matrix): Reorder calls to R_registerRoutines
988            and R_useDynamicSymbols (suggested by B.D.Ripley).
989    
990    2004-12-14  Douglas Bates  <bates@wisc.edu>
991    
992            * R/sscMatrix.R: Add determinant methods
993    
994            * src/triplet.[ch],src/init.c (triplet_to_matrix): Add a coercion
995            for tripletMatrix to matrix.
996    
997    2004-12-13  Douglas Bates  <bates@wisc.edu>
998    
999            * R/AllClass.R (.onLoad): Eliminate the bbCrosstab class, which is
1000            no longer used.
1001    
1002            * src/R_ldl.c: Created an R-specific version of the ldl.[ch] files
1003            with dynamic allocation of scratch arrays.
1004    
1005            * src/ssclme.c (ssclme_copy_ctab): Fixed bug in creation of ZtZ
1006            for multivariate random effects with multiple grouping factors.
1007            Fixes part but not all of #15.
1008    
1009    2004-12-03  Douglas Bates  <bates@wisc.edu>
1010    
1011            * src/lmeRep.c (lmeRep_factor): order of operations for multiple
1012            scalar grouping factors corrected.
1013    
1014    2004-11-29  Douglas Bates  <bates@wisc.edu>
1015    
1016            * src/bCrosstab.c: remove diag_update which is no longer used
1017    
1018    2004-11-16  Douglas Bates  <bates@wisc.edu>
1019    
1020          * src/Metis_utils.c: Move metis.h include to C sources so that the          * src/Metis_utils.c: Move metis.h include to C sources so that the
1021          .h file can be included.          .h file can be included.
1022    
1023  2004-11-12  Douglas Bates  <bates@bates1-home>  2004-11-12  Douglas Bates  <bates@wisc.edu>
1024    
1025          * src/LU.c,geMatrix.c,trMatrix.c, etc.:          * src/LU.c,geMatrix.c,trMatrix.c, etc.:
1026          Complete allocation of slots in NEW_OBJECT.          Complete allocation of slots in NEW_OBJECT.
1027    
1028          * src/Mutils.h: Moved list of symbols to an include file          * src/Mutils.h: Moved list of symbols to an include file
1029    
1030  2004-11-11  Douglas Bates  <bates@bates1-home>  2004-11-11  Douglas Bates  <bates@wisc.edu>
1031    
1032          * src/geMutils.c (Matrix_init): remove unused function          * src/geMutils.c (Matrix_init): remove unused function
1033    
1034  2004-11-10  Douglas Bates  <bates@bates1-home>  2004-11-10  Douglas Bates  <bates@wisc.edu>
1035    
1036          * src/cscMatrix.c (csc_to_imagemat): removed unused function          * src/cscMatrix.c (csc_to_imagemat): removed unused function
1037    
1038  2004-11-05  Douglas Bates  <bates@bates1-home>  2004-11-05  Douglas Bates  <bates@wisc.edu>
1039    
1040          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile          * src/Makefile.win (SOURCES_C): Keep consistent with Makefile
1041    
1042  2004-10-27  Douglas Bates  <bates@bates1-home>  2004-10-27  Douglas Bates  <bates@wisc.edu>
1043    
1044          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls          * R/pdmatrix.R: remove PACKAGE="Matrix" in .Call calls
1045    
1046  2004-10-04  Douglas Bates  <bates@bates1-home>  2004-10-04  Douglas Bates  <bates@wisc.edu>
1047    
1048          * src/init.c: Created R_init_Matrix and added registration of C          * src/init.c: Created R_init_Matrix and added registration of C
1049          routines.          routines.
1050    
1051  2004-10-02  Douglas Bates  <bates@bates1-home>  2004-10-02  Douglas Bates  <bates@wisc.edu>
1052    
1053          * R/tripletMatrix.R: Force a require(lattice) for the image methods.          * R/tripletMatrix.R: Force a require(lattice) for the image methods.
1054    
1055  2004-06-15  Douglas Bates  <bates@bates7>  2004-06-15  Douglas Bates  <bates@wisc.edu>
1056    
1057          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.          * man/trMatrix-class.Rd: Escape the % chars in .Rd files.
1058    

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