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revision 1213, Tue Feb 7 23:44:07 2006 UTC revision 1365, Thu Aug 10 18:52:55 2006 UTC
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1    2006-08-10  Douglas Bates  <bates@R-project.org>
2    
3            * src/lmer.c: adjust checks in glmer_init for S4SXP
4            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
5            before S4SXP but for the wrong reasons.
6    
7    2006-08-08  Douglas Bates  <bates@R-project.org>
8    
9            * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.
10            Later modified to return the upper triangle only.
11            * R/dgTMatrix.R: Remove vestigial crossprod and tcrossprod methods.
12    
13    2006-08-07  Douglas Bates  <bates@R-project.org>
14    
15            * src/Csparse.c (Csparse_crossprod): Set stype on result to avoid
16            R-level conversion to a sparse symmetric class.
17            * R/Tsparse.R,R/Csparse.R (crossprod and tcrossprod methods):
18            Remove conversion to sparse symmetric classes (now done in C code).
19    
20    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dgCMatrix.R: disable old crossprod and tcrossprod methods
23            * man/band.Rd:  adapt the \dontshow{} unit test.
24    
25    2006-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * DESCRIPTION (Version): 0.995-14  for CRAN
28    
29            * tests/other-pkgs.R: oops: library(Matrix) outside *if* !
30    
31            * R/sparseMatrix.R (Tsp2grNEL): fixed Tsparse -> graph coercion
32            * tests/other-pkgs.R:  more checks, sparseMatrix -> graph
33    
34            * R/Auxiliaries.R (as_Tsparse, as_Rsparse): new
35            * R/Tsparse.R (tril, triu, band): methods
36            * R/dgRMatrix.R (tril, ...):    ditto
37            * man/band.Rd:                  ditto
38    
39    2006-08-04  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Matrix.R (head, tail): directly use utils:::head.matrix
42                    to be up-to-date automatically.
43    
44    2006-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * DESCRIPTION (Version): 0.995-13 to be released to CRAN
47    
48            * DESCRIPTION (Lazydata): no, instead of 'yes' because it fails for:
49            * data/CAex.R, inst/external/CAex_slots.rda: replacing data/CAex.rda
50            * data/KNex.R, inst/external/KNex_slots.rda: replacing data/KNex.rda
51            such that the S4 objects are always created by the current version
52            of R and 'Matrix' class definitions.
53    
54    2006-08-01  Douglas Bates  <bates@R-project.org>
55    
56            * R/lmer.R (LMEoptimize method), tests/lmer.R,
57            inst/external/test3comp.rda: Added warnings for convergence on
58            boundary and test cases.
59    
60            * src/lmer.c (mer_postVar): Modified to return the variances that
61            are marginal to the fixed effects, not conditional on them (which
62            is what the bVar slot contents represent).
63    
64    2006-07-31  Douglas Bates  <bates@R-project.org>
65    
66            * NAMESPACE, src/lmer.c, R/lmer.R (hatTrace):  Add the hatTrace
67            function which calls the C function mer_hat_trace2.
68    
69            * man/ranef.Rd: Include description of "postVar" argument and
70            producing a caterpillar plot.
71    
72    2006-07-31  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * NAMESPACE:    change  "correlation" to "corMatrix"
75            * R/AllClass.R: to avoid clash with S3 class in 'nlme'.
76            * R/dpoMatrix.R: ditto
77            * R/lmer.R:      ditto
78    
79    2006-07-28  Douglas Bates  <bates@R-project.org>
80    
81            * src/lmer.c (internal_mer_RZXinv): Split the calculation of the
82            RZXinv slot's contents into a separate internal function that can
83            be used in mer_hat_trace.
84    
85    2006-07-22  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Matrix.R: Coercions "Matrix" -> (sparse|dense)Matrix
88            via new smart
89            * R/Auxiliaries.R (as_Csparse, as_dense, .M.shapse): new
90            utility functions.
91    
92    
93    2006-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/Csparse.R (tril, triu, band): do return *triangular* classed
96            matrices when appropriate; band() even symmetric ones.
97            (replCmat): extend to potentially all "CsparseMatrix"
98            * R/Tsparse.R (replTmat): extend to all "TsparseMatrix"; hence
99            allow subassignment for special sparse matrices.
100    
101            * R/Auxiliaries.R (as_geClass): factor out the  .M.kind() functionality
102    
103            * src/lmer.c (mer_MCMCsamp, glmer_MCMCsamp): new 'verbose'
104            argument; in glmer_*(): print only if(verbose).
105    
106            speed-optimize a few places by moving REAL(.) out of loops.
107    
108            * src/lmer.h, src/init.h, R/lmer.R:  related to above.
109    
110    2006-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Matrix.R("["): disable ("Matrix", i = "logical", j = "missing"),
113                    since that wrongly triggers also for M[ logi , ]
114    
115            * R/denseMatrix.R: "[" methods now also work e.g. when indexing
116            a symmetric matrix that results in a non-symmetric one.
117            * R/Auxiliaries.R (as_geClass): new function used in "[" above.
118    
119            * R/dMatrix.R: make round(M) work as round(M, 0)
120    
121            * R/dgTMatrix.R (image): coordinate system and axis now use
122            1-based indices, not 0-based ones.
123    
124            * R/Tsparse.R (.ind.prep for "["): get rid of max(<empty>) warning.
125            * tests/indexing.R: test it.
126    
127            * NAMESPACE: export isSymmetric(); has been a generic in "base" for a while;
128            * man/isSymmetric-methods.Rd: and document it.
129    
130            * R/SparseM-conv.R: added coercion methods for some 'SparseM' matrices.
131            * man/SparseM-conv.Rd: docu them
132    
133            * tests/other-pkgs.R: renamed from tests/graph.R and add example
134                    for 'SparseM' conversions
135    
136    2006-07-17  Douglas Bates  <Douglas.Bates@R-project.org>
137    
138            * R/Matrix.R (head): added head() and tail() methods.
139    
140    2006-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * DESCRIPTION (Version): 0.995-12 released to CRAN
143    
144    2006-07-15  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * tests/simple.R: add check for correct dsT -> dgT coercion;
147                    add check for correct printing of symmetric sparse matrices.
148    
149            * R/Auxiliaries.R (non0ind): return *all* non-0 entry indices also
150            for sparse symmetric matrices.
151    
152            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): do not copy the
153            diagonal twice.
154    
155    2006-07-11  Douglas Bates  <Douglas.Bates@R-project.org>
156    
157            * src/dsTMatrix.c (dsTMatrix_as_dgTMatrix): Fix a case of INTEGER
158            being applied to the x slot (detected by Brian Ripley).
159    
160    2006-07-10  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * src/dgCMatrix.c (dgCMatrix_validate): 'p' slot must have correct length.
163    
164            * R/Auxiliaries.R (isTriC): fix buglet (we were 1-based!)
165    
166    2006-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/lgCMatrix.c (lgCMatrix_diag): new function
169            * R/lgCMatrix.R (diag): for new method
170    
171            * R/AllClass.R (TsparseMatrix): do use Tsparse_validate
172                 ==> construction of illegal "*gTMatrix" via new() should
173                 now be much less easy:
174            * tests/Class+Meth.R: assertError() for some illegal "dgT*"
175    
176            * R/Matrix.R (Matrix): Matrix(0, nrow,ncol) now "goes sparse"
177                    directly.
178            * man/Matrix.Rd: documents it.
179    
180    2006-07-06  Douglas Bates  <bates@R-project.org>
181    
182            * src/pedigree.c (pedigree_inbreeding): Correction in
183            initialization.  This function is not currently being used and is
184            not fully tested.
185    
186            * NAMESPACE, R/{AllClass.R,lmer.R}, src/{init.c,lmer.c}:
187            Introduced the glmer class.  Added code for mcmcmsamp on glmer
188            objects.  Modified validity check on pedigree objects to account
189            for nonparallel patterns of missingness of parents.
190    
191            * man/{lmer-class.Rd,mcmcsamp.Rd}: Update documentation for glmer
192            class.
193    
194    2006-07-01  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/pMatrix.R: coercion pMatrix -> Tsparse
197    
198    2006-06-12  Douglas Bates  <bates@R-project.org>
199    
200            * DESCRIPTION (Version): 0.995-11 released to CRAN
201    
202            * R/lmer.R (mcmcsamp method): Corrected arrangments of names on
203            the output from mcmcsamp.
204    
205    2006-06-10  Douglas Bates  <bates@R-project.org>
206    
207            * R/lmer.R (simulestimate): added C code for calculating the trace
208            of the hat matrix.
209    
210    2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
213            classes.
214            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
215    
216    2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/dgTMatrix.R (colSums): etc. All four of
219            colSums(), rowSums(), colMeans(), rowMeans() now should work for
220            all "Matrices".
221    
222    2006-06-01  Douglas Bates  <bates@stat.wisc.edu>
223    
224            * R/lmer.R (panel.ci): Add a reference line at zero and a
225            background grid to the qqmath plot of ranef.lmer.
226    
227    2006-05-30  Douglas Bates  <bates@stat.wisc.edu>
228    
229            * R/lmer.R (expandSlash): Functions (non-exported) to allow nested
230            grouping factors to be specified in the formula as (1|foo/bar).
231    
232    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
233    
234            * R/lmer.R (findbars and others): Change check of is.numeric to
235            !is.language to resolve the bug reported by Jacob Wegelin.
236    
237            * src/pedigree.c (pedigree_inbreeding): Initial implementation of
238            code to evaluate inbreeding coefficients without calculating T,
239            based on code in Sargolzaei and Iwaisaki's paper.
240    
241    2006-05-27  Douglas Bates  <bates@stat.wisc.edu>
242    
243            * R/{lmer.R,AllGeneric.R}, src/{init.c,lmer.[ch]}: Added local
244            generic and mer methods for isNested and denomDF. This denomDF was
245            an attempt to emulate that in lme but I don't think that makes
246            sense.  Use the trace of the hat matrix instead.
247    
248    2006-05-17  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
251            the C code depending on a slot structure that's no longer valid.
252            * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
253    
254    
255    2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
256    
257            *  R/{AllGeneric.R,Csparse.R},man/band.Rd,NAMESPACE: changed name
258            of lowerTriMatrix generic and methods to tril (also upper to triu)
259            and added a general band extractor.
260    
261    2006-05-16  Douglas Bates  <bates@stat.wisc.edu>
262    
263            * R/pedigree.R (pedigree): Replace sire and dam values outside the
264            allowable range with NAs. Added a corresponding check in the
265            validity check for the pedigree class.
266    
267            * R/[CT]sparse.R ([t]crossprod): The result of single-argument
268            crossprod methods now inherits from symmetricMatrix.
269    
270    2006-05-15  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * R/AllGeneric.R (lowerTriMatrix): Added (but did not export)
273            generics lowerTriMatrix and upperTriMatrix along with methods for
274            the Csparse virtual class.  Also added a C function Csparse_band
275            that implements these methods by calling cholmod_band.
276    
277    2006-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Tsparse.R ("["): column or row subsetting; @Dimnames[k] got
280            erased when it was NULL.  This led to invalid subselections!
281    
282    2006-04-25  Douglas Bates  <bates@stat.wisc.edu>
283    
284            * R/dtCMatrix.R: avoid coercion of dtCMatrix object to dgCMatrix
285            in method for "t" so as not to lose the unit diagonal property.
286    
287    2006-04-19  Douglas Bates  <bates@stat.wisc.edu>
288    
289            * R/lmer.R, R/AllGeneric.R, NAMESPACE: Remove the postVar generic
290            and methods.  This is now an option to the ranef method for the
291            mer class.
292    
293            * src/cs_utils.c: Ensure that the nz component is -1 for a
294            compressed column-oriented matrix.  Minor formatting cleanup.
295    
296            * man/lmer-class.Rd: Document the qqmath method for ranef.lmer
297            objects.
298    
299    2006-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/Auxiliaries.R (diagU2N): new for the solve() methods in
302            * R/dtCMatrix.R: where dgC -> dgT coercion now preserves diag = "U".
303    
304    2006-04-15  Douglas Bates  <bates@stat.wisc.edu>
305    
306            * src/cs.[ch],src/cs_utils.[ch] : Added Tim Davis' CSparse library
307            in cs.[ch] and utilities to interface to that code in cs_utils.[ch].
308    
309            * R/dtCMatrix.R, src/dtCMatrix.[ch] : CSparse-based solve methods
310            for the dtCMatrix class.
311    
312    2006-04-12  Douglas Bates  <bates@stat.wisc.edu>
313    
314            * R/pedigree.R, R/AllClass.R, NAMESPACE: added a pedigree class
315            and methods for it.
316    
317    2006-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/dgCMatrix.R: add  storage.mode(.) <- "double" for "matrix"
320            arguments, such that M %*% 1:6 now works
321            * Tests/matprod.R: test the above
322    
323    2006-04-03  Douglas Bates  <bates@stat.wisc.edu>
324    
325            * R/lmer.R (qqmath,ranef.lmer-method): added a qqmath method for
326            the ranef.lmer class.
327    
328            * R/AllClass.R, NAMESPACE, R/lmer.R: Added a postVar generic and
329            methods to extract the posterior variances from the bVar slot.
330    
331    2006-03-30  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/dtCMatrix.R: allow coercion from  dgC* to triangular (dtC*)
334            * R/dsCMatrix.R: and symmetric (dsC*) 'Csparse' matrices.
335    
336            * R/Tsparse.R: Tsparse* -> Csparse* coercion now works and is tested in
337            * tests/simple: (extended)
338    
339            * R/sparseMatrix.R (isTriangular): now using much improved
340            * R/Auxiliaries.R (isTriC): new triangularity check for *CMatrix
341    
342    2006-03-23  Douglas Bates  <bates@stat.wisc.edu>
343    
344            * src/dsyMatrix.c (dsyMatrix_as_dspMatrix): Propagate DimNames
345            (problem report from Franklin Parlamis).  This should be done
346            generally.
347    
348    2006-03-21  Douglas Bates  <bates@stat.wisc.edu>
349    
350            * R/AllClass.R,lmer.R: Change the name of the lmer.ranef class to
351            ranef.lmer (like summary.lmer).  Add the coef.lmer class and
352            update the plot methods.
353    
354    2006-03-20  Douglas Bates  <bates@stat.wisc.edu>
355    
356            * R/lmer.R (resid and ranef methods):  Added methods for the
357            "residuals" and "resid" generic but only for linear mixed model
358            fits.  Changed the ranef method to return a list of data frames so
359            that the plot methods now work.
360    
361    2006-03-16  Douglas Bates  <bates@bates2>
362    
363            * src/dpoMatrix.c (dpoMatrix_chol): Require n > 0 in call to
364            dpotrf - otherwise the BLAS on Mac OS X complains and quits.
365    
366            * DESCRIPTION (Date): New release
367    
368    2006-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * DESCRIPTION (Version): 0.995-6  -- to be released to CRAN
371    
372            * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
373            * man/KNex.Rd: and other help files
374            * tests/*.R: several ones needed adaption
375            * inst/doc/Comparisons.Rnw: ditto
376    
377    2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/dgCMatrix.R (replCmat): "[<-" methods for dgCMatrix
380    
381            * tests/indexing.R: tests for new [<- methods for sparse matrices.
382    
383    2006-03-10  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/dgTMatrix.R (replTmat): "[<-" methods for dgTMatrix
386    
387            * R/Tsparse.R (.ind.prep): fix out-of-range indexing
388    
389    2006-03-08  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/dMatrix.R: enable things like  M [ M < 10 ]
392            * R/dgeMatrix.R: implement it
393    
394    2006-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/AllClass.R: define "summary.mer" and "*.lmer"
397            * R/lmer.R (summary): summary(<mer>) computes & returns the above;
398            * R/lmer.R (show): now works with summary()
399    
400    2006-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/dgCMatrix.R: finally direct "Arith"  dgC o dgC
403            * R/Auxiliaries.R (WhichintersectInd): and other utilities to
404                    support the above
405    
406  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>  2006-02-07  Douglas Bates  <bates@stat.wisc.edu>
407    
408          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.          * R/lmer.R (lmer): fix initial values of offset and weights for glm.fit.
# Line 171  Line 576 
576  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578          * R/Matrix.R:  added first "[<-" methods; not yet functional          * R/Matrix.R:  added first "[<-" methods; not yet functional
579          * R/denseMatrix.R: dito          * R/denseMatrix.R: ditto
580          * man/Subassign-methods.Rd: new help file for these          * man/Subassign-methods.Rd: new help file for these
581    
582  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>  2005-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>

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