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revision 1298, Sat Jun 10 19:56:18 2006 UTC revision 1365, Thu Aug 10 18:52:55 2006 UTC
# Line 1  Line 1 
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>  2006-06-10  Douglas Bates  <bates@R-project.org>
206    
207          * R/lmer.R (simulestimate): added          * 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>  2006-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix          * R/diagMatrix.R (setAs): define coercion methods to sparse matrix
213          classes.          classes.
214            * R/sparseMatrix.R etc: multiplication of diagonal and sparse
215    
216  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-06-08  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
# Line 43  Line 249 
249    
250          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use          * R/sparseMatrix.R: Matrix <-> graph methods: can no longer use
251          the C code depending on a slot structure that's no longer valid.          the C code depending on a slot structure that's no longer valid.
252          * src/dgTMatrix.c: dito (also: src/init.c src/dgTMatrix.h)          * src/dgTMatrix.c: ditto (also: src/init.c src/dgTMatrix.h)
253    
254    
255  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>  2006-05-17  Douglas Bates  <bates@stat.wisc.edu>
# Line 166  Line 372 
372          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)          * data/KNex.rda: replacing 'mm' and 'y' by KNex <- list(mm=mm, y=y)
373          * man/KNex.Rd: and other help files          * man/KNex.Rd: and other help files
374          * tests/*.R: several ones needed adaption          * tests/*.R: several ones needed adaption
375          * inst/doc/Comparisons.Rnw: dito          * inst/doc/Comparisons.Rnw: ditto
376    
377  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-03-11  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
# Line 370  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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