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[matrix] Annotation of /pkg/Done
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Annotation of /pkg/Done

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Revision 1228 - (view) (download)

1 : maechler 511 - check to see if the .onLoad function to require the methods package
2 :     (in the AllClass.R file) is needed
3 :     -- no, it is not: "Depends: " in DESCRIPTION suffices.
4 : bates 529
5 :     - Should the uplo and diag slots continue to be stored as character?
6 :     An alternative is to use a factor as in the enum values for the
7 :     cblas.
8 :     -- Leave as character but use care in determining the default cases
9 :     -- E.g. Checks for diag slot should check for 'U' or 'u' vs. anything else
10 :    
11 :     - Organization of the source code files - right now they are organized
12 :     according to class (e.g. dgeMatrix.R, dgeMatrix.h, dgeMatrix.c). Is
13 :     there a better way?
14 :     -- This seems ok.
15 :    
16 :     - Fix the calculation of the Dim slot for the crossprod method for
17 :     dgCMatrix objects (too tired to do that now).
18 :     -- Done
19 : bates 530
20 :     - spelling style: Should "coersion" be "coercion" ?
21 :     -- Yes. Watch for this.
22 :    
23 : bates 536 - src/Metis/ : one of the two Makefiles needs fixing, as changing
24 :     src/Metis/*.c does not lead to recompilation.
25 :     --DB - it seems both Makefiles need fixing. I think I have the
26 :     src/Metis/Makefile fixed but not src/Makefile
27 :     --DB - now have both working, I believe.
28 : bates 530
29 : maechler 538 - man/Matrix.Rd : has example with dimnames, but we just drop them!
30 :     MM thinks dimnames should be supported (but then ...)
31 :     -- added 'Dimnames' slot (2005-02-10)
32 : maechler 540
33 :     - bCrosstab(): yes, we really do want the diagonal "V:V" crosstabs.
34 :     -- explained a bit more in man/bCrosstab.Rd
35 :    
36 : bates 561 - Clean up vestigial functions (pdFactor, pdMatrix, matrix<-) from the
37 :     nlme package.
38 : maechler 675
39 :     - create a class of permutation matrices for use in expand. The
40 :     current expand method for the LU factorization is not complete
41 :     because it does not provide the permutation.
42 :    
43 :     - tcrossprod() now works: C code now "exported" via init.c
44 : maechler 869
45 : maechler 946 - Fixed: dtpMatrix(... diag = "U") (i.e., unit-diagonal packed triangular)
46 :     *does* need 'x' entries for the diagonal but these are never looked at.
47 : maechler 869 -> changed doc -- Lapack also says they are not referenced but assumed 1.
48 : bates 881
49 :    
50 :     - in lmer.c check all instances of the use of ZtX and XtX and change
51 :     them so that having a negative last element of nc means use the
52 :     response only (but look for it in the right place).
53 : maechler 935
54 :     - Solved:
55 :    
56 :     Currently the show() method fail sometime after coercion:
57 :     e.g. 'sy' show()s wrongly, even though it "str()" fine :
58 :    
59 :     (po <- crossprod(Matrix(0:3, 2))) # ok
60 :     (ge <- as(po, "dgeMatrix")) # ok
61 :     (sy <- as(po, "dsyMatrix")) # BAD
62 :     str(sy) # looks fine
63 :    
64 :     or
65 :     example(expand) # -> ex$L and ex$U look bad, however
66 :     as(ex$L, "dgeMatrix") # `works'
67 :    
68 :     {Of course, we don't need a workaround but must understand
69 :     and solve the problem}
70 :    
71 : maechler 976 - slot "factors" maybe should move up to "Matrix" -- done, 2005-09-28
72 : maechler 935
73 : maechler 976 - group generics: "Arith", also "Compare", "Math" etc;
74 :     see ?Math and the examples in ?SetGeneric
75 :    
76 :     - methods for rbind and cbind where they make sense:
77 :     R 2.2.0 (and newer) provide cbind2() and rbind2() generics and default
78 :     methods [following John Chambers's proposition], and we have implemented
79 :     methods for them.
80 :    
81 : maechler 935 - arithmetic for sparse matrices:
82 :     done for <sparseMatrix> o <scalar>
83 :     {more needed: see TODO}
84 :    
85 : maechler 1109 - rcond() of a singular dpoMatrix gives a LaPack error instead of just 0:
86 :     MM <- crossprod(M <- Matrix(c(1:4,9:6), 2,4)) ; rcond(MM)
87 :     Done(2005-10-03): The error message is more helpful now.
88 : maechler 976
89 : maechler 1109 - implement diagonal Matrix class "ddiMatrix" etc
90 :     using constructor function Diagonal() {and extractor diag()}.
91 :     Done(2006-01-03)
92 :    
93 :     - new("ltTMatrix") now at least prints
94 : bates 1224
95 :     -- Done by version 0.995-1 ---
96 :    
97 :    
98 :     - Migration of lmer from the mer representation to the mer2
99 :     representation and the use of the CHOLMOD code for the sparse
100 :     matrix decomposition. Some of the things that need to be done.
101 :    
102 :     - Matrices in the mer2 representation are classed matrices, in the
103 :     mer representation they were unclassed. Any parts inside the C
104 :     code that would access, for example,
105 :     REAL(GET_SLOT(x, Matrix_RXXSym))
106 :     need to be modified to access
107 :     REAL(GET_SLOT(GET_SLOT(x, Matrix_RXXSym), Matrix_xSym))
108 :     This is especially important for Omega but I think I have done
109 :     those changes already.
110 :    
111 :     - The components named *X* in an mer object refers to an augmented
112 :     design matrix of p+1 columns. In the mer2 object there are
113 :     separate slots for rZy and rXy. The scalar y'y is the first
114 :     element of devComp.
115 :    
116 :     - Presently nc is of length nf+1 and the last element is n, the
117 :     number of observations. This value should be moved to devComp and
118 :     nc made of length nf.
119 :    
120 :     - The slot L is a list of length 1 that contains an ExternalPointer
121 :     to a cholmod_factor object. This contains a permutation which is
122 :     most easily accessible through cholmod_solve(CHOLMOD_P,...) or
123 :     cholmod_solve(CHOLMOD_Pt,...). The ZtX, Zty, RZX and rZy slots actually
124 :     contain P%*%RZX and P%*%rZy
125 :    
126 : maechler 1226 - "[<-" Methods for dgC* and dgT* the former building on the latter
127 :     using j = .Call("Matrix_expand_pointers", x@p, PACKAGE = "Matrix")
128 :     where needed
129 : bates 1224
130 : maechler 1228 - Put the matrix 'mm' and the response vector 'y' into 'KNex', a list.
131 :     Modified all examples and tests that used them and the Comparisons vignette.

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