Annotation of /pkg/Done

Parent Directory | Revision Log

---

Revision 1226 - (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

---

root@r-forge.r-project.org	ViewVC Help
Powered by ViewVC 1.0.0