R devel - Jan 2018 - resolving a names conflict

The survival package uses a generalized cholesky decompostition throughout.? If
A is a
symmetric matrix A= LDL' where L is lower triangular with 1s on the
diagonal, D is
diagonal, and D[i,i] =0 if column i of A is redundant.? Being able to read the
rank and
dependencies directly off of D is very handy.

The bdsmatrix package uses the same, but exposes it to the user as gchol and
solve methods
in the NAMESPACE file.

I'd like to expose it in survival as it would make some current development
easier.

How do I do this without causing warning messages for anyone who loads both,
e.g., anyone
using the coxme package?? The S4 structures are identical, but bdsmatrix has a
superset of
methods.?? Adding importFrom(bdsmatrix, gchol) is one solution, of course, but
it runs
afoul of the current requirement that recommended packages import only from the
core set.

Terry T.

Dear Terry,

Why not have the required code in survival and use
importFrom(survival, gchol) in bdsmatrix? Since you maintain both,
that shouldn't be too complicated.

Best regards,

ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx at inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///////////////////////////////////////////////////////////////////////////////////////////
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more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given body
of data. ~ John Tukey
///////////////////////////////////////////////////////////////////////////////////////////




2018-01-09 16:37 GMT+01:00 Therneau, Terry M., Ph.D. <therneau at
mayo.edu>:
> The survival package uses a generalized cholesky decompostition throughout.
> If A is a symmetric matrix A= LDL' where L is lower triangular with 1s
on
> the diagonal, D is diagonal, and D[i,i] =0 if column i of A is redundant.
> Being able to read the rank and dependencies directly off of D is very
> handy.
>
> The bdsmatrix package uses the same, but exposes it to the user as gchol
and
> solve methods in the NAMESPACE file.
>
> I'd like to expose it in survival as it would make some current
development
> easier.
>
> How do I do this without causing warning messages for anyone who loads
both,
> e.g., anyone using the coxme package?  The S4 structures are identical, but
> bdsmatrix has a superset of methods.   Adding importFrom(bdsmatrix, gchol)
> is one solution, of course, but it runs afoul of the current requirement
> that recommended packages import only from the core set.
>
> Terry T.
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel