From thierry.onkelinx at inbo.be  Tue Jan  9 16:45:00 2018
From: thierry.onkelinx at inbo.be (Thierry Onkelinx)
Date: Tue, 9 Jan 2018 16:45:00 +0100
Subject: [Rd] resolving a names conflict
In-Reply-To: <375144$8krhb9@ironport10.mayo.edu>
References: <375144$8krhb9@ironport10.mayo.edu>
Message-ID: <CAJuCY5xjqPSGQ1vOF6DTTQSkd5Nunj+qojMxzBgACo6oj_H6EA@mail.gmail.com>

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

///////////////////////////////////////////////////////////////////////////////////////////
To call in the statistician after the experiment is done may be no
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



[Rd] resolving a names conflict
Thierry Onkelinx