[Phylobase-commits] r584 - pkg/R

[Peter D. Cowan]

Well this is really a one line change for APE, perhaps after we've actually got a package on CRAN we can convince Emmanuel to change it.

Peter

On Mon, Aug 24, 2009 at 11:03:21PM -0400, Ben Bolker wrote:
> 
>   at present we're only warning on export (phylo4 -> phylo), not
> vice versa.
> 
>   at present i'm pretty certain that trying to plot a badly ordered
> tree in ape can crash R.
> 
>   Ben
> 
> Steve Kembel wrote:
> > I'm also in favour of not automatically reordering trees on phylo <>
> > phylo4 conversion. There are cases where I would really like to
> > maintain tree order (because I have some information about nodes that
> > is in Newick string order).
> > 
> > I am not sure of a better solution. Am I correct that unknown ordering
> > is only really a potential problem on export *to* ape where it could
> > break some functions (i.e. plotting)? Could we warn in this case but
> > not on phylo -> phylo4 conversion?
> > 
> > -Steve
> > On Mon, Aug 24, 2009 at 7:23 PM, Ben Bolker<bolker at ufl.edu> wrote:
> >>  hmmm.
> >>  you may be right, but this will presumably break round-trip capability
> >> -- i.e. if we import a tree with unknown ordering and automatically
> >> re-order it when we export, the round trip will have changed it.
> >> Am I being too obsessive about this?  Is there a better solution?
> >>
> >>  Ben
> >>
> >> Peter D. Cowan wrote:
> >>> On Tue, Aug 25, 2009 at 02:58:59AM +0200, noreply at r-forge.r-project.org wrote:
> >>>> Author: bbolker
> >>>> Date: 2009-08-25 02:58:59 +0200 (Tue, 25 Aug 2009)
> >>>> New Revision: 584
> >>>>
> >>>> Modified:
> >>>>    pkg/R/setAs-Methods.R
> >>>> Log:
> >>>>   added error if unknown ordering imported from ape
> >>>>   added warning if unknown ordering exported to ape
> >>>>
> >>> How about reordering unknown trees before exporting them?  This seems likely to flood users with warnings.
> >>>
> >>> peter
> >>>
> >>>> Modified: pkg/R/setAs-Methods.R
> >>>> ===================================================================
> >>>> --- pkg/R/setAs-Methods.R    2009-08-25 00:51:06 UTC (rev 583)
> >>>> +++ pkg/R/setAs-Methods.R    2009-08-25 00:58:59 UTC (rev 584)
> >>>> @@ -26,11 +26,11 @@
> >>>>          }
> >>>>      }
> >>>>      oldorder <- attr(from,"order")
> >>>> -    neworder <- if (is.null(oldorder)) { "unknown" } else {
> >>>> -      switch(oldorder,
> >>>> -             pruningwise="pruningwise",
> >>>> -             cladewise="preorder")
> >>>> -    }
> >>>> +    neworder <- if (is.null(oldorder)) { "unknown" } else
> >>>> +    if (!oldorder %in% phylo4_orderings) {
> >>>> +      stop("unknown ordering '",oldorder,"' in ape object")
> >>>> +    } else if (oldorder=="cladewise") "preorder"
> >>>> +    else oldorder
> >>>>      attr(from,"order") <- NULL
> >>>>      newobj <- phylo4(from$edge, from$edge.length, from$tip.label,
> >>>>                       node.label = from$node.label,
> >>>> @@ -113,9 +113,10 @@
> >>>>                                     preorder  = 'cladewise',
> >>>>                                     unknown = 'unknown',
> >>>>                                     pruningwise = 'pruningwise')
> >>>> -    } else {
> >>>> -      ## warning ??
> >>>> -    }
> >>>> +      } else {
> >>>> +        ## warning ??
> >>>> +        warning("trees with unknown order may be unsafe in ape")
> >>>> +      }
> >>>>      if (length(y$edge.length) == 0)
> >>>>          y$edge.length <- NULL
> >>>>      if (length(y$node.label) == 0)
> >>>>
> >>>> _______________________________________________
> >>>> Phylobase-commits mailing list
> >>>> Phylobase-commits at lists.r-forge.r-project.org
> >>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-commits
> >>
> >> --
> >> Ben Bolker
> >> Associate professor, Biology Dep't, Univ. of Florida
> >> bolker at ufl.edu / www.zoology.ufl.edu/bolker
> >> GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
> >>
> >>
> >> _______________________________________________
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> >> Phylobase-commits at lists.r-forge.r-project.org
> >> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/phylobase-commits
> >>
> >>
> > 
> > 
> > 
> 
> 
> -- 
> Ben Bolker
> Associate professor, Biology Dep't, Univ. of Florida
> bolker at ufl.edu / www.zoology.ufl.edu/bolker
> GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc
>