[Phylobase-devl] Nexus class library v2.1 finally has some documentation about what has changed since v2.0

Fri Apr 2 01:09:30 CEST 2010

Hello all,

  I think we are ready for a new CRAN release of phylobase. Since 0.5
(and 79 commits later), the main changes are:
- update to the newest NCL and new approach in the way we build NCL
- readNexus works well and has a few new functionalities
- labels don't have to be unique
- there are global options that can be accessed and modified with
phylobase.options()
- number-like labels are now imported as numeric if
check.node.labels="asdata"
- there is a new nData method that indicates how many data sets are
associated with the tree
- checkTree builds and returns messages consistently

  What do you think? Are there any bugs/functionalities that should be
addressed before a new CRAN release?

  Cheers,
  -- François 

On Mon, 2010-03-29 at 09:36 -0500, Mark Holder wrote:
> Note, that too use some of the newest features mentioned in the docs,
> someone with phylobase write access will have to sync the version of
> the NCL code in phylobase with what is now in NCL's repo.
> 
> 
> 
> 
> all the best,
> 
> 
> Mark
> 
> 
> 
> 
> 
> On Mar 29, 2010, at 9:34 AM, Brian O'Meara wrote:
> 
> > Mark Holder has updated the documentation for NCL, which should make
> > using it in phylobase easier. Thanks, Mark!
> > 
> > 
> > Brian
> > 
> > Begin forwarded message:
> > 
> > > From: Mark Holder <mtholder at ku.edu>
> > > Date: March 27, 2010 3:17:38 PM EDT
> > > To: Brandon Chisham <bchisham at cs.nmsu.edu>, "Brian O'Meara"
> > > <bcomeara at nescent.org>, Dave Swofford <david.swofford at duke.edu>,
> > > Paul Lewis <paul.lewis at uconn.edu>, dz <zwickl at ku.edu>, Jeet
> > > Sukumaran <jeet at ku.edu>, Paul van der Mark <paulvdm at scs.fsu.edu>,
> > > Peter Cowan <pdc at berkeley.edu>, Michael Sanderson
> > > <sanderm at email.arizona.edu>, Arlin Stoltzfus
> > > <arlin.stoltzfus at nist.gov>, William Piel <william.piel at yale.edu>,
> > > Rutger Vos <rutgeraldo at gmail.com>, David Maddison
> > > <beetle at ag.arizona.edu>, Wayne Maddison
> > > <wmaddisn at interchange.ubc.ca>, Hilmar Lapp <hlapp at duke.edu>,
> > > Fredrik Ronquist <ronquist at csit.fsu.edu>, John Huelsenbeck
> > > <johnh at berkeley.edu>
> > > Subject: Nexus class library v2.1 finally has some documentation
> > > about what has changed since v2.0
> > > 
> > > 
> > > Hi NCL users (and other folks who may be interested in NEXUS
> > > parsing),
> > > 
> > > Short message:
> > > - I have finally forced myself to update the NCL documentation to
> > > reflect the changes to the API that accompanied the v2.1 branch.
> > > 
> > > - Check out the high level overview at:
> > > http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/index.html
> > > 
> > > - Checkout the example code at:
> > > http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/simpleNCLClient/simpleNCLClient.cpp
> > >  and its Makefile:
> > > http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/simpleNCLClient/Makefile
> > > 
> > > - Please let me know if you find errors/typos in the docs
> > > ( mtholder at gmail.com ).  I'm sure there are plenty of typos.
> > > 
> > > - I pushed a new release to sourceforge (v2.1.11). Some of the
> > > docs refer to convenience functions that I just added to the
> > > library, so you'll need that version of the library.
> > > 
> > > 
> > > 
> > > 
> > > 
> > > Longer message:
> > > 
> > > As you probably know the currently-developed branches of NCL
> > > (https://ncl.svn.sourceforge.net/svnroot/ncl/branches/v2.1
> > > and https://ncl.svn.sourceforge.net/svnroot/ncl/branches/v2.2)
> > > have changed considerably since version 2.0 of the library.
> > > 
> > > Paul Lewis is the author of NCL, and for a few years now I've been
> > > helping expand and maintain the library. Unfortunately, while Paul
> > > is very disciplined about documenting his code, I'm not a very
> > > good commenter/documenter.  So the documentation has become much
> > > less useful of late because of my additions to the library.
> > > 
> > > We have really tried to make the new API backward compatible, so
> > > Paul's docs are still useful.
> > > 
> > > However:
> > > - The newer API can be considerably easier to use and more robust
> > > for complex NEXUS files (those which contain multiple instances of
> > > the same block).
> > > 
> > > - There are some substantial performance improvements in the newer
> > > version.  Admittedly most of our software is not limited by
> > > parsing time, but if you are writing an application that needs to
> > > crunch a lot of files or big files (or both) you should be using
> > > NCL v2.1.
> > > 
> > > - v2.1 and later supports quite a few more commands and options
> > > (including Mesquite's LINK/TITLE syntax for dealing with multiple
> > > blocks, Mesquite's extension to the CHARSET commands, and MrBayes'
> > > extensions to NEXUS such as datatype=mixed and dataype=restriction
> > > in the FORMAT command).
> > > 
> > > - v2.2 is now generated from v2.1 using a simple script.  v2.2
> > > provides support for SWIG bindings to NCL.  Currently only python
> > > bindings have been tested, but other languages should be usable
> > > without too much tweaking.
> > > 
> > > So, I think that the jump from 2.0 to 2.1 is worth making.
> > > 
> > > 
> > > I've just made a push on documenting the newer API at a high
> > > level.  It is still a work in progress, but if you've been
> > > frustrated by my poor documentation of NCL, you should check out:
> > > http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/index.html
> > > 
> > > The logic of the newer API and new features are described much
> > > better than they have been before now.
> > > 
> > > You may also want to look at the at the example files at:
> > > http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/simpleNCLClient/simpleNCLClient.cpp
> > > 
> > > which can be built using the Makefile at:
> > > http://phylo.bio.ku.edu/ncldocs/v2.1/funcdocs/simpleNCLClient/Makefile
> > > if you use g++, have installed NCL and put NCL_INSTALL_DIR in your
> > > env.
> > > 
> > > 
> > > all the best,
> > > Mark
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > Mark Holder
> > > 
> > > mtholder at ku.edu
> > > http://phylo.bio.ku.edu/mark-holder
> > > 
> > > ==============================================
> > > Department of Ecology and Evolutionary Biology
> > > University of Kansas
> > > 6031 Haworth Hall
> > > 1200 Sunnyside Avenue
> > > Lawrence, Kansas 66045
> > > 
> > > lab phone:  785.864.5789
> > > 
> > > fax (shared): 785.864.5860
> > > ==============================================
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > 
> > ------------------------------------------------------
> > Brian O'Meara
> > http://www.brianomeara.info
> > Assistant Prof.
> > Dept. Ecology & Evolutionary Biology
> > U. of Tennessee, Knoxville
> > 
> > 
> 
> Mark Holder
> 
> 
> mtholder at ku.edu
> http://phylo.bio.ku.edu/mark-holder
> 
> 
> ==============================================
> Department of Ecology and Evolutionary Biology
> University of Kansas
> 6031 Haworth Hall
> 1200 Sunnyside Avenue
> Lawrence, Kansas 66045
> 
> 
> lab phone:  785.864.5789
> 
> 
> fax (shared): 785.864.5860
> ==============================================
> 
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