Difference between revisions of "R Hackathon 1/Programming Goals"

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The community needs stable standards: trees (with uncertainty, character mapping), networks, data, perhaps model descriptions or analysis settings. Also metadata standards?
 
The community needs stable standards: trees (with uncertainty, character mapping), networks, data, perhaps model descriptions or analysis settings. Also metadata standards?
We have a test set of trees and datasets.
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We have a test set of sample trees and datasets which contain various formats for input (trees with and without branch lengths, rooting, labels, etc.). In order to better get an idea of the structure of trees and data within each package, we'd like to get the internal representation of the files from each package, as well as notes regarding the procedure for loading the files and what was lost (for example, is it clear which trees are rooted and unrooted?). See, for an example of a description of a format, Paradis' description of the [http://pbil.univ-lyon1.fr/R/ape/misc/FormatTreeR_4Dec2006.pdf phylo class] (pdf) or the scheme for coding [http://pbil.univ-lyon1.fr/R/ape/misc/BitLevelCodingScheme_20April2007.pdf nucleotides] (pdf) in [http://pbil.univ-lyon1.fr/R/ape/ APE].
  
  
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     * Mesquite calling R modules.
 
     * Mesquite calling R modules.
 
     * R calling Mesquite modules.
 
     * R calling Mesquite modules.
     * R calling existing software (PAUP? MrBayes? others? [Brownie?])
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     * R calling existing software (PAUP? MrBayes? others?)
  
 
New functions
 
New functions

Revision as of 16:15, 12 November 2007

The community needs stable standards: trees (with uncertainty, character mapping), networks, data, perhaps model descriptions or analysis settings. Also metadata standards?

We have a test set of sample trees and datasets which contain various formats for input (trees with and without branch lengths, rooting, labels, etc.). In order to better get an idea of the structure of trees and data within each package, we'd like to get the internal representation of the files from each package, as well as notes regarding the procedure for loading the files and what was lost (for example, is it clear which trees are rooted and unrooted?). See, for an example of a description of a format, Paradis' description of the phylo class (pdf) or the scheme for coding nucleotides (pdf) in APE.


Interaction:

   * Mesquite calling R modules.
   * R calling Mesquite modules.
   * R calling existing software (PAUP? MrBayes? others?)

New functions

   * [What's missing]

Visualization