Difference between revisions of "R Hackathon 1/Current Data Representations"

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 +
== DPUT files ==
  
  
  
== Ade4 ==
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== Other info ==
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=== Ade4 ===
  
== Ape ==
+
=== Ape ===
 
There are two main data classes in ape: "phylo" and "DNA.bin". They are both described in [http://pbil.univ-lyon1.fr/R/ape/ ape Web pages] (->Development section). Some features of "phylo" are summarized in the [[R_Hackathon_1/Data Standards]] page. Both classes have associated functions to read/write files on the disk, manipulate them and compute with in R, and ways to pass them to C.
 
There are two main data classes in ape: "phylo" and "DNA.bin". They are both described in [http://pbil.univ-lyon1.fr/R/ape/ ape Web pages] (->Development section). Some features of "phylo" are summarized in the [[R_Hackathon_1/Data Standards]] page. Both classes have associated functions to read/write files on the disk, manipulate them and compute with in R, and ways to pass them to C.
  
== apTreeshape ==
+
=== apTreeshape ===
  
== ComPairWise ==
+
=== ComPairWise ===
  
== Geiger ==
+
=== Geiger ===
  
== Laser ==
+
=== Laser ===
  
== OUCH ==
+
=== OUCH ===
  
== PaleoTS ==
+
=== PaleoTS ===
  
== PhyloGR ==
+
=== PhyloGR ===
  
== PhySim ==
+
=== PhySim ===
  
 
[[Category:R Hackathon 1]]
 
[[Category:R Hackathon 1]]

Revision as of 13:26, 28 November 2007

On this page, for the test set of sample trees and datasets and any other relevant files, describe success/failure in loading the file, any information lost, and how the objects are represented in R (pending a different/better idea, we could use a similar format as used for the 'phylo' class (pdf) or the scheme for coding nucleotides (pdf)).

Summary

Package altnexus_simple.tre altnexus_treewts.tre nexus_rooted_brlen.tre nexus_simple.tre notes_multitrees.nex (has labels and notes) phylip.tre samplefile.nex (has trees and data)
ape

ok

WEIGHTS NOT STORED

ok

ok

WILL NOT LOAD ("Error in edge[j, 1] <<- current.node : subscript out of bounds")

ok

tree ok, DATA WILL NOT LOAD ("samplefiledata<-read.nexus.data(file="samplefile.nex") Error in read.nexus.data(file = "samplefile.nex") : nexus parser does not handle spaces in sequences or taxon names (ts>2)")

ade4

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apTreeshape

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ComPairWise

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Geiger

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Laser

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OUCH

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PaleoTS

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PhyloGR

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PhySim

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DPUT files

Other info

Ade4

Ape

There are two main data classes in ape: "phylo" and "DNA.bin". They are both described in ape Web pages (->Development section). Some features of "phylo" are summarized in the R_Hackathon_1/Data Standards page. Both classes have associated functions to read/write files on the disk, manipulate them and compute with in R, and ways to pass them to C.

apTreeshape

ComPairWise

Geiger

Laser

OUCH

PaleoTS

PhyloGR

PhySim