R Hackathon 1/Current Data Representations

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Revision as of 13:19, 28 November 2007 by Bco (talk)
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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

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