R Hackathon 1/Current Data Representations

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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

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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

File ape ade4 apTreeshape ComPairWise Geiger Laser OUCH PaleoTS PhyloGR PhySim
altnexus_simple.tre
structure(
	list(
	edge = structure(
		c(8, 9, 10, 10, 9, 11, 11, 8, 12, 12, 13, 13, 9, 10, 1, 2, 11, 3, 4, 12, 5, 13, 6, 7),
		.Dim = c(12L, 2L)
	), 
	tip.label = c("taxon_1", "taxon_3", "taxon_2", "taxon_6", "taxon_4", "taxon_5", "taxon_7"), Nnode = 6L), 
	.Names = c("edge", "tip.label", "Nnode"),
	class = "phylo", 
	origin = "/Users/bcomeara/Desktop/RHackTrees/altnexus_simple.tre"
)
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altnexus_treewts.tre
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nexus_rooted_brlen.tre
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nexus_simple.tre
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notes_multitrees.nex
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phylip.tre
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samplefile.nex
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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