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

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On this page, for the [[Media:RHackTrees.zip|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 [http://pbil.univ-lyon1.fr/R/ape/misc/FormatTreeR_4Dec2006.pdf 'phylo' class] (pdf) or the [http://pbil.univ-lyon1.fr/R/ape/misc/BitLevelCodingScheme_20April2007.pdf scheme for coding nucleotides] (pdf)).
 
On this page, for the [[Media:RHackTrees.zip|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 [http://pbil.univ-lyon1.fr/R/ape/misc/FormatTreeR_4Dec2006.pdf 'phylo' class] (pdf) or the [http://pbil.univ-lyon1.fr/R/ape/misc/BitLevelCodingScheme_20April2007.pdf scheme for coding nucleotides] (pdf)).
 +
 +
== Summary ==
 +
{| border=1 cellspacing=0
 +
|-
 +
! 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")
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Error in read.nexus.data(file = "samplefile.nex") :
 +
nexus parser does not handle spaces in sequences or taxon names
 +
(ts>2)")
 +
|-
 +
|}
 +
 +
  
 
== Ade4 ==
 
== Ade4 ==

Revision as of 13:19, 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

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