Carl Boettiger

TREEBASE PACKAGE: Mod­i­fied tree­base pack­age to return the tree­base id in the phylo class as phy$id, so that I can use the id to query the appro­pri­ate meta data. Mod­i­fied the pack­age with the option to return only max num­ber of trees, try(xpathApply(search_returns, paste(“//rdf:li[position()< “, max_trees, ”]”, sep=””), function(x){ … Mod­i­fied to check for branch lengths and …

Next Steps Tree­base (See Sunday’s post) — Phylo-ws imple­mented, but a few extra func­tions would strengthen the inter­face a bit: limit the num­ber of trees returned, query­ing trees for branch lengths, RaXML pipeline for return­ing rough branch lengths con­di­tioned on the given topol­ogy, user doc­u­men­ta­tion, more test exam­ples. Imple­ment OAI-PMH test cases for tree­base: For …

Work­ing on a few updates to the Tree­BASE pack­age.  This flushes out the basic func­tion­al­ity pro­vided by the phylo-ws API now. Needs a bit more test­ing of the pos­si­ble queries and some bells and whis­tles options.  Mean­while, going to start look­ing at the meta­data side with the OAI-PMH API.  With this I should be able …

Light­ning Talk Pro­posal I will present the R pack­age tree­BASE, which pro­vides an R imple­men­ta­tion of the tree­BASE phy­lows API.   This pack­age makes it pos­si­ble to search and import data from this data­base of pub­lished phy­lo­ge­netic trees eas­ily from within an R script.  Recent data archiv­ing require­ments at major evo­lu­tion­ary jour­nals such as The …

I’ve recently1 begun a project to see if I can search for and load phy­lo­ge­nies from Tree­BASE directly into R. Thanks to the rather bril­liant API in place (doc­u­mented on the tree­BASE wiki) for Tree­BASE, some advice from Rut­ger Vos (Tree­BASE devel­oper), and some xpaths R code from Gabe Becker (stats grad stu­dent, UC Davis), …