Wednesday: Treebase

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 remove trees without branch lengths from the returned set. Still has to download all trees, so in this case max_trees is the number attempted, not the number returned.

XPATH AND METADATA

Trying to learn XPath from the W3 tutorial in order to parse the OAI-PMH output (like this, for a single treebase entry). Not much success.  Oooh, Duncan introduced me to getNodeSet() and xmlToList(), now I can query the metadata for the tree(!)

     tree <- search_treebase("1234", "id.tree")
     metadata(tree$id)

  • Since the metadata  API is quite small, (see treebase wiki on OAI-PMH) just about done with treebase implementation, short of testing, documentation and use cases.

  • Grabbing study by date could be useful (supports at least “until” and “after”.)  Can “ListRecord” or “GetIdentifier”.  The latter can be useful to get ids to feed into search_treebase(), allowing the user to query all studies after a certain date, for instance. (DONE – see examples.)

  • And now the treebase server for OAI-PMH seems to be down. Maybe a sign I should return to some real work.

  • Managing the to-do lists for treeBASE under github-issues (much more sensible than flipping through notebook pages).

DRYAD

Implemented the basic Dryad metadata query GetRecord given an ID.  (forms the api query and parses output).  Uses the same OAI function as the treebase query:

dryad_metadata("10255/dryad.12")

Now I just need:

  • a way to get Dryad IDs from the TreeBASE query, (server-side issue)

  • a way to grab the doi pointing to each data file (not the paper doi, or the study doi.  This is returned in $relation, along with other stuff such as the journal title, so will need a grep on doi at the moment).

  • A way to get from the webpage returned to get the actual url of the data (also a server-side issue ) Actually was already in the documentation on the wiki.   DONE, see 2011-05-12

RFlickr

  1. Revisiting Rflickr now that Duncan has added write permissions.  install.packages(“Rflickr”, repos = “https://www.omegahat.org/R”)

  2. Look up key and secret for my registered app (others mustregister an app)

  3. Authenticate with write permissions – Go quickly after issuing this command into browser and approve access before the timeout. NOTE: PERMISSION IS SINGULAR - - won’t error if it is plural.   tok <- Rflickr::authenticate(api_key, secret, permission=“write”)

  4. We can use the full flickr api just as described, except that we need to start everything with secret, tok, and then as specified in the API (api_key, other options).  I.e. for flickr.people.getInfo we would do: flickr.people.getInfo(secret, tok, api_key, “30385402@N05”)

  5. Instead we can use the clever interface to avoid having to give these keys each time.  (See documentation): we make a session once: > session = flickrSession(secret, tok, api_key)

  6. and can now call with session$ and skip the “flickr” everywhere it occurs, and skip the keys, i.e.:  session$people.getInfo(“46456847@N08”)

  7. Note: we could have left flickr in too: session$flickr.people.getInfo(“46456847@N08”).  Partial matching in R is fantastic.

  8. All this is great but having trouble with write permissions still... farther thanlast time though.  Working, should have used singular, as noted above.  ToDo: integrate into socialR package.

Wordpress, RWordpress

There’s a JSON API for Wordpress, that allows downloading post data, also optionally making posts, editing posts and tags, etc from the API.  An implementation of this in R would be straight forward using RCurl and RJSONIO.  Duncan has an RWordpress package (on Omegahat) that does this the official/direct way for blogs as well.

CHATS AND READING

Discussing with Brian Anackner some ways of looking for evidence of correlations in transition rates using contrasts. Taking an example from [cite source=‘pubmed’ rel=“cito:DisagreesWith”]16261729[/cite] the method proposed in [cite source=‘pubmed’ rel=“cito:UsesMethod”]7583692[/cite], which combines independent contrasts in discrete and continuous traits. Say categorical traits are E and N and continuous trait is affinity for precipitation level. This method pairs them so that contrasts are taken only between E and N, and in the the same order each time, E - N (or vice versa). It seems to me this simply suggests that large values means E’s tend to be found more often in higher-precipitation climates.

Rebecca Best suggests I take a look at [cite rel=“cito:UsesMethod”]10.1890/10-1264.1[/cite].

UPGRADING TO A VPS

Time to upgrade this site to a virtual private server on DreamHost.  We’ll see how it goes, hopefully things get faster now.

mathjax

Meanwhile, Jason Moore suggested just adding the mathjax to the header file, as described on the MathJax homepage. Doesn’t need any libraries installed as it uses their CDN, and so is quite fast. Won’t convert my wp-latex but will work with inline equations, \(y=mx+b\), and displayed equations. Wonder if I’ll have to manually edit the header file if I upgrade my theme.

[ = 1+ {1+ {1+ {1+ {1+} } } }]

\[\begin{aligned} \nabla \times \vec{\mathbf{B}} -\, \frac1c\, \frac{\partial\vec{\mathbf{E}}}{\partial t} & = \frac{4\pi}{c}\vec{\mathbf{j}} \\ \nabla \cdot \vec{\mathbf{E}} & = 4 \pi \rho \\ \nabla \times \vec{\mathbf{E}}\, +\, \frac1c\, \frac{\partial\vec{\mathbf{B}}}{\partial t} & = \vec{\mathbf{0}} \\ \nabla \cdot \vec{\mathbf{B}} & = 0 \end{aligned}\]

$ $    
$$ $$ or $$ $$

To give credit where it’s due: now, powered by: Powered by MathJax