User:Carl Boettiger/Notebook/Comparative Phylogenetics/2010/04/09

{| width="800"
 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Comparative Phylogenetics
 * style="background-color: #F2F2F2" align="center"|  |Main project page
 * style="background-color: #F2F2F2" align="center"|  |Main project page


 * colspan="2"|
 * colspan="2"|

Research

 * Working on bootstrapping theta parameters
 * bootstrapping multiple parameters doesn't seem effective in the context of the boot package, despite claiming it can use a vector of stats. Certainly part of challenge is that different models have different numbers of parameters, so this isn't a fixed size vector.  Approaching manually for the moment, inhibits use of bootstrap confidence intervals function from the boot package.
 * Some irregular behavior in bootstrapping parameters -- have to load package and then reload likelihood_bootstrap library source file or else bootstraps are NAs, needs further investigation.
 * formatting bootstrapping meaningfully -- following the ouch style for the moment
 * Sent Peter Wainwright a rough draft of Bio Let. manuscript.

Goals / ToDo

 * Add bootstraps of parameters to manuscript,
 * Function to bootstrap all parameters given list of all models. Plotting function also.
 * Write up Evolution note on AIC.
 * Conference registrations
 * NESCent whitepaper

Primates

 * Graham pointed out a rather promising looking chronogram from a supermatrix for Primate phylogenetic trees
 * Contacted Helen Chatterjee re: primate phylogenies.
 * Also see project details in Daniel's notebook

Reading & Notes

 * Embedding google spreadsheets sounds much more promising than formatting tables in OWW/html: Example from Anthony / Koch Lab
 * OWW Stats
 * FF discussion on Chelsea's Open Science article
 * Embedding/Transclusion in OWW/mediawiki and examples


 * Exploring gist for code fragments. Embeddable gist:


 * }