- 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: