- Friday 09 Dec 2011
- Thursday 08 Dec 2011
- Wednesday - wrightscape runs and various other things 07 Dec 2011
- Tuesday -- two insights 06 Dec 2011
- Monday - wrightscape meetings, PDG meeting 05 Dec 2011
- More labrid plots 05 Dec 2011
- Release of constraint 04 Dec 2011
- Friday - updated wrightscape results - simulated examples 02 Dec 2011
- Thrusday - corrected calculation, implementing. 01 Dec 2011
- Wednesday - various logistics, then checking likelihood calculation 30 Nov 2011
- Tuesday debugging 29 Nov 2011
- Monday: submodels for full traits 28 Nov 2011
- Friday: wrightscape, ggplot, wp memory 25 Nov 2011
- wrightscape and sensitivity to initial conditions 17 Nov 2011
- Wainwright Retreat to Hastings Reserve 12 Nov 2011
- Auteur plots for reef fish jaws and monkey brains -- needs tweaking 10 Nov 2011
- Friday's reading 04 Nov 2011
- Labrids & Parrotfish, method1 01 Nov 2011
- Labrid submodels 26 Oct 2011
- Tuesday notes: package work mostly. 25 Oct 2011
- Treebase Package On Cran 25 Oct 2011
- Thursday - some parrotfish & labrid runs on method2 20 Oct 2011
- Matt Helmus visit 07 Oct 2011
- Tuesday 04 Oct 2011
- Friday, wordpress backups, pmc edits 30 Sep 2011
- Thursday 29 Sep 2011
- Phylogenetics - Research Proposal 29 Sep 2011
- Wednesday - Berkeley visits 28 Sep 2011
- Monday 26 Sep 2011
- Friday: ropensci, manuscript edits 23 Sep 2011
- Thursday 22 Sep 2011
- Likelihood expressions for branching processes 10 Sep 2011
- discriminating early bursts 08 Sep 2011
- rfishbase demo: Are there more Goby or Labrid species on reefs? 02 Sep 2011
- Wednesday 31 Aug 2011
- Tuesday 30 Aug 2011
- Monday: scaling wrightscape examples 29 Aug 2011
- Sunday: scaling, runs 28 Aug 2011
- rropensci and some taxonomy in R with taxize 26 Aug 2011
- Tuesday: rropensci, Rmpi, manuscripts, ... 23 Aug 2011
- Academic Year 2011 Summary 21 Aug 2011
- Thursday: reviewing edits, ropensci, computers. 18 Aug 2011
- Wrightscape: a brief tutorial 17 Aug 2011
- Tuesday: 16 Aug 2011
- Monday: Evolution manuscript revisions; early burst models, etc 16 Aug 2011
- Monday: ESA, appendix, etc 25 Jul 2011
- Showcasing the latest phylogenetic methods: AUTEUR 20 Jul 2011
- #ievobio Day 2 22 Jun 2011
- Evolution Day 4 / #ievobio Day 1 21 Jun 2011
- Evolution Day 3 20 Jun 2011
- Slides from my talk at Evolution 2011 20 Jun 2011
- Evolution Day 2 19 Jun 2011
- Evolution Conference Day 1 18 Jun 2011
- Friday: more labrid & parrotfish wrightscape examples 17 Jun 2011
- Wrightscape labrid/parrotfish results; Evolution pres 16 Jun 2011
- Wednesday MCMC and MLEs for wrightscape 15 Jun 2011
- Tuesday - Evolution/wrightscape talk & sundry 14 Jun 2011
- Monday - 13 Jun 2011
- mcmc and bootstrapped likelihood runs on parrotfish tree 09 Jun 2011
- Wednesday: Simulated model fit analysis on wrightscape, parrotfish tree 08 Jun 2011
- Tuesday: Parrotfish/wrightscape runs and code modification 07 Jun 2011
- Parrotfish in wrightscape 06 Jun 2011
- Saturday: git with latexdiff, TreeBASE and PMC package updates, bounds on lambda 04 Jun 2011
- Friday 03 Jun 2011
- Tuesday: PMC, confidence intervals; screen code-tricks 31 May 2011
- Monday 30 May 2011
- Sunday 29 May 2011
- End of NCEAS & the legacy of synthetic data 22 May 2011
- Algorithms group: MCMCMC 19 May 2011
- Thursday 19 May 2011
- Birth-death Tutorial for PBG Core 18 May 2011
- Tuesday: Parrotfish results, MCMCMC testing, APIs 17 May 2011
- TreeBASE in R: a first tutorial 16 May 2011
- Thursday: Fun with databases continued 12 May 2011
- Wednesday: Treebase 11 May 2011
- Interfaces for databases: TreeBASE, Dryad, DataONE 10 May 2011
- Monday: meetings, notebook 09 May 2011
- Sunday: a few Treebase R package updates 08 May 2011
- Thursday: parrotfish analysis 05 May 2011
- Weds: Parrotfish data set analysis 04 May 2011
- Tuesday: phylogenetics- wrightscape coding 03 May 2011
- treeBASE R interface: proposal for #iEvoBio 03 May 2011
- Monday 03 May 2011
- Friday: Notes on Labrids, notes on Transforms and size-corrections 29 Apr 2011
- Reading Notes, presentation prep treebase error handling 28 Apr 2011
- Wednesday 27 Apr 2011
- Accessing phylognenies in TreeBASE from R 26 Apr 2011
- TreeBASE interface continued... 25 Apr 2011
- wrightscape profiling 24 Apr 2011
- Release of constraint in labrids? 22 Apr 2011
- Wednesday 20 Apr 2011
- TreePar: changing rates of evolution 17 Apr 2011
- Friday 16 Apr 2011
- TreeBase: exploratory exercises in database-driven phylogenetics 08 Apr 2011
- Comparative methods paper status/to-do 06 Apr 2011
- evolution manuscript revisions 04 Apr 2011
- A few large data problems in Ecology & Evolution 31 Mar 2011
- Brian O'Meara discusses new algorithms approaches on Phylo 30 Mar 2011
- Approximate Bayesian Computing (algorithms) methods 19 Mar 2011
- Sam's Practice talk 18 Mar 2011
- Model identifiability in phylogenetic inference GTR+I+G 15 Mar 2011
- Peter's talk 14 Mar 2011
- Bodega evolution Tutorial: behind the scenes difficulties in R packages 07 Mar 2011
- Is BM nested in OU? Understanding likelihoods of ouch 25 Feb 2011
- Phylo: Luke Harmon 25 Feb 2011
- Bodega evolution Workshop: Continuous Characters R session planning 19 Feb 2011
- Friday 18 Feb 2011
- Thursday 17 Feb 2011
- Monday 14 Feb 2011
- Thursday 10 Feb 2011
- Phylogenetic Monte Carlo for the Laser package 09 Feb 2011
- Notes during revisions on phylogenetics manuscript 08 Feb 2011
- more Phylogenetic signal metrics & Brownie comparison 31 Jan 2011
- Notes on Bokma 2010: evolution in drifts and jumps 31 Jan 2011
- Phylogenetic Signal metrics 28 Jan 2011
- Felsenstein (web) seminar 24 Jan 2011
- Shape as well as size influence power of phylogeny 21 Jan 2011
- Estimating phylogenetic signal (lambda) on large trees 20 Jan 2011
- evolution- wrightscape 11 Jan 2011
- Phylo Monte Carlo for diversification rates 09 Jan 2011
- Finishing up my #SICB Presentation 02 Jan 2011
- Monday 12 Dec 2011
- Friday 09 Dec 2011
- Thursday 08 Dec 2011
- Wednesday - wrightscape runs and various other things 07 Dec 2011
- Optimal control -- costs to policy shifts 07 Dec 2011
- Tuesday -- two insights 06 Dec 2011
- Monday - wrightscape meetings, PDG meeting 05 Dec 2011
- Wednesday - various logistics, then checking likelihood calculation 30 Nov 2011
- Handling other sources of noise 28 Nov 2011
- Getting the right distributions 23 Nov 2011
- Friday 18 Nov 2011
- Steve Pacala - Storer lecture 17 Nov 2011
- Tues: Sources of stochastic variation in optimal control 15 Nov 2011
- non-optimal outcomes of optimal solutions 13 Nov 2011
- Thursday 10 Nov 2011
- Crashing stocks and optimal harvesting effort on Allee effects 09 Nov 2011
- SDP solution for allee model 08 Nov 2011
- Friday's reading 04 Nov 2011
- Warning signals - noise response 03 Nov 2011
- Stochastic Optimal Control 02 Nov 2011
- pdg-control Conference Call 01 Nov 2011
- Training Problem 2 update 01 Nov 2011
- Monday: openfisheries & ggplot 31 Oct 2011
- Optimal Control examples continued: Bellman, Dynamic Programming 28 Oct 2011
- Optimal control sample problems (Mostly continuous time by Pontryagin principle) 27 Oct 2011
- Monday, misc notes 26 Oct 2011
- Training problem 2: the economist's problem statement 24 Oct 2011
- Friday: Optimal Control 21 Oct 2011
- Mathematical Elements of Attack Risk Analysis for Mountain Pine tribolium 18 Oct 2011
- Rewrites 17 Oct 2011
- Friday, more runs 17 Oct 2011
- Thursday, Fisheries course 13 Oct 2011
- Wednesday 12 Oct 2011
- Loo Botsford, CPB seminar 11 Oct 2011
- Wednesday - forage fish & cascades 05 Oct 2011
- Tuesday 04 Oct 2011
- Thursday 29 Sep 2011
- Tuesday - Berkeley visits 27 Sep 2011
- Saturday 24 Sep 2011
- Thursday 22 Sep 2011
- Wednesday 21 Sep 2011
- Colored noise: some classic results in ecology 21 Sep 2011
- Van Kampen Expansion and Stochastic population dynamics 21 Sep 2011
- Tuesday: Visit to Berkeley 21 Sep 2011
- Monday 19 Sep 2011
- pdg-control pdg-control: Thursday 15 Sep 2011
- pdg-control PDG group, Tasks 15 Sep 2011
- Training Problem II 14 Sep 2011
- pdg-control pdg-control: Wednesday 14 Sep 2011
- pdg-control pdg-control, Tuesday 13 Sep 2011
- Pretty Darn Good Control Working Group 12 Sep 2011
- Wednesday 07 Sep 2011
- Thursday Reading 01 Sep 2011
- Wednesday 31 Aug 2011
- Tuesday 30 Aug 2011
- Academic Year 2011 Summary 21 Aug 2011
- ESA personal notes: people, goals 13 Aug 2011
- Saturday: Post ESA, NSF Intersections post-doc? 13 Aug 2011
- ESA Friday 12 Aug 2011
- ESA Thursday 11 Aug 2011
- ESA Wednesday 10 Aug 2011
- ESA Tuesday 09 Aug 2011
- Monday: ESA Conference 08 Aug 2011
- Fisheries stock assessments for early warning 02 Aug 2011
- Monday 02 Aug 2011
- Saturday: Fisheries Data Survey, Warning Signals 30 Jul 2011
- Friday: ESA Practice Talk 29 Jul 2011
- Weds: Manuscript 27 Jul 2011
- Wednesday: ESA presentation, manuscript/appendix edits 27 Jul 2011
- Tues: ESA presentation 26 Jul 2011
- Monday: ESA, appendix, etc 25 Jul 2011
- Sunday: Appendix edits 24 Jul 2011
- Sunday: Warning Signals 17 Jul 2011
- Saturday - back to Warning Signals MS 17 Jul 2011
- Thursday: sending off paper draft, starting applications 07 Jul 2011
- Early warning signals presentation notes 07 Jul 2011
- Exact Simulation by the Gillespie Algorithm 06 Jul 2011
- Wednesday: Data wrangling into graphs 06 Jul 2011
- Tuesday: Warning Signals Data Wrangling 05 Jul 2011
- Warning Signals writing, organization, appendices 04 Jul 2011
- Friday, warning signals writing, etc 01 Jul 2011
- Thursday: Warning Signals writing, figures, segue 30 Jun 2011
- Warning signals: summary statistic performance at varying sampling effort 29 Jun 2011
- Warning Signals writing 29 Jun 2011
- Monday: Warning Signals Manuscript 27 Jun 2011
- Sunday 12 Jun 2011
- Friday 10 Jun 2011
- Sunday -- warning signals manuscript (mostly) 05 Jun 2011
- Thursday: Warning Signals 02 Jun 2011
- Warning Signals Literature: when stats are and aren't attempted 01 Jun 2011
- Matt Potts: Conserving Diversity in Tropical Landscapes 27 May 2011
- Thursday Meetings: Duncan; Alan 26 May 2011
- Wednesday 25 May 2011
- Tuesday 24 May 2011
- Sunday 22 May 2011
- End of NCEAS & the legacy of synthetic data 22 May 2011
- Monday 03 May 2011
- Reading Notes, presentation prep treebase error handling 28 Apr 2011
- Early Warning Signals in Coral Dynamics -- Economic analysis of risk 19 Apr 2011
- Thursday: submitting warning signals manuscript 18 Apr 2011
- Weds: Final round edits 13 Apr 2011
- Tuesday: manuscript and appendix edits 12 Apr 2011
- Monday: Warning Signals - Updated graphs 11 Apr 2011
- Sunday: Warning signals edits continue 11 Apr 2011
- Warning signals 08 Apr 2011
- Steve Ellner's seminar 07 Apr 2011
- Warning Signals - Manuscript touch-ups 06 Apr 2011
- Thursday finishing up appendices(?) 01 Apr 2011
- A few large data problems in Ecology & Evolution 31 Mar 2011
- Wednesday: appendices; parameter distributions 30 Mar 2011
- Tuesday, simulations & appendix 29 Mar 2011
- Monday, appendices continue... 29 Mar 2011
- Sunday -- edits and appendices 27 Mar 2011
- Saturday-- Appendices 26 Mar 2011
- Friday 25 Mar 2011
- Thursday 24 Mar 2011
- Wednesday 23 Mar 2011
- Tuesday: Figures, figures, figures 23 Mar 2011
- Monday -- Edits and organization 22 Mar 2011
- Sunday - manuscript and simulations 21 Mar 2011
- Writing: Warning Signals Mansucript 20 Mar 2011
- Warning Signals examples and tracking graphs 19 Mar 2011
- Warning Signals in Ecological Systems: Revisions and Drake & Griffen Data 17 Mar 2011
- Wednesday 16 Mar 2011
- Tuesday 15 Mar 2011
- Warning Signals, Monday 14 Mar 2011
- Warning signals: summary stats vs likelihood on real and simulated data 11 Mar 2011
- Numerical challenges in likelihood estimation of time-dep OU models 10 Mar 2011
- Warning Signals data examples 09 Mar 2011
- Warning Signals: Comparing Methods on Climate Data 01 Mar 2011
- Warning Signals on Real data continued 28 Feb 2011
- Warning Signals on Real Data? 27 Feb 2011
- ESA 2011 Abstract: Limits to Detection of Early Warning Signals 23 Feb 2011
- Friday 18 Feb 2011
- Weds & Framing warning signals manuscript 16 Feb 2011
- Tuesday 15 Feb 2011
- Monday 14 Feb 2011
- Warning signals & hpc 04 Feb 2011
- Progress on warning signals 03 Feb 2011
- Warning signals: Indicators vs Likelihood continued 31 Jan 2011
- Warning signals of differing stregths by likelihood and by indicator 28 Jan 2011
- Warning signals vs model choice 27 Jan 2011
- McElreath: A Bayesian approach to hierarchical modeling, using R to build our own estimator from scratch 26 Jan 2011
- McElreath Hierarchical Models 24 Jan 2011
- Robert Hijmans on Models to predict sp response to climate change 19 Jan 2011
- Warning Signals, Power and Sufficient Statistics 10 Jan 2011
- Two routes to adaptive branching 06 Jan 2011
- Better dynamic documents (Sweave) with syntax highlighting, caching, etc 12 Dec 2011
- Friday: wrightscape, ggplot, wp memory 25 Nov 2011
- some configuration notes: RStudio setup, syntax highlighting in sweave 22 Nov 2011
- Parallel hpc on clusters in R, MPI 10 Nov 2011
- Sunday 06 Nov 2011
- Sparkleshare configuration 04 Nov 2011
- server file management from bowser: ajaxplorer, mollify 01 Nov 2011
- Optimal Control Exploration 19 Oct 2011
- Algorithms Group: Literate programming 17 Oct 2011
- rfishbase Tutorial - updated & extended 12 Oct 2011
- Algorithms Group, HMM meets EM 10 Oct 2011
- Friday, wordpress backups, pmc edits 30 Sep 2011
- memory management, cron 07 Sep 2011
- Algorithms group: Hidden Markov Models 29 Aug 2011
- Monday: scaling wrightscape examples 29 Aug 2011
- Sunday: scaling, runs 28 Aug 2011
- Saturday: working on computational scaling, ion, etc 27 Aug 2011
- rropensci and some taxonomy in R with taxize 26 Aug 2011
- FishBASE from R: some XML parsing 26 Aug 2011
- Tuesday: rropensci, Rmpi, manuscripts, ... 23 Aug 2011
- Wednesday: migrating codes into MPI 17 Aug 2011
- Monday: Algorithms Discussion Group, EM finished 25 Jul 2011
- CSGF Conference Notes 24 Jul 2011
- CSGF 2010 Computing Practices Survey Summary 24 Jul 2011
- Segue: Easy cloud hpc in R, now with custom packages 07 Jul 2011
- EM Algorithm 13 Jun 2011
- Thursday Meetings: Duncan; Alan 26 May 2011
- Monday: some code-tricks, Algorithms group planning 23 May 2011
- Algorithms Discussion Group: MCMC 04 May 2011
- wrightscape profiling 24 Apr 2011
- Algorithms Discussion Group: algorithms Continued 18 Apr 2011
- Monday: algorithms Meeting 11 Apr 2011