Notebook entries in 2011

(301 entries)

Monday 12 Dec 2011
Better dynamic documents (Sweave) with syntax highlighting, caching, etc 12 Dec 2011
Some Notes on Open Notebooks, Open peer review practices. 11 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
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
Handling other sources of noise 28 Nov 2011
Friday: wrightscape, ggplot, wp memory 25 Nov 2011
Getting the right distributions 23 Nov 2011
some configuration notes: RStudio setup, syntax highlighting in sweave 22 Nov 2011
Friday 18 Nov 2011
Steve Pacala - Storer lecture 17 Nov 2011
wrightscape and sensitivity to initial conditions 17 Nov 2011
Tues: Sources of stochastic variation in optimal control 15 Nov 2011
non-optimal outcomes of optimal solutions 13 Nov 2011
Wainwright Retreat to Hastings Reserve 12 Nov 2011
Thursday 10 Nov 2011
Auteur plots for reef fish jaws and monkey brains -- needs tweaking 10 Nov 2011
Parallel hpc on clusters in R, MPI 10 Nov 2011
Crashing stocks and optimal harvesting effort on Allee effects 09 Nov 2011
SDP solution for allee model 08 Nov 2011
Sunday 06 Nov 2011
Sparkleshare configuration 04 Nov 2011
Friday's reading 04 Nov 2011
Warning signals - noise response 03 Nov 2011
Stochastic Optimal Control 02 Nov 2011
server file management from bowser: ajaxplorer, mollify 01 Nov 2011
pdg-control Conference Call 01 Nov 2011
Training Problem 2 update 01 Nov 2011
Labrids & Parrotfish, method1 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
Labrid submodels 26 Oct 2011
Monday, misc notes 26 Oct 2011
Tuesday notes: package work mostly. 25 Oct 2011
Treebase Package On Cran 25 Oct 2011
Training problem 2: the economist's problem statement 24 Oct 2011
Friday: Optimal Control 21 Oct 2011
Thursday - some parrotfish & labrid runs on method2 20 Oct 2011
Optimal Control Exploration 19 Oct 2011
Mathematical Elements of Attack Risk Analysis for Mountain Pine tribolium 18 Oct 2011
Algorithms Group: Literate programming 17 Oct 2011
Rewrites 17 Oct 2011
Friday, more runs 17 Oct 2011
Thursday, Fisheries course 13 Oct 2011
Wednesday 12 Oct 2011
rfishbase Tutorial - updated & extended 12 Oct 2011
Loo Botsford, CPB seminar 11 Oct 2011
Algorithms Group, HMM meets EM 10 Oct 2011
Matt Helmus visit 07 Oct 2011
Wednesday - forage fish & cascades 05 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
Tuesday - Berkeley visits 27 Sep 2011
Monday 26 Sep 2011
Saturday 24 Sep 2011
Friday: ropensci, manuscript edits 23 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
Likelihood expressions for branching processes 10 Sep 2011
How google views me: by search terms or citation counts? 09 Sep 2011
discriminating early bursts 08 Sep 2011
memory management, cron 07 Sep 2011
Wednesday 07 Sep 2011
rfishbase demo: Are there more Goby or Labrid species on reefs? 02 Sep 2011
Thursday Reading 01 Sep 2011
Wednesday 31 Aug 2011
Tuesday 30 Aug 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
DataCite Day 2 25 Aug 2011
DataCite Day 1 24 Aug 2011
Tuesday: rropensci, Rmpi, manuscripts, ... 23 Aug 2011
Academic Year 2011 Summary 21 Aug 2011
Thursday: reviewing edits, ropensci, computers. 18 Aug 2011
Wednesday: migrating codes into MPI 17 Aug 2011
Wrightscape: a brief tutorial 17 Aug 2011
Tuesday: 16 Aug 2011
Monday: Evolution manuscript revisions; early burst models, etc 16 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
Monday: Algorithms Discussion Group, EM finished 25 Jul 2011
Sunday: Appendix edits 24 Jul 2011
CSGF Conference Notes 24 Jul 2011
CSGF 2010 Computing Practices Survey Summary 24 Jul 2011
Showcasing the latest phylogenetic methods: AUTEUR 20 Jul 2011
Sunday: Warning Signals 17 Jul 2011
Saturday - back to Warning Signals MS 17 Jul 2011
The Case for Better Data Citation Practices? 14 Jul 2011
UC Davis Student Assembled Panel on Data Management Issues 13 Jul 2011
141 scientists can't be wrong? 08 Jul 2011
Friday: writing post-doc applications 08 Jul 2011
Thursday: sending off paper draft, starting applications 07 Jul 2011
Segue: Easy cloud hpc in R, now with custom packages 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
Open F1000 reviews? 04 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
#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
EM Algorithm 13 Jun 2011
Monday - 13 Jun 2011
Sunday 12 Jun 2011
Friday 10 Jun 2011
Workflows that Work: making it "easy enough" 10 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
Sunday -- warning signals manuscript (mostly) 05 Jun 2011
Saturday: git with latexdiff, TreeBASE and PMC package updates, bounds on lambda 04 Jun 2011
Friday 03 Jun 2011
Thursday: Warning Signals 02 Jun 2011
Warning Signals Literature: when stats are and aren't attempted 01 Jun 2011
Tuesday: PMC, confidence intervals; screen code-tricks 31 May 2011
Monday 30 May 2011
Sunday 29 May 2011
Site configuration: file sharing notes 28 May 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
Monday: some code-tricks, Algorithms group planning 23 May 2011
Sunday 22 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
MathJax the smart way: Child Themes 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
Building a semantic notebook 08 May 2011
Reproducible Research, Large data sets, and SI2 06 May 2011
Mendeley API in R 06 May 2011
Thursday: parrotfish analysis 05 May 2011
Weds: Parrotfish data set analysis 04 May 2011
Algorithms Discussion Group: MCMC 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
Tuesday: Reading and thoughts 19 Apr 2011
Early Warning Signals in Coral Dynamics -- Economic analysis of risk 19 Apr 2011
Thursday: submitting warning signals manuscript 18 Apr 2011
Algorithms Discussion Group: algorithms Continued 18 Apr 2011
TreePar: changing rates of evolution 17 Apr 2011
Friday 16 Apr 2011
Weds: Final round edits 13 Apr 2011
Tuesday: manuscript and appendix edits 12 Apr 2011
A bit of work on my socialR package for reproducible research 12 Apr 2011
Monday: Warning Signals - Updated graphs 11 Apr 2011
Monday: algorithms Meeting 11 Apr 2011
Sunday: Warning signals edits continue 11 Apr 2011
Warning signals 08 Apr 2011
TreeBase: exploratory exercises in database-driven phylogenetics 08 Apr 2011
Some reproducible research practices in journals 08 Apr 2011
Steve Ellner's seminar 07 Apr 2011
Warning Signals - Manuscript touch-ups 06 Apr 2011
Comparative methods paper status/to-do 06 Apr 2011
Updates to socialR package 05 Apr 2011
evolution manuscript revisions 04 Apr 2011
Thursday finishing up appendices(?) 01 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
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
Data Management Workshop at UC Davis Center for Population Biology: Video archive 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
Challenges with Collaboration in Open Science 21 Mar 2011
Writing: Warning Signals Mansucript 20 Mar 2011
Warning Signals examples and tracking graphs 19 Mar 2011
Approximate Bayesian Computing (algorithms) methods 19 Mar 2011
Sam's Practice talk 18 Mar 2011
Warning Signals in Ecological Systems: Revisions and Drake & Griffen Data 17 Mar 2011
Wednesday 16 Mar 2011
Tuesday 15 Mar 2011
Model identifiability in phylogenetic inference GTR+I+G 15 Mar 2011
Peter's talk 14 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
Bodega evolution Tutorial: behind the scenes difficulties in R packages 07 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
Is BM nested in OU? Understanding likelihoods of ouch 25 Feb 2011
Phylo: Luke Harmon 25 Feb 2011
ESA 2011 Abstract: Limits to Detection of Early Warning Signals 23 Feb 2011
Monday: Writing, Mendeley groups, Notebook plugin tweaks 21 Feb 2011
Bodega evolution Workshop: Continuous Characters R session planning 19 Feb 2011
Friday 18 Feb 2011
Thursday 17 Feb 2011
Weds & Framing warning signals manuscript 16 Feb 2011
Citation tools & Future of Publishing 16 Feb 2011
Data Mangement on UC3 Merritt Repository 16 Feb 2011
Tuesday 15 Feb 2011
Monday 14 Feb 2011
Thursday 10 Feb 2011
Phylogenetic Monte Carlo for the Laser package 09 Feb 2011
Why ONS? From a discussion with friends 08 Feb 2011
Notes during revisions on phylogenetics manuscript 08 Feb 2011
Warning signals & hpc 04 Feb 2011
Progress on warning signals 03 Feb 2011
To podcast or not to podcast university lectures 01 Feb 2011
The Future of Data: Plans for a UC Davis workshop 01 Feb 2011
Warning signals: Indicators vs Likelihood continued 31 Jan 2011
more Phylogenetic signal metrics & Brownie comparison 31 Jan 2011
Notes on Bokma 2010: evolution in drifts and jumps 31 Jan 2011
Warning signals of differing stregths by likelihood and by indicator 28 Jan 2011
Phylogenetic Signal metrics 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
Intro Ecology Lecture at University of the Pacific 25 Jan 2011
McElreath Hierarchical Models 24 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
Robert Hijmans on Models to predict sp response to climate change 19 Jan 2011
Reflections from #scio11: Saturday's Open Science Track 15 Jan 2011
evolution- wrightscape 11 Jan 2011
Warning Signals, Power and Sufficient Statistics 10 Jan 2011
Phylo Monte Carlo for diversification rates 09 Jan 2011
Two routes to adaptive branching 06 Jan 2011
Finishing up my #SICB Presentation 02 Jan 2011