Notebook entries in 2010

(271 entries)

Comparative evolution: Is the data informative? 31 Dec 2010
Stochastic limits to evolutionary branching 30 Dec 2010
Open Notebook Science Abstract 30 Dec 2010
Parameter exploration in adaptive dynamics branching 30 Dec 2010
adaptive-dynamics Simulations 29 Dec 2010
DoE renewal and a year in review 24 Dec 2010
Writing, Cloud Computing, and #scio11 23 Dec 2010
Sun: Visualizing my coding over the past year 20 Dec 2010
Thurs: writing section on comparing to AIC 16 Dec 2010
Weds: Example sets & more EC2 15 Dec 2010
Tues: evolution thoughts while writing... 14 Dec 2010
Back to Writing 13 Dec 2010
Citations 11 Dec 2010
socialR: Reproducible Research & Notebook integration with R 11 Dec 2010
Warning signals manuscript 10 Dec 2010
Exploring Power in Warning Signals 09 Dec 2010
Practice SICB Presentation 08 Dec 2010
Mapping out SICB Presentation: Is your phylogeny informative? 07 Dec 2010
follow up from Fri discussions: Revisiting post-predictive evaluation 06 Dec 2010
Identifying Warning Signals 04 Dec 2010
Thoughts on the New Policies for Data Archiving at NSF and in Common Journals 03 Dec 2010
CPB : David Collar 01 Dec 2010
Tues: Fitting the limiting OU models to each bifurcation 30 Nov 2010
Further treatment of the limiting models 29 Nov 2010
Challenges in estimating phylogenetic signal 29 Nov 2010
Likelihoods for quadratic models cont 28 Nov 2010
Implementing Likelihoods for quadratic models 27 Nov 2010
Tweets from an Ecology Field class 25 Nov 2010
Warning signals: Likelihoods Straight-up 24 Nov 2010
Power in simple tests 22 Nov 2010
Two questions 21 Nov 2010
Making R twitter? 21 Nov 2010
Sat: evolution -- porting tree transformations to OUCH? 20 Nov 2010
Fri: extending Geiger to Monte Carlo method 19 Nov 2010
Thurs: evolution likelihood 18 Nov 2010
Weds 18 Nov 2010
Tues seminar 16 Nov 2010
evolution today: Discussion groups, writing, etc 15 Nov 2010
Thursday: Post-predictive verification exploration; writing and figures 11 Nov 2010
evolution statistics 11 Nov 2010
Tuesday - SDEs then back to phylogenetics 10 Nov 2010
Monday and some phylogenetics 08 Nov 2010
Welcome to my Lab Notebook 08 Nov 2010
Friday: Evolution reading, writing 05 Nov 2010
Thursday 05 Nov 2010
Getting the details right on the Fourier Transform approach to likelihood 03 Nov 2010
Reviews, organization, rewrites 03 Nov 2010
Short note: Trait diversification rates controlled by other traits 30 Oct 2010
A new twist on the approach 28 Oct 2010
Red Noise (aside exercise) 28 Oct 2010
Warning Signals -- Where are we now? 27 Oct 2010
Correcting for the mean dynamics 26 Oct 2010
Wrong picture, wrong model: why warning signals don't look like rare events 25 Oct 2010
Warning Signals 2 21 Oct 2010
Spatial Warning Signals, power, etc 21 Oct 2010
ecology Abstract 20 Oct 2010
Adaptive Dynamics Abstract 20 Oct 2010
Warning Signals 19 Oct 2010
Teaching 18 Oct 2010
Status update 15 Oct 2010
Writing continues 14 Oct 2010
Wednesday 13 Oct 2010
a day of writing 12 Oct 2010
Still writing 11 Oct 2010
LR Manuscript 05 Oct 2010
Monday 04 Oct 2010
Likelihood Ratio Paper 03 Oct 2010
Thursday 30 Sep 2010
Adaptive Dynamics Updates 30 Sep 2010
Writing 15 Sep 2010
Writing 14 Sep 2010
Power plots 14 Sep 2010
Peter meeting 13 Sep 2010
Meeting with Alan 10 Sep 2010
Lab Notebooks 07 Sep 2010
Meeting with Sam 07 Sep 2010
evolution Research Abstract 04 Sep 2010
Updating examples of stochastic structured population dynamics 02 Sep 2010
Entry title 01 Sep 2010
Tuesday 31 Aug 2010
Summer Review 30 Aug 2010
Adaptive Dynamics 30 Aug 2010
Likelihood ratio ToDo 27 Aug 2010
Likelihood Ratio Paper- Power in Trees 26 Aug 2010
Likelihood Ratio Manuscript 25 Aug 2010
Writing 19 Aug 2010
Entry title 19 Aug 2010
Warning Signals -- still in code development 18 Aug 2010
Warning Signals 17 Aug 2010
Warning Signals 16 Aug 2010
Warning Signals 15 Aug 2010
Adaptive Dynamics 13 Aug 2010
Warning Signals 12 Aug 2010
Adaptive Dynamics 12 Aug 2010
Adaptive Dynamics 11 Aug 2010
Warning Signals 10 Aug 2010
Likelihood ratio update 10 Aug 2010
Warning Signals by model choice 09 Aug 2010
Warning Signals 08 Aug 2010
Reading 07 Aug 2010
Batch Data 05 Aug 2010
Data Format functions 04 Aug 2010
Writing 03 Aug 2010
Open Science Summit Day 3 31 Jul 2010
Open Science Summit day 2 30 Jul 2010
Open Science Summit 29 Jul 2010
Cetartiodactyle data 28 Jul 2010
Parameter Estimates for Labrid-Parrotfish model 27 Jul 2010
Parrotfish Model choice 26 Jul 2010
Writing 23 Jul 2010
Writing 22 Jul 2010
Writing 21 Jul 2010
Writing 20 Jul 2010
Wainwright Meeting 19 Jul 2010
Parrotfish-Wrasse example 15 Jul 2010
Organizing analyses, data, codes 14 Jul 2010
Bootstrapping the independent alpha-sigma models 13 Jul 2010
Multivariate normal random variables 12 Jul 2010
Status - Thoughts 09 Jul 2010
Evolutionary Regime Shift examples 08 Jul 2010
Multitype OU process interfaces 07 Jul 2010
Ensemble simulations of beetle dynamics 07 Jul 2010
Generalizing the multi-type OU process- continued 02 Jul 2010
Multitype OU Processes with varying alpha and sigma 01 Jul 2010
iEvoBio day two 30 Jun 2010
iEvoBio day one 29 Jun 2010
Evolution 2010 Day 3 28 Jun 2010
Evolution 2010 Day 2 27 Jun 2010
Evolution 2010 26 Jun 2010
CSGF Conference Thursday 24 Jun 2010
CSGF Conference Day 2 23 Jun 2010
CSGF Conference- Tuesday 22 Jun 2010
CSGF Conference- HPC Workshop 21 Jun 2010
Wainwright Lab Meeting 16 Jun 2010
Questions 10 Jun 2010
Graham & Peter Meeting 09 Jun 2010
Making slides for Evolution meeting 08 Jun 2010
Implementing the new approach 06 Jun 2010
Likelihood Calculation 05 Jun 2010
Comparative Phylogenetics Talk 04 Jun 2010
Entry title 03 Jun 2010
Actually starting at Arkin Lab 02 Jun 2010
Gamma Waiting times on individual level 01 Jun 2010
CSGF Survey 31 May 2010
Individual based simulation with gamma waiting times 29 May 2010
Conference call w- Bob and Brett 28 May 2010
Summary of Structured Population noise so far 27 May 2010
Rethinking Beetles Noise 26 May 2010
Bug fixed! 25 May 2010
Status on Structured Populations 24 May 2010
Puzzled over the two-step jump process results 21 May 2010
Beetle dynamics exploration & adjustments 20 May 2010
Noisy Beetles 19 May 2010
Noisy beetles 18 May 2010
Annual Progress Report 17 May 2010
General matrix form and correcting equations 16 May 2010
Large Intrinsic Noise 15 May 2010
Structured Population Dynamics 14 May 2010
Beetles workshop Day 2 13 May 2010
Adaptive Dynamics 13 May 2010
Roi and Sam Comparative Phylogenetics R Workshop 12 May 2010
Hastings Beetle Workshop 12 May 2010
Peter Meeting 11 May 2010
Demographic Noise 11 May 2010
Alan Meeting 10 May 2010
Warning Signals with SDEs 09 May 2010
Likelihood calculation 07 May 2010
Goals 06 May 2010
Wednesday 05 May 2010
Primates 05 May 2010
Alan Meeting 04 May 2010
Adaptive Dynamics 04 May 2010
Adaptive Dynamics 03 May 2010
Phase1 01 May 2010
Coexistence Of The Early Dimorphism 01 May 2010
Adaptive Dynamics 30 Apr 2010
Adaptive Dynamics 29 Apr 2010
Meetings 28 Apr 2010
iEvoBio lightning talk 27 Apr 2010
Teaching 26 Apr 2010
Adaptive Dynamics 26 Apr 2010
Adaptive Dynamics 23 Apr 2010
Adaptive Dynamics 22 Apr 2010
Adaptive Dynamics 21 Apr 2010
Waiting Time 20 Apr 2010
R-sig-phylo 20 Apr 2010
Alan Meeting 20 Apr 2010
Research 19 Apr 2010
MATICCE 18 Apr 2010
iEvoBio Submission 16 Apr 2010
Branching Paper 15 Apr 2010
Wednesday 14 Apr 2010
Tuesday 13 Apr 2010
Teaching 13 Apr 2010
Teaching 12 Apr 2010
Primate chronogram 12 Apr 2010
Effective warning signals 11 Apr 2010
Research 09 Apr 2010
Research 08 Apr 2010
Comparative Phylogenetics Notebook 08 Apr 2010
Research 07 Apr 2010
Towards a meaningful warning signal metric 06 Apr 2010
Research 06 Apr 2010
Research 05 Apr 2010
Research 04 Apr 2010
Warning Signals Research 03 Apr 2010
Warning Signals 02 Apr 2010
Research 02 Apr 2010
Research 01 Apr 2010
Research 31 Mar 2010
Comparative Phylogenetics Notebook 31 Mar 2010
Research 30 Mar 2010
Still puzzling on LR 26 Mar 2010
Research 25 Mar 2010
Entry title 25 Mar 2010
Parallel R 24 Mar 2010
Bootstrapping Likelihood ratios 23 Mar 2010
Phylogenetic Tree formats 22 Mar 2010
Research 20 Mar 2010
Research 19 Mar 2010
Research 18 Mar 2010
Research 17 Mar 2010
Graham & Peter Meeting 16 Mar 2010
Computing 15 Mar 2010
Post-Workshop 14 Mar 2010
Bodega Workshop Presentations 12 Mar 2010
Phylogenetics Workshop Day 5 11 Mar 2010
Bodega Workshop Day 4 10 Mar 2010
Bodega Phylogenetics Workshop Day 3 09 Mar 2010
Bodega Phylogenetics Workshop Day 2 08 Mar 2010
Bodega Phylogenetics Workshop Day 1 07 Mar 2010
Meeting 05 Mar 2010
Friday 05 Mar 2010
Big Picture Comparative Phylogenetics 04 Mar 2010
Solution to the strange behavior in ouch 03 Mar 2010
Power in trees 02 Mar 2010
Teaching 01 Mar 2010
Parallel at last 01 Mar 2010
Parallelizing Code 28 Feb 2010
Friday 26 Feb 2010
Thursday 25 Feb 2010
The Ergodicity Question- Time averaging vs Ensemble averaging 25 Feb 2010
Derin And Alan Meeting 24 Feb 2010
Comparing to Analytic Dynamics 23 Feb 2010
Teaching 22 Feb 2010
Monday 22 Feb 2010
Implementing an example of low and high power trees 20 Feb 2010
Teaching 19 Feb 2010
Power in trees continues 19 Feb 2010
Power in Trees 18 Feb 2010
Meeting Goals 17 Feb 2010
Hastings Meeting 17 Feb 2010
Updating manuscript 16 Feb 2010
Parametric bootstrapping 15 Feb 2010
Implementing warning signals metrics 15 Feb 2010
Speciation 14 Feb 2010
Teaching 11 Feb 2010
Meeting w- Alan 10 Feb 2010
Follow-up on Parametric Bootstrapping 10 Feb 2010
Meeting with Graham and Peter 09 Feb 2010
Code Development for Exploring Regimes Shifts 09 Feb 2010
Updates to Code 08 Feb 2010
Exploring Difficulties with Existing Methods continued 08 Feb 2010
Exploring Difficulties with Existing Methods 07 Feb 2010
Lunch with Wainwright Lab 05 Feb 2010
Teaching 04 Feb 2010
Hastings Meeting 03 Feb 2010
The Lab Notebook Goes Open 02 Feb 2010
Teaching 25 Jan 2010
Progresschallenges 18 Jan 2010
CPB thesis proposal 10 Jan 2010