Carl Boettiger

Q: What Schools Are Affiliated With Carl Boettiger

Carl Boettiger is affiliated with the following schools: University of California, Berkeley, University of Wollongong, Princeton University, University of California, Davis, University of California, Santa Cruz

Carl Boettiger's AcademicInfluence.com Rankings

Carl Boettiger

Biology

#11008

World Rank

#14381

Historical Rank

Ecology

#639

World Rank

#699

Historical Rank

biology Degrees

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Biology

Carl Boettiger's Degrees

PhD Ecology University of California, Santa Cruz
Masters Environmental Studies University of California, Santa Cruz
Bachelors Biology University of California, Santa Cruz

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Carl Boettiger's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

An introduction to Docker for reproducible research (2014) (772)
MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN–UHLENBECK MODEL OF ADAPTIVE EVOLUTION (2012) (521)
IS YOUR PHYLOGENY INFORMATIVE? MEASURING THE POWER OF COMPARATIVE METHODS (2011) (220)
rfishbase: exploring, manipulating and visualizing FishBase data from R. (2012) (197)
Quantifying limits to detection of early warning for critical transitions (2012) (158)
Early warning signals: the charted and uncharted territories (2013) (144)
An introduction to Docker for reproducible research, with examples from the R environment (2014) (118)
Tipping points: From patterns to predictions (2013) (103)
Early warning signals and the prosecutor's fallacy (2012) (98)
Taxonomic Information from Around the Web (2015) (83)
Packaging Data Analytical Work Reproducibly Using R (and Friends) (2018) (83)
Making ecological models adequate. (2018) (82)
R Python, and Ruby clients for GBIF species occurrence data (2017) (76)
Skills and Knowledge for Data-Intensive Environmental Research (2017) (58)
Building Software, Building Community: Lessons from the rOpenSci Project (2014) (49)
An Introduction to Rocker: Docker Containers for R (2017) (45)
Optimal management of a stochastically varying population when policy adjustment is costly. (2015) (44)
From noise to knowledge: how randomness generates novel phenomena and reveals information. (2018) (43)
No early warning signals for stochastic transitions: insights from large deviation theory (2013) (37)
Is your phylogeny informative (2012) (35)
Rebuilding global fisheries under uncertainty (2019) (33)
Avoiding tipping points in fisheries management through Gaussian process dynamic programming (2014) (32)
Enforcing public data archiving policies in academic publishing: A study of ecology journals (2018) (32)
Software vs. data in the context of citation (2016) (30)
After the games are over: life‐history trade‐offs drive dispersal attenuation following range expansion (2016) (25)
The Shape, Multiplicity, and Evolution of Superclusters in ΛCDM Cosmology (2006) (24)
Adaptive management of ecological systems under partial observability (2018) (19)
Treebase: an R package for discovery, access and manipulation of online phylogenies (2012) (17)
ASCARIS LUMBRICOIDES FOUND IN THE CAVITY OF THE HUMAN HEART (1929) (15)
Revealing biases in the sampling of ecological interaction networks (2017) (12)
Algorithmic conservation in a changing climate (2021) (12)
Client for Various 'CrossRef' 'APIs' (2016) (11)
A Community of Practice Around Peer Review for Long-Term Research Software Sustainability (2019) (10)
PNEUMONIA AND SOME OF ITS COMPLICATIONS AT CAMP BOWIE (1919) (9)
taxadb: A high‐performance local taxonomic database interface (2020) (9)
Fluctuation domains in adaptive evolution. (2010) (8)
How to Read a Research Compendium (2018) (8)
Interface to the Search 'API' for 'PLoS' Journals (2015) (7)
Resolving the Measurement Uncertainty Paradox in Ecological Management (2018) (6)
The principles of tomorrow's university (2018) (6)
The forecast trap. (2022) (6)
Promoting equity in the use of algorithms for high-seas conservation (2021) (6)
Client for Various 'CrossRef' 'APIs' [R package rcrossref version 1.1.0] (2020) (6)
Grazer behavior can regulate large-scale patterning of community states (2019) (6)
Deep reinforcement learning for conservation decisions (2021) (5)
PRIMARY SUPPURATION OF LIVER DUE TO FRIEDLAENDER'S BACILLUS (1940) (5)
A Shiny r app to solve the problem of when to stop managing or surveying species under imperfect detection (2020) (5)
Social-ecological feedbacks drive tipping points in farming system diversification (2022) (4)
Bifurcation or state tipping: assessing transition type in a model trophic cascade (2020) (4)
Managing Larger Data on a GitHub Repository (2018) (4)
R Interface to 'FishBase' (2015) (4)
Generating CodeMeta Metadata for R Packages (2017) (4)
Teaching machines to anticipate catastrophes (2021) (4)
Interface to PLoS Journals search API (2014) (3)
A Community Convention for Ecological Forecasting: Output Files and Metadata (2021) (3)
Case Study 3: A Reproducible R Notebook Using Docker (2019) (3)
Ecological Metadata as Linked Data (2019) (3)
Demographic Noise (2008) (2)
Semantic Citations For The Notebook And Knitr (2013) (2)
What I look for in 'Software Papers' (2013) (2)
RNeXML: a package for reading and writing richly annotated phylogenetic, character and trait data in r (2015) (2)
Citations for 'Knitr' Markdown Files (2015) (2)
Implementing the new approach (2010) (2)
Limits to ecological forecasting: Estimating uncertainty for critical transitions with deep learning (2022) (2)
Ecological management of stochastic systems with long transients (2020) (2)
Comparing numerical methods (2012) (1)
Priorities for synthesis research in ecology and environmental science (2023) (1)
Power and accountability in reinforcement learning applications to environmental policy (2022) (1)
Active adaptive management solutions: Belief SDP (2012) (1)
Welcome to my Lab Notebook - Reloaded (2012) (1)
Open Science Summit (2010) (1)
Article Formats for R Markdown (2016) (1)
an R interface to figshare.com (2014) (1)
Reviewing Software Revisited (2013) (1)
ropensci/arkdb: arkdb: Archive and Unarchive Databases Using Flat Files (2018) (1)
Promoting equity in scientific recommendations for high seas governance (2021) (1)
rocker/geospatial: a flexible runtime environment for geoscientific data analysis (2018) (1)
Citing Lab Notebook Entries (2012) (1)
R Interface to the DataONE REST API [R package dataone version 2.2.1] (2020) (1)
Citing R packages (2012) (1)
Stochastic limits to evolutionary branching (2010) (1)
The NEON Ecological Forecasting Challenge (2023) (1)
Basic regression in Gaussian processes (2012) (1)
Plos Data Sharing Policy Reflections (2014) (1)
TreeBASE in R: a first tutorial (2011) (0)
Comparative methods paper status/to-do (2011) (0)
Labrids & Parrotfish, method1 (2011) (0)
Migrating Oww Posts To Jekyll (2012) (0)
Figure For Summarizing Simulations (2013) (0)
mcmc and bootstrapped likelihood runs on parrotfish tree (2011) (0)
Different ways of visualizing distribution overlap (2012) (0)
The Case for Better Data Citation Practices (2011) (0)
Likelihood expressions for branching processes (2011) (0)
Policy functions and value functions under multiple uncertainty (2012) (0)
Warning Signals 2 (2010) (0)
Data to Knowledge Day II and other notes (2012) (0)
manuscript reviews on github (2013) (0)
Sdp Reed Controls Comparisons (2015) (0)
Warning signals - noise response (2011) (0)
Gamma Waiting times on individual level (2010) (0)
Segue: Easy cloud hpc in R, now with custom packages (2011) (0)
Thursday Meetings: Duncan; Alan (2011) (0)
Monday: ESA, appendix, etc (2011) (0)
Further Examples Managing Tipping Points With Gp (2013) (0)
Evolution Day 4 / #ievobio Day 1 (2011) (0)
Coexistence Of The Early Dimorphism (2010) (0)
Prosecutor's fallacy notes (2012) (0)
Evolutionary Regime Shift examples (2010) (0)
Thursday: Post-predictive verification exploration; writing and figures (2010) (0)
My Prosecutor's Fallacy paper and other recent warning signals literature (2012) (0)
General matrix form and correcting equations (2010) (0)
Multiple Uncertainty Corrections (2012) (0)
Phylogenetics Workshop Day 5 (2010) (0)
Peter's talk (2011) (0)
Access for Dryad Web Services [R package rdryad version 1.0.0] (2020) (0)
Isees Day 2 (2013) (0)
pdg-control Conference Call (2011) (0)
Multiple Uncertainty Notes (2014) (0)
rfishbase Tutorial - updated & extended (2011) (0)
Tuesday: Visit to Berkeley (2011) (0)
Some reproducible research practices in journals (2011) (0)
Parallel hpc on clusters in R, MPI (2011) (0)
Resilience seminar course plan (2012) (0)
Tweets from an Ecology Field class (2010) (0)
rOpenSci- Open Tools to Facilitate Data Driven Science in Ecology and Evolution (2013) (0)
Back to Writing (2010) (0)
more Phylogenetic signal metrics & Brownie comparison (2011) (0)
Beetles workshop Day 2 (2010) (0)
Likelihood ratio ToDo (2010) (0)
Friday: Evolution reading, writing (2010) (0)
Analytic Marginalizing For Posteriors (2013) (0)
Steve Ellner's seminar (2011) (0)
Solution to the strange behavior in ouch (2010) (0)
Evolution Conference Day 1 (2011) (0)
Graham & Peter Meeting (2010) (0)
Leveraging private lands to meet 2030 biodiversity targets in the United States (2023) (0)
Draft Wssspe Thoughts (2014) (0)
ews-review: Published version (2015) (0)
Measurement uncertainty matters: ecological management using POMDPs (2016) (0)
Visit To Whoi (2013) (0)
Too Much Fun With Docker (2014) (0)
Saturday - back to Warning Signals MS (2011) (0)
Monday - wrightscape meetings, PDG meeting (2011) (0)
Tues: ESA presentation (2011) (0)
wrightscape and sensitivity to initial conditions (2011) (0)
Brian O'Meara discusses new algorithms approaches on Phylo (2011) (0)
Bodega evolution Workshop: Continuous Characters R session planning (2011) (0)
Tuesday: pmc package, latex to word attempts (2012) (0)
Thursday, Fisheries course (2011) (0)
Friday: more labrid & parrotfish wrightscape examples (2011) (0)
Data Mangement on UC3 Merritt Repository (2011) (0)
Warning signals vs model choice (2011) (0)
Colored noise: some classic results in ecology (2011) (0)
Sunday: Appendix edits (2011) (0)
Organizing analyses, data, codes (2010) (0)
Tuesday: Reading and thoughts (2011) (0)
Elegant & fast data manipulation with data.table (2012) (0)
Mapping out SICB Presentation: Is your phylogeny informative? (2010) (0)
Reading Notes, presentation prep treebase error handling (2011) (0)
evolution manuscript revisions (2011) (0)
Gp Nimble Setup (2015) (0)
Wednesday - Berkeley visits (2011) (0)
Forage Fish course plan (2012) (0)
Monday -- Edits and organization (2011) (0)
pdg-control, Training Problem 2 update to group (2012) (0)
Warning Signals, Monday (2011) (0)
Challenges with Collaboration in Open Science (2011) (0)
Warning Signals writing, organization, appendices (2011) (0)
Further examples for appendices (2012) (0)
pdg-control pdg-control, Tuesday (2011) (0)
A Clever Derivation On Realized Escape Times (2013) (0)
The Lab Notebook Goes Open (2010) (0)
Regime shifts in ecology and evolution (2012) (0)
Model identifiability in phylogenetic inference GTR+I+G (2011) (0)
Robust control & uncertainty - reading notes (2012) (0)
Wednesday: ESA presentation, manuscript/appendix edits (2011) (0)
Roi and Sam Comparative Phylogenetics R Workshop (2010) (0)
Ews Review Paper Chat (2013) (0)
Rnexml Metadata Queries (2013) (0)
Thursday finishing up appendices( (2011) (0)
Nonparametric Bayes Notes (2012) (0)
Do we need a culture of Data Science in Academia (2013) (0)
Sensitivity Of Gp Comparisons In Further Examples (2013) (0)
Thursday: submitting warning signals manuscript (2011) (0)
Steps To A More Portable Workflow (2014) (0)
Showcasing the latest phylogenetic methods: AUTEUR (2011) (0)
server file management from bowser: ajaxplorer, mollify (2011) (0)
Server Security Basics (2014) (0)
Comparative evolution: Is the data informative? (2010) (0)
Parrotfish in wrightscape (2011) (0)
My experiment with open science: Why the benefits of sharing go beyond source code (2010) (0)
Discovery, Access and Manipulation of 'TreeBASE' Phylogenies (2015) (0)
Release of constraint in labrids (2011) (0)
Crashing stocks and optimal harvesting effort on Allee effects (2011) (0)
Notes of the Week (1921) (0)
knitr, github, and a new phase for the lab notebook (2012) (0)
Esa 2013 Notes For Week (2013) (0)
Evolution Day 3 (2011) (0)
Evolution and iEvobio conference notes (2012) (0)
We Need More Object Oriented Design In Comparative Methods (2013) (0)
Ensemble Behavior from Individual Dynamics in Multispecies Forest Populations (2013) (0)
Mathematical Elements of Attack Risk Analysis for Mountain Pine tribolium (2011) (0)
Mendeley API in R (2011) (0)
Prosecutor Fallacy As Large Deviations (2013) (0)
Tutorial On Likelihood And Roc Methods For Early Warning Signals (2013) (0)
Tues: Sources of stochastic variation in optimal control (2011) (0)
Citations in markdown using knitr (2012) (0)
Wainwright Retreat to Hastings Reserve (2011) (0)
Finishing Comparison Parametric And Nonparametric (2013) (0)
Notes For Van Noorden Chat (2013) (0)
Adaptive Dynamics Updates (2010) (0)
Treebase Package On Cran (2011) (0)
OU model in Nimble (2014) (0)
Monday, appendices continue... (2011) (0)
Multitype OU Processes with varying alpha and sigma (2010) (0)
Saturday: git with latexdiff, TreeBASE and PMC package updates, bounds on lambda (2011) (0)
Steve Pacala - Storer lecture (2011) (0)
Optimal policy with assymetric costs to changing harvest quotas (2012) (0)
ESA 2011 Abstract: Limits to Detection of Early Warning Signals (2011) (0)
Near‐term forecasts of NEON lakes reveal gradients of environmental predictability across the US (2023) (0)
Monday: scaling wrightscape examples (2011) (0)
Scientific Computing Notes (2014) (0)
McElreath: A Bayesian approach to hierarchical modeling, using R to build our own estimator from scratch (2011) (0)
Warning signals & hpc (2011) (0)
the week so far (2012) (0)
Semantic Lab Notebook (2012) (0)
Pdg Controlfest Notes (2014) (0)
Automated feeds in notebook entries (2012) (0)
Bayesian Gp Regression By Metropolis Hastings (2013) (0)
Nimble On Dai Model (2015) (0)
Docker And User Permissions Crazyness (2014) (0)
socialR: Reproducible Research & Notebook integration with R (2010) (0)
Tuesday: Parrotfish results, MCMCMC testing, APIs (2011) (0)
Using knitr and RWordPress to publish results directly from R (2012) (0)
Warning Signals on Real data continued (2011) (0)
Dockerizing Fishbase Api (2015) (0)
Gp Nimble V2 (2015) (0)
Policy Costs Work (2012) (0)
early results in nonparametric-bayes approaches to optimal policy (2012) (0)
Monday: openfisheries & ggplot (2011) (0)
Algorithms Group: Literate programming (2011) (0)
Further exploration of RAM Legacy Stock Assessment data (2015) (0)
A general model of continuous character evolution (2011) (0)
Results Comparing Gp To Parametric (2012) (0)
Likelihood ratio update (2010) (0)
Friday, wordpress backups, pmc edits (2011) (0)
Matt Potts: Conserving Diversity in Tropical Landscapes (2011) (0)
Shape as well as size influence power of phylogeny (2011) (0)
Cran And Package Dependencies (2014) (0)
Tuesday: rropensci, Rmpi, manuscripts, ... (2011) (0)
The Ergodicity Question- Time averaging vs Ensemble averaging (2010) (0)
TreePar: changing rates of evolution (2011) (0)
pdg-control pdg-control: Wednesday (2011) (0)
Adaptive Dynamics: Branching Phenomena and the Canonical Equation (2007) (0)
Evolution Day 2 (2011) (0)
Lsn Model Comparisons (2015) (0)
Friday, more runs (2011) (0)
Warning Signals by model choice (2010) (0)
Coreos Cluster Gotchas (2014) (0)
Notes On Leveraging The Ecological Markup Language (2013) (0)
Friday: ropensci, manuscript edits (2011) (0)
Mbi Day Five Notes (2013) (0)
Mbi Day Three (2013) (0)
Computing the value of information in management of a stochastic resource (2012) (0)
Nceas Workflows Day3 (2014) (0)
Data Format functions (2010) (0)
Still puzzling on LR (2010) (0)
Notebook tweaks: APIs in Ruby, Github hosting (2013) (0)
141 scientists can't be wrong? (2011) (0)
Tools to Manipulate and Query Semantic Data [R package rdflib version 0.2.3] (2020) (0)
Gitlab And Other Configuration Notes (2014) (0)
Monday: Warning Signals - Updated graphs (2011) (0)
Question-and-Answer-post on my use of Docker in research (2015) (0)
Warning Signals: Comparing Methods on Climate Data (2011) (0)
iEvoBio lightning talk (2010) (0)
Sam's Practice talk (2011) (0)
Semantic Markup Examples For The Lab Notebook (2012) (0)
Thursday, Friday, Saturday (2012) (0)
Practice SICB Presentation (2010) (0)
R interface for fisheries data (2014) (0)
Stochastic Optimal Control (2011) (0)
Monday: submodels for full traits (2011) (0)
Response To Software Discovery Index Report (2014) (0)
Nonparametric Bayes Summary Ideas (2013) (0)
ESA personal notes: people, goals (2011) (0)
Reading and potential examples for talk to ERE next week (2013) (0)
Meeting with Alan (2010) (0)
rrdf: Release 2.2.1 (2015) (0)
adaptive-dynamics Simulations (2010) (0)
Warning Signals -- still in code development (2010) (0)
Saturday: projects, reading, markdown notebook-technology (2012) (0)
Monday: Warning Signals Manuscript (2011) (0)
Gaussian process inference on sample functions (2012) (0)
Friday's reading (2011) (0)
Figures 3 And 4 For Policycosts (2012) (0)
Tuesday notes: package work mostly. (2011) (0)
Optimal control -- costs to policy shifts (2011) (0)
Bootstrapping the independent alpha-sigma models (2010) (0)
Lab Notebook, 2010 (2012) (0)
varying recruitment function, noise form, and harvesting cost (2012) (0)
Are open lab notebooks considered prior publication (2012) (0)
Open F1000 reviews (2011) (0)
Coreos And Other Infrastructure Notes (2014) (0)
Prep for ERE talk (2013) (0)
Tuesday -- two insights (2011) (0)
Xml Parsing Strategies (2013) (0)
Data to Knowledge Day 1 (2012) (0)
Warning Signals Research (2010) (0)
rrdf: Release 2.1.2 (2015) (0)
Formal Semantics With Reml (2013) (0)
Limits to the detection of early warning signals of population collapse (2012) (0)
Stochastic Dynamic Programming With Gaussian Process Approx (2012) (0)
Ecological Metadata as Linked Data [R package emld version 0.5.1] (2020) (0)
Implementing warning signals metrics (2010) (0)
Real World Challenges In Reproducible Research Code (2014) (0)
Collected notes from past few days (2013) (0)
Weds & Framing warning signals manuscript (2011) (0)
Alex Pfaff seminar, meeting (2012) (0)
Wednesday - various logistics, then checking likelihood calculation (2011) (0)
Article Formats for R Markdown [R package rticles version 0.17] (2020) (0)
Optimal Control examples continued: Bellman, Dynamic Programming (2011) (0)
Revisions on Prosecutors Fallacy (2012) (0)
cboettig/pmc: PMC v1.0.2 released to CRAN (2017) (0)
follow up from Fri discussions: Revisiting post-predictive evaluation (2010) (0)
Updates On Managing References (2013) (0)
Create Lightweight Schema.org Descriptions of Data [R package dataspice version 1.0.0] (2020) (0)
NEON Data Store [R package neonstore version 0.3.3] (2020) (0)
pdg-control Training Problem II update (2012) (0)
Exploring Jekyll layout (2012) (0)
Relevant initiatives from today's Big Data press release (2012) (0)
Bifurcation or state tipping: assessing transition type in a model trophic cascade (2019) (0)
DataCite Day 1 (2011) (0)
Empirical Demonstration Of That Clever Derivation (2013) (0)
Reflecting on five years of the open lab notebook (2015) (0)
Training Problem 2 update (2011) (0)
Tuesday: active adaptive management, a first solution (2012) (0)
Tgp Mcmc For Gaussian Processes (2012) (0)
Tuesday - Evolution/wrightscape talk & sundry (2011) (0)
'Programmatic Interface to the 'openfisheries.org' API' (2016) (0)
Tuesday - Berkeley visits (2011) (0)
Docker Machine Notes (2015) (0)
Notebook features: reproducible code (2013) (0)
Scholarly Infrastructure Thoughts (2013) (0)
DoE renewal and a year in review (2010) (0)
Migrating From Wordpress To Jekyll (2012) (0)
Whitehouse Open Data Memorandum (2013) (0)
Thursday: Warning Signals (2011) (0)
More labrid plots (2011) (0)
Monday: some code-tricks, Algorithms group planning (2011) (0)
Journey to freedom - a code's tale of open source license migration (2012) (0)
Some Notes on Open Notebooks, Open peer review practices. (2011) (0)
Exit Seminar to Center for Population Biology: Regime Shifts in Ecology and Evolution (2012) (0)
To podcast or not to podcast university lectures (2011) (0)
Friday: writing post-doc applications (2011) (0)
Notes of the Week (1921) (0)
Power in trees continues (2010) (0)
Thursday: Warning Signals writing, figures, segue (2011) (0)
Notebook Design Notes (2014) (0)
The Evolutionary Seesaw: Origins of biodiversity? (2012) (0)
Algorithms group: MCMCMC (2011) (0)
Exploring Difficulties with Existing Methods continued (2010) (0)
pdg-control PDG group, Tasks (2011) (0)
Warning signals: summary statistic performance at varying sampling effort (2011) (0)
Warning Signals in Ecological Systems: Revisions and Drake & Griffen Data (2011) (0)
Bodega Workshop Day 4 (2010) (0)
Generalizing the multi-type OU process- continued (2010) (0)
Two routes to adaptive branching (2011) (0)
Monday: Writing, Mendeley groups, Notebook plugin tweaks (2011) (0)
Monday: ESA Conference (2011) (0)
R Client for the Lagotto Altmetrics Platform (2015) (0)
The promise of U.S. private lands for reaching 21st century conservation targets (2021) (0)
Notebook features: digital archiving (2013) (0)
Robert Hijmans on Models to predict sp response to climate change (2011) (0)
Exploring Approximate Dynamic Programming Approaches (2013) (0)
Containerizing My Development Environment (2014) (0)
Tuesday, simulations & appendix (2011) (0)
Phylo Monte Carlo for diversification rates (2011) (0)
Sunday: scaling, runs (2011) (0)
Wainwright Lab Meeting (2010) (0)
ropensci/rdflib: v0.2.3 (2020) (0)
Nimble Model Construction (2015) (0)
Thoughts on the New Policies for Data Archiving at NSF and in Common Journals (2010) (0)
Weds: Final round edits (2011) (0)
Tues: Research, seminar (managing for resilience), talk (future of libraries), etc... (2012) (0)
Data Uris For Image Archives (2013) (0)
Misc Notes On Cloud Providers (2015) (0)
Software Sustainability Issues In R (2014) (0)
Warning Signals, Power and Sufficient Statistics (2011) (0)
After the games are over: decay of the Olympic Village effect following invasion implies a trade-off between dispersal and fitness (2015) (0)
TreeBASE interface continued... (2011) (0)
Archive and Unarchive Databases Using Flat Files [R package arkdb version 0.0.12] (2021) (0)
Multivariate normal random variables (2010) (0)
Meeting with Graham and Peter (2010) (0)
Effective warning signals (2010) (0)
Implementing an example of low and high power trees (2010) (0)
nonparametric-bayes: v0.2.0 (2014) (0)
Reflections from #scio11: Saturday's Open Science Track (2011) (0)
Forking The R Journal (2013) (0)
Monday Treebase Manuscript Writing (2012) (0)
Thursday: sending off paper draft, starting applications (2011) (0)
Meeting with Sam (2010) (0)
Parametric Bayesian Example (2013) (0)
Starting An Eml Package For R (2013) (0)
iEvoBio day two (2010) (0)
Lab Notebook, 2012 (2013) (0)
Writing reproducibly in the open with knitr (2012) (0)
Dryad API interface (2013) (0)
Wednesday: Simulated model fit analysis on wrightscape, parrotfish tree (2011) (0)
Further treatment of the limiting models (2010) (0)
Stability analysis on fished and unfished dynamics. (2012) (0)
SDP solution for allee model (2011) (0)
Red Noise (aside exercise) (2010) (0)
Daniel Gp Example (2015) (0)
Notes on value of information runs with uniform noise (2012) (0)
Sunday: Warning signals edits continue (2011) (0)
Wednesday: migrating codes into MPI (2011) (0)
wrightscape / release of constraint (2012) (0)
Note On Notebook Figures (2012) (0)
Big Picture Comparative Phylogenetics (2010) (0)
Isees Training Workshop Day 1 (2013) (0)
Workflows Working Group Day 1 (2014) (0)
Exploring Gp Model Space (2012) (0)
Scratch Notes While Outlining Talk (2014) (0)
Comparative Phylogenetics Notebook (2010) (0)
Ropensci Unconf Teaching Session (2015) (0)
Sunday: a few Treebase R package updates (2011) (0)
A few large data problems in Ecology & Evolution (2011) (0)
Coreos Docker Registries Etc (2014) (0)
F1000-Research publishing for ecologists (2013) (0)
Short note: Trait diversification rates controlled by other traits (2010) (0)
Multiple uncertainty corrected (2012) (0)
Tuesday: Figures, figures, figures (2011) (0)
CPB thesis proposal (2010) (0)
Towards a meaningful warning signal metric (2010) (0)
Pdg Control Updates (2012) (0)
a day of writing (2010) (0)
Nonparametric Bayes Comparisons (2012) (0)
CSGF Conference Thursday (2010) (0)
TreeBase: exploratory exercises in database-driven phylogenetics (2011) (0)
Policy costs to changing mangement, TP 1b: Apples to Apples (2012) (0)
Actually starting at Arkin Lab (2010) (0)
Jordan's bigdata talk in Math/Stats series (2012) (0)
Additional sources of noise (Sethi 2005) (2012) (0)
Intro Ecology Lecture at University of the Pacific (2011) (0)
ESA 2012 Abstract (2012) (0)
Synthesizing forecasts to inform decision‐making and advance ecological theory (2023) (0)
Parameter uncertainty in stochastic control problems (2012) (0)
Title Early warning signals : The charted and uncharted territories Permalink (2013) (0)
memory management, cron (2011) (0)
My research workflow, based on Github (2012) (0)
Challenges in estimating phylogenetic signal (2010) (0)
evolution Research Abstract (2010) (0)
Algorithms Discussion Group: algorithms Continued (2011) (0)
UPS and data vs optimal control (2014) (0)
A High-Performance Local Taxonomic Database Interface [R package taxadb version 0.1.0] (2020) (0)
From Theory to Application: Addressing Outstanding Challenges to Operationalizing Resilience (2018) (0)
Data to Knowledge Conference, UC Berkeley: application (2012) (0)
Semi Analytic Posteriors (2013) (0)
Self Destroy Droplet On Completion (2014) (0)
Lunch with Wainwright Lab (2010) (0)
Notes during revisions on phylogenetics manuscript (2011) (0)
UC Davis graduate student symposium proposal (2012) (0)
Handling other sources of noise (2011) (0)
Extending ape::phylo class to NeXML: (2013) (0)
Estimating phylogenetic signal (lambda) on large trees (2011) (0)
Lsn Model Considerations (2015) (0)
Notes of the Week (1921) (0)
Popbio Core Review Notes (2008) (0)
Notes from chat with Duncan (2013) (0)
Implementing Likelihoods for quadratic models (2010) (0)
Power in trees (2010) (0)
An R Interface to 'figshare' (2015) (0)
Monday and some phylogenetics (2010) (0)
Updating examples of stochastic structured population dynamics (2010) (0)
Discrete Grid Notes (2014) (0)
Summarizing Earlier Warning Signal Under Control Notes (2013) (0)
Parrotfish Model choice (2010) (0)
Training problem 2: the economist's problem statement (2011) (0)
Training Problem II (2011) (0)
Open Science Post Doc (2015) (0)
Wednesday: appendices; parameter distributions (2011) (0)
Numerical challenges in likelihood estimation of time-dep OU models (2011) (0)
Conference call w- Bob and Brett (2010) (0)
Optimal control sample problems (Mostly continuous time by Pontryagin principle) (2011) (0)
Rnexml Semantic Considerations (2013) (0)
Docker tricks of the trade and best practices thoughts (2014) (0)
Thurs: evolution likelihood (2010) (0)
Exploring Power in Warning Signals (2010) (0)
Value of information, cost of bias (2012) (0)
Code Development for Exploring Regimes Shifts (2010) (0)
Notebook Features: parsing linked data in the semantic notebook (2013) (0)
Wednesday - forage fish & cascades (2011) (0)
Monday, misc notes (2011) (0)
Gp Nimble Explore (2015) (0)
ievobio Day 2 (2011) (0)
Friday - updated wrightscape results - simulated examples (2011) (0)
Warning Signals examples and tracking graphs (2011) (0)
Warning signals of differing stregths by likelihood and by indicator (2011) (0)
ISEES software lifecycle and components workshop, Day 1 (2013) (0)
Multitype OU process interfaces (2010) (0)
Friday: some random notes (2012) (0)
Thurs: writing section on comparing to AIC (2010) (0)
CSGF Conference Day 2 (2010) (0)
End of NCEAS & the legacy of synthetic data (2011) (0)
Startup Culture And Platforms For The Academy (2014) (0)
Lazy Evaluation Thoughts (2015) (0)
Tues: evolution thoughts while writing... (2010) (0)
Bodega Phylogenetics Workshop Day 3 (2010) (0)
Avoiding tipping points in the management of ecological systems: a non-parametric Bayesian approach (2013) (0)
Weds: Parrotfish data set analysis (2011) (0)
Warning Signals -- Where are we now? (2010) (0)
Thursday: parrotfish analysis (2011) (0)
Early warning signals: the charted and uncharted territories (2013) (0)
Infering Partially Observable Markov Processes with Iterative Particle Filtering (2012) (0)
Saturday: working on computational scaling, ion, etc (2011) (0)
treeBASE R interface: proposal for #iEvoBio (2011) (0)
Bayesian Parametric Uncertainty Sdp (2013) (0)
CPB : David Collar (2010) (0)
Finishing up my #SICB Presentation (2011) (0)
Exploring Difficulties with Existing Methods (2010) (0)
Sunday: Warning Signals (2011) (0)
Warning Signals on Real Data (2011) (0)
Ensemble simulations of beetle dynamics (2010) (0)
An rfigshare tutorial (2012) (0)
RDF Library Bindings in R [R package redland version 1.0.17-14] (2020) (0)
Robust information from phylogenetic trees (2010) (0)
Is it time to retire Pagel's lambda? (2013) (0)
Wrong picture, wrong model: why warning signals don't look like rare events (2010) (0)
Tuesday: manuscript and appendix edits (2011) (0)
Sckott/Gbifms: Gbif Ms Preprint (2017) (0)
Analytic Solution To Multiple Uncertainty (2012) (0)
Early Warning Signals in Coral Dynamics -- Economic analysis of risk (2011) (0)
Simpler Nimble Dai Model (2015) (0)
Sckott/Gbifms Preprint (2017) (0)
Some Collaborative Tools for Science (2012) (0)
Interfaces for databases: TreeBASE, Dryad, DataONE (2011) (0)
Monday - Sweave workflow (2012) (0)
Writing, Cloud Computing, and #scio11 (2010) (0)
a drat repository for rOpenSci (draft for ropensci blog) (2015) (0)
Approximate Bayesian Computing (algorithms) methods (2011) (0)
RNeXML v2.0.0 (2014) (0)
Gpdd And Kalman Exploration Continued (2015) (0)
Reflections on the Mozilla Science Code Review Pilot (2013) (0)
Sat: evolution -- porting tree transformations to OUCH? (2010) (0)
discriminating early bursts (2011) (0)
Notebook Maintenance And Scaling (2015) (0)
Data Management Workshop at UC Davis Center for Population Biology: Video archive (2011) (0)
Accessing phylognenies in TreeBASE from R (2011) (0)
Comparative Phylogenetics Talk (2010) (0)
prosecutor's fallacy initial look (2012) (0)
Summary of Structured Population noise so far (2010) (0)
Notes On Tricks In Manuscript Submission And Collaboration (2014) (0)
Status on Structured Populations (2010) (0)
Puzzled over the two-step jump process results (2010) (0)
Sunday -- warning signals manuscript (mostly) (2011) (0)
Making slides for Evolution meeting (2010) (0)
A comparison of nonparametric Bayesian Gaussian process estimates to standard the parametric Bayesian approach (2013) (0)
Semantically Rich I/O for the 'NeXML' Format (2015) (0)
Thursday: Fun with databases continued (2011) (0)
Download and Parse Github Issues (2015) (0)
Thoughts On Harte Interview (2014) (0)
Matt Helmus visit (2011) (0)
Bodega evolution Tutorial: behind the scenes difficulties in R packages (2011) (0)
Tuesday: Warning Signals Data Wrangling (2011) (0)
Theoretical Limits to Forecasting in Ecological Systems (And What to Do About It) (2019) (0)
Loo Botsford, CPB seminar (2011) (0)
Integrating Github Project Repos Into The Notebook (2014) (0)
Ievobio Lightning Talk Proposal (2012) (0)
Correcting for the mean dynamics (2010) (0)
Algorithms group: Hidden Markov Models (2011) (0)
Progress this week, by project (2012) (0)
Mbi Day Two (2013) (0)
Structured Population Dynamics (2010) (0)
Ram Legacy Database Explore (2015) (0)
Phylogenetic Signal metrics (2011) (0)
Lessons Learned In Writing Dockerfiles (2014) (0)
getting signal from autocorrelation (2012) (0)
Individual based simulation with gamma waiting times (2010) (0)
Gpdp Via Mdptoolbox Cont (2015) (0)
Read and Write Ecological Metadata Language Files [R package EML version 2.0.4] (2020) (0)
some configuration notes: RStudio setup, syntax highlighting in sweave (2011) (0)
Spatial Warning Signals, power, etc (2010) (0)
Notes on Bokma 2010: evolution in drifts and jumps (2011) (0)
packrat and rmarkdown (2014) (0)
RDF Library Bindings in R (2016) (0)
Comparing to Analytic Dynamics (2010) (0)
Deep challenges to dynamic documentation in daily workflows (2014) (0)
CSGF 2010 Computing Practices Survey Summary (2011) (0)
Mdptoolbox Allen Model (2015) (0)
Warning signals manuscript (2010) (0)
Esa Changes Arxiv Policy Following Community Comments (2012) (0)
Meeting w- Alan (2010) (0)
Why ONS? From a discussion with friends (2011) (0)
Tipping Points Comment In Nature (2013) (0)
Isees Workforce Development Day 2 (2013) (0)
Notebook features: an introduction (2013) (0)
Warning signals: Indicators vs Likelihood continued (2011) (0)
Automated Knitr In Jekyll (2015) (0)
Tuesday - SDEs then back to phylogenetics (2010) (0)
Friday: wrightscape, ggplot, wp memory (2011) (0)
Van Kampen Expansion and Stochastic population dynamics (2011) (0)
Exact Simulation by the Gillespie Algorithm (2011) (0)
Pretty Darn Good Control Working Group (2011) (0)
Early warning signals presentation notes (2011) (0)
A new phylogenetic comparative method: detecting niches and transitions with continuous characters (2010) (0)
Tues: Fitting the limiting OU models to each bifurcation (2010) (0)
Difficulties with tgp; taking custom mcmc approach for GPs (2013) (0)
Building a semantic notebook (2011) (0)
Better Tagging Practices (2012) (0)
A new twist on the approach (2010) (0)
Sunday - manuscript and simulations (2011) (0)
Haldanes Sieve Guest Post (2013) (0)
Multiple Uncertainty Value Function Iteration (2012) (0)
Reviews, organization, rewrites (2010) (0)
DIMACS Workshop on Global Change (2014) (0)
Wrightscape: a brief tutorial (2011) (0)
Writing: Warning Signals Mansucript (2011) (0)
Open Science Summit Day 3 (2010) (0)
CSGF Conference- HPC Workshop (2010) (0)
Reproducible research environments with Docker (2014) (0)
Testing out a Jekyll-based notebook (2012) (0)
Friday, warning signals writing, etc (2011) (0)
Monday: Algorithms Discussion Group, EM finished (2011) (0)
Wrightscape labrid/parrotfish results; Evolution pres (2011) (0)
Delayed Release Archives (2013) (0)
rropensci and some taxonomy in R with taxize (2011) (0)
An Interface for Content-Based Identifiers [R package contentid version 0.0.9] (2021) (0)
Welcome to my Lab Notebook (2010) (0)
Auteur plots for reef fish jaws and monkey brains -- needs tweaking (2011) (0)
Generate 'CodeMeta' Metadata for R Packages [R package codemetar version 0.1.9] (2020) (0)
finer sampling in prosecutor's fallacy (2012) (0)
Getting the details right on the Fourier Transform approach to likelihood (2010) (0)
Open Notebook Science Abstract (2010) (0)
Rethinking Beetles Noise (2010) (0)
Phylogenetic Monte Carlo for the Laser package (2011) (0)
Review Of Progress On Packages (2014) (0)
Santa Cruz Postdoc (2012) (0)
Deviations from S = D (2012) (0)
Hastings Beetle Workshop (2010) (0)
Thursday: reviewing edits, ropensci, computers. (2011) (0)
Tuesday: phylogenetics- wrightscape coding (2011) (0)
[Rp] Fluctuation domains in adaptive evolution (2020) (0)
FishBASE from R: some XML parsing (2011) (0)
Follow-up on Parametric Bootstrapping (2010) (0)
Nonparametric Bayes Wrapping Up Sensitivity (2013) (0)
Updates to Code (2010) (0)
Thursday - some parrotfish & labrid runs on method2 (2011) (0)
Citation tools & Future of Publishing (2011) (0)
Academic Year 2011 Summary (2011) (0)
Phylogenetics - Research Proposal (2011) (0)
Knitr with flickr and wordpress (2012) (0)
Esa 2012 Conference (2012) (0)
Adaptive Dynamics Abstract (2010) (0)
Fisheries stock assessments for early warning (2011) (0)
Mdptoolbox Ex 2 (2015) (0)
The Future of Data: Plans for a UC Davis workshop (2011) (0)
Monday: Evolution manuscript revisions; early burst models, etc (2011) (0)
pdg-control Day 1 goals by training problem (2012) (0)
Archiving the lab notebook on figshare (2013) (0)
Site configuration: file sharing notes (2011) (0)
Sun: Visualizing my coding over the past year (2010) (0)
Nsf Math Bio Postdoc (2013) (0)
Wednesday: Data wrangling into graphs (2011) (0)
Likelihood Ratio Manuscript (2010) (0)
Bodega Workshop Presentations (2010) (0)
iEvoBio day one (2010) (0)
DataCite Day 2 (2011) (0)
Beetle dynamics exploration & adjustments (2010) (0)
Warning signals: summary stats vs likelihood on real and simulated data (2011) (0)
Parameter exploration in adaptive dynamics branching (2010) (0)
Lab Notebook, 2008 (2015) (0)
Using TreeBASE from R (2012) (0)
Dear DockerHub users: please configure your repository links (2014) (0)
Reading the Secrets of Biological Fluctuations (2010) (0)
CSGF Conference Notes (2011) (0)
Thursday: writing; some latexdiff notes (2012) (0)
UC Davis Student Assembled Panel on Data Management Issues (2011) (0)
Is statistical software harmful (2014) (0)
Github Issues Tracker: The Perfect Research Todo List (2012) (0)
Project tracking (Ecology) (2012) (0)
Better dynamic documents (Sweave) with syntax highlighting, caching, etc (2011) (0)
Warning Signals writing (2011) (0)
Large Intrinsic Noise (2010) (0)
Derin And Alan Meeting (2010) (0)
Bridging adaptive management and reinforcement learning for more robust decisions (2023) (0)
Notebook features: SHA Hashes (2013) (0)
MathJax the smart way: Child Themes (2011) (0)
Friday: Notes on Labrids, notes on Transforms and size-corrections (2011) (0)
Tuesday: Parrotfish/wrightscape runs and code modification (2011) (0)
Solarized Colors with Twitter-Bootstrap? (2012) (0)
Wednesday MCMC and MLEs for wrightscape (2011) (0)
Null Distribution Width Minor Puzzle (2013) (0)
Slides from my talk at Evolution 2011 (2011) (0)
Fun Standardizing Non Standard Evaluation (2015) (0)
Weds: Example sets & more EC2 (2010) (0)
Visuals for Communicating Uncertainty (2012) (0)
Access for Dryad Web Services (2015) (0)
Release of constraint (2011) (0)
Parrotfish-Wrasse example (2010) (0)
Stochastic impediments to biological diversification (2009) (0)
Regime Vs State (2013) (0)
Managing Larger Data on a GitHub Repository [R package piggyback version 0.0.11] (2020) (0)
Jekyll vs Wordpress (2012) (0)
A bit of work on my socialR package for reproducible research (2011) (0)
nonparametric-bayes: framing the issues for the manuscript (2013) (0)
Bootstrapping Likelihood ratios (2010) (0)
non-optimal outcomes of optimal solutions (2011) (0)
Friday: Optimal Control (2011) (0)
Musings On Conservation Literature (2013) (0)
Admb Basic Example (2013) (0)
Identifying Warning Signals (2010) (0)
Warning Signals - Manuscript touch-ups (2011) (0)
Open Science Literature Highlights (2014) (0)
evolution today: Discussion groups, writing, etc (2010) (0)
Warning signals: Likelihoods Straight-up (2010) (0)
McElreath Hierarchical Models (2011) (0)
Likelihood Ratio Paper- Power in Trees (2010) (0)
Wednesday - wrightscape runs and various other things (2011) (0)
Three Interfaces For Docker (2014) (0)
Stochastic policy costs (2012) (0)
Mbi Day Four Notes (2013) (0)
Progress on warning signals (2011) (0)
Notes of the Week (1921) (0)
Updates Across Various Projects (2013) (0)
Extending Data Frame Class (2013) (0)
2015: Carl Boettiger's Open Lab Notebook, Archive for 2015 (2016) (0)
Reproducible Research, Large data sets, and SI2 (2011) (0)
Fri: extending Geiger to Monte Carlo method (2010) (0)
Integrating Open Lab Notebooks with Online Databases (2012) (0)
Warning Signals Literature: when stats are and aren't attempted (2011) (0)
linking binaries from other containers (2014) (0)
rfishbase demo: Are there more Goby or Labrid species on reefs? (2011) (0)
Evolution 2012 Conference, Day 1 (2012) (0)
Likelihoods for quadratic models cont (2010) (0)
Algorithms Discussion Group: MCMC (2011) (0)
Integrating Over Posterior Gp (2013) (0)
Monday: algorithms Meeting (2011) (0)
Drone Ci And Docker (2014) (0)
Warning Signals In Management (2012) (0)
Tuesday: pandoc citations notes, various (2012) (0)
Project tracking (Evolution) (2012) (0)
Saturday: Post ESA, NSF Intersections post-doc? (2011) (0)
Power in simple tests (2010) (0)
Parallel at last (2010) (0)
Felsenstein (web) seminar (2011) (0)
Tuesday: PMC, confidence intervals; screen code-tricks (2011) (0)
Friday: ESA Practice Talk (2011) (0)
How google views me: by search terms or citation counts? (2011) (0)
Warning Signals with SDEs (2010) (0)
Saturday: Fisheries Data Survey, Warning Signals (2011) (0)
Updates to socialR package (2011) (0)
Monday: meetings, notebook (2011) (0)
Warning Signals in Fish Collapse (2012) (0)
ropensci/RNeXML: RNeXML 2.0.8 (2017) (0)
Birth-death Tutorial for PBG Core (2011) (0)
Optimal Control Exploration (2011) (0)
a few notes on various projects (2013) (0)
Getting the right distributions (2011) (0)
Evolution 2010 Day 3 (2010) (0)
Prior Distributions For Tgp Mcmc (2012) (0)
Lab Notebook, 2011 (2012) (0)
Warning Signals data examples (2011) (0)
Some Rfishbase Updates (2013) (0)
Thrusday - corrected calculation, implementing. (2011) (0)
Algorithms Group, HMM meets EM (2011) (0)
Parameter Estimates for Labrid-Parrotfish model (2010) (0)
So, you're active on Research Gate? (2013) (0)
Friday (lab group meeting notes) (2012) (0)
Phylogenetic Tree formats (2010) (0)
Data Management Plan (2012) (0)
Data Science Regional Hubs (2015) (0)
Likelihood Ratio Paper (2010) (0)
Sunday -- edits and appendices (2011) (0)
Comforting Trends In Scientific Software Use (2013) (0)
Is BM nested in OU? Understanding likelihoods of ouch (2011) (0)
why I sign my reviews (2014) (0)
An appropriate amount of fun with docker (2014) (0)

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