Recent Posts

More Posts

Overview Setup Initial data examination Injuries by date Injuries by cause Overview This is an exploration of the TidyTuesday dataset on “Amusement Park Injuries”, done as part of the Wednesday coding clinic for Research Bazaar Gainesville. Setup ## load packages library(tidyverse) ## ── Attaching packages ──────────────────────────────────────────────────────────── tidyverse 1.2.1 ── ## ✔ ggplot2 3.2.1 ✔ purrr 0.3.2 ## ✔ tibble 2.1.3 ✔ dplyr 0.8.3 ## ✔ tidyr 0.

CONTINUE READING

Agenda Resources Installation and Setup Backup option Data Formats Determine embedding dimension using Simplex Projection Identify nonlinearity using S-map Multivariate Models Convergent Cross Mapping Surrogate Analysis with CCM Extra topics These are the notes for the rEDM tutorial I gave at the November 13-15 Nonlinear Dynamics and Fisheries Workshop at the NMFS Southwest Fisheries Science Center in Santa Cruz. Agenda Time 900-915 set up computers 915-930 data formats 930-945 simplex, plotting rho vs.

CONTINUE READING

While on my visit to the University of Nebraska, Lincoln, I had the pleasure of taking over Chris Chizinski’s R class on Friday (2018-11-02). I demo’d a few things about setting up RStudio, using RStudio packages and the here package, and then walked through a workflow of doing data analysis, converting code into functions, and writing scripts and functions to be more accessible for readers. For reference, here are my slides.

CONTINUE READING

For my rEDM package, I’ve been using the pkgdown package to build a website comprising all the documentation and vignettes, for easy reference from a web browser. The normal workflow for this is something like: Make updates to the package. Run pkgdown::build_site() to generate the website files into a docs folder. Commit changes and upload to GitHub. Use GitHub Pages, configured to source the files from the docs folder on the master branch.

CONTINUE READING

Motivation What I used to do Why use an R package? How-to Guide Requirements Tutorial Setup Workflow Bonus steps Other Readings Motivation I’ve been wondering about the best way to organize (reproducible) research projects in R for a while now. I figured this might be a good spot to write up some thoughts. What I used to do Initially my projects would consist of just a few R files that separate out functions from a main script that calls the functions.

CONTINUE READING

Recent Publications

More Publications

. portalr: an R package for summarizing and using the Portal Project Data. In JOSS, 2019.

PDF WWW

. The intrinsic predictability of ecological time series and its potential to guide forecasting. In Ecol Monogr, 2019.

PDF WWW

. Comprehensive incentives for reducing Chinook salmon bycatch in the Bering Sea walleye Pollock fishery: Individual tradable encounter credits. In Reg Stud Mar Sci, 2018.

PDF WWW

. Ecosystem‐based forecasts of recruitment in two menhaden species. In Fish Fish, 2018.

PDF WWW

. Fluctuating interaction network and time-varying stability of a natural fish community. In Nature, 2018.

PDF WWW

Projects

GPEDM

Gaussian Process Regression for Empirical Dynamic Modeling

MATSS

R package for Macroecological Analysis of Time Series Structure

MATSS-forecasting

Analyzing Ecological Predictability using MATSS

portalR

R package for downloading and summarizing the Portal data

rEDM

R package for empirical dynamic modeling

Causal inference

Identifying causal interactions among time series.

Forecasting

Predicting the future state of ecosystems.

Empirical Dynamic Modeling

Inferring system dynamics from time series

Dynamic stability

Dynamic quantification of stability in ecosystems.

Teaching

Computational Training

I have taught or assisted with The Carpentries workshops at the University of Minnesota, the University of Florida, and the University of California San Diego.

In addition to teaching, I was a board member for the UF Carpentries Club from 2017-2019, which organizes computational workshops and related events at the University of Florida. I have also led the organization of two Research Bazaar events at UF that include: talks, panel discussions, tutorials, and more: ResBaz2018 ResBaz2019.

As part of the Open Data Science at SIO, I also led the following informal seminars:

Pedagogy

I have formal training in pedagogy via “Teaching + Learning at the College Level”, a course on evidence-based teaching practices taught by UCSD’s Teaching + Learning Commons. (The course is now called “Introduction to College Teaching”.)

In addition, I am a certified instructor for The Carpentries.

Experience

I have been a teaching assistant for the following courses:

Contact