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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.

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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.

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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.

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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.

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Introduction Package Setup Data Forecasting Generate data to plot Figure Introduction Since I’m writing R code to make certain figures for this website, I thought I could go ahead and annotate some of it in R markdown to serve as blog posts. Package Setup library(tidyverse) ## ── Attaching packages ────────────────────────────────────────────────────────────── tidyverse 1.2.1 ── ## ✔ ggplot2 3.0.0.9000 ✔ purrr 0.2.5 ## ✔ tibble 1.4.2 ✔ dplyr 0.

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Recent Publications

More Publications

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

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

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

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. Quantitative argument for long-term ecological monitoring. In MEPS, 2017.

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. Predicting coastal algal blooms in southern California. In Ecol, 2017.

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Projects

Causal inference

Identifying causal interactions among time series.

Dynamic stability

Dynamic quantification of stability in ecosystems.

Empirical Dynamic Modeling

Inferring system dynamics from time series

Forecasting

Predicting the future state of ecosystems.

portalR

R package for downloading and summarizing the Portal data

rEDM

R package for empirical dynamic modeling

Teaching

The Carpentries

I am a certified instructor for The Carpentries and have taught at and assisted with several workshops at both the University of Florida and the University of California San Diego.

In addition to teaching, I am also a board member for the UF Carpentry Club, which organizes workshops and other events at UF. In August 2018, we organized a series of talks, career panel, and mini-tutorials as part of Research Bazaar at UF.

Training

I have formal training in pedagogy from completing “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”.)

Experience

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

I have also been a teaching assistant for the following courses:

Contact