RcourseMidwest2018

Workshop Description

This one-day workshop is for those interested in expanding their R skills to estimate basic population dynamic rate parameters. Through a sequence of short lectures, code demonstrations, and hands-on application exercises, participants will use R to construct and apply an age-length key to estimate ages of individual fish from their lengths, estimate mortality rates and compare rates among groups, fit a von Bertalanffy growth function (VBGF) and compare function parameters among groups, and fit weight-length relationships and compare parameters among groups. A short demonstration for creating reproducible reports will also be demonstrated. Participants should be familiar with the fundamentals of R. See the workshop announcement.

Pre-Workshop Preparation - REQUIRED

• Install R: Install at least version 3.4.0 of R (note that 3.4.3 is the latest version) on your laptop. Directions for a first install are here for Windows or here for MacOS. If you are using Windows and already have R installed, then here is an easy method to upgrade. [The MacOS installation directions may be dated. Simply following the installation defaults should be fine.]
• Install RStudio: RStudio is not required for this workshop but I strongly encourage you to use it to interact with R. Directions to install and prepare RStudio are here for Windows and here for MacOS. [The MacOS installation directions may be dated. Simply following the installation defaults should be fine.]
• Install R Packages: Install the FSA, FSAdata, AICcmodavg, captioner, dplyr, magrittr, minpack.lm, and nlstools packages. Directions for installing packages are here if you plan to use RStudio and here for Windows and here for MacOS if you plan to use R directly. Test your package installations by seeing if this script runs without error.
• Get Workshop Materials: Download (to one folder/directory on your computer) each of these six items:
  • Lecture Slides (PowerPoint)
  • Pygmy Whitefish R Script and data
  • Walleye Assignments and data
  • Reproducible Reports Example

Pre-Workshop Preparation - OPTIONAL

• Get Book: The materials for this workshop are based on my Introduction to Fisheries Analysis with R book (IFAR). This book is NOT required for the workshop but is available at a 20% discount for workshop participants in this workshop. Contact me for how to order with the discount.
• Read Book Chapters: You may want to (re)familiarize yourself with R basics (IFAR Chapters 1-3), age-length keys (IFAR Chapter 5), estimating mortality rates (IFAR Chapter 11), von Bertalanffy growth functions (IFAR Chapter 12), and weight-length relationships (IFAR Chapter 7).
• Can You Knit?: If you want to try the reproducible reports example (see above) on your own computer, then, to prepare your computer, you should select the File menu, New File submenu, and R Markdown submenu; select the PDF option on the ensuing dialog box and press OK; save the document that opens onto your computer (don’t give the filename an extension); and then press the “Knit” icon on the RStudio script pane toolbar. Install some packages if prompted to do so. If a PDF document is produced then your computer is prepared to compile the reproducible reports example (assuming that you successfully followed the installation instructions above).

Post-Workshop Follow-up

• Please complete this survey regarding this workshop.
• Here is the answer key to the Escanaba Walleye exercises.
• If you have any questions please feel free to contact me.