This one-day course is for students 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 several stock-recruitment functions. Depending on time, participants may also fit weight-length relationships and compare parameters among groups. Participants should be familiar with the fundamentals of R. See the workshop announcement.
- Install at least version 3.4.0 of R 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.]
- I use RStudio to interact with R (but RStudio is not required for this course). 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 the
nlstoolspackages. 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.
- Download the slides, R scripts, and data for the course (available below).
- 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. However, the book is available at a 20% discount for participants in this workshop. Contact me if you would like details about how to receive this discount.
- 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), stock-recruitment functions (IFAR Chapter 13), and weight-length relationships (IFAR Chapter 7).