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
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.
- Get Workshop Materials: Download (to one folder/directory on your computer) each of these six items:
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).