I am in the process of moving the fishR website to derekogle.com/fishR/ Please update your bookmarks/favorites/etc. The new page will be hosted through GitHub pages and will allow me to keep the page updated more easily and to write more … Continue reading → [Read more...]

In the last few months I have received queries about whether a “fish bioenergetics” model has been implemented in R.  Here is what I am aware of. Fish Bioenergtics 4.0 (an update of the Fish Bioenergetics program distributed by Wisconsin Sea … Continue reading → [Read more...]

I have submitted a draft of the Introduction to Fisheries Analyses with R to the publisher.  It will now be submitted to a thorough editorial review in preparation for a late 2015 publication (fingers are crossed).  The draft, as a whole … Continue reading → [Read more...]

I am nearly ready to submit a draft of the Introduction to Fisheries Analysis with R book to the publisher.  Relatedly, I am preparing the FSA package to be version 1.0.0 by the time the book is released.  As part … Continue reading → [Read more...]

I (and Northland alum Taylor Stewart) will be leading a continuing education course on using R for typical age and growth analyses as part of the national American Fisheries Society conference in Portland, OR.  Here is the announcement on the conference webpage … Continue reading → [Read more...]

Hadley Wicham has announced two new package for reading external data into R that will likely be of great interest to fisheries scientists. readr — Several new functions that replace the traditional read.csv() and read.table() (among others).  Hadley’s announcement is here, … Continue reading → [Read more...]

I have added a very rough draft of the Recruitment chapter to the Introduction to Fisheries Analysis with R (IFAR) page.  This chapter is a complete re-working of the old Stock-Recruitment vignette and includes a section on fitting non-linear stock-recruitment … Continue reading → [Read more...]

In previous versions of FSA, growthModelSim() was used to produce a scatterplot of length-age data with a von Bertalanffy model superimposed where the parameters of the model were linked to slider bars that allowed the model to be dynamically changed … Continue reading → [Read more...]

Thanks to some very thoughtful reviews, I have dramatically updated the Mortality and Age Comparisons chapters in the Introduction to Fisheries Analysis with R book. Changes to the Age Comparisons chapter in particular resulted in major changes to the FSA … Continue reading → [Read more...]

Thanks to a couple of great reviews, I have updated the Weight-Length and Condition chapters of the forthcoming Introduction to Fisheries Analysis with R book. The suggestions resulted in some changes to the FSA package so you may want to … Continue reading → [Read more...]

A week or so ago I participated in the “Data Wrangling” webinar provided by RStudio.  I found Garret Gromelund’s descriptions of the functions in tidyr and dplyr to be fantastic.  A recording of the webinar is available here on the RStudio … Continue reading → [Read more...]

I have uploaded a draft of Chapter 3 — Plotting Fundamentals — for the Introduction to Fisheries Analyses with R (IFAR) book (note the new name).  This chapter is meant to be a quick introduction to plotting in base R for plots … Continue reading → [Read more...]

I have uploaded a draft of Chapter 1 — A Very Brief Introduction to R — to Introduction to Fisheries Science with R book.  This chapter is very bare bones as there are many great introductions to R on the … Continue reading → [Read more...]

I have added two new drafts of chapters for the Introductory Fisheries Science with R book.  Both chapters are still rough, but feedback would be greatly appreciated. The first chapter is an introduction to basic data manipulations, largely using the … Continue reading → [Read more...]

In this post on RPubs, I demonstrate how to use new functions (psdAdd() and wrAdd()) in the FSA package, along with functions in the dplyr package, to efficiently add Gabelhouse length category and relative weight variables for all species in … Continue reading → [Read more...]

Over the summer I made two posts about using the dplyr package.  The first was an example of the dplyr verbs applied to fish data.  The second was an example of modifications that I had made to lencat() to work better … Continue reading → [Read more...]

I have added a (very rough) first draft to the Size Structure chapter of the forthcoming Introductory Fisheries Science with R book on the book’s fishR webpage.  Accompanying this chapter are major changes to all of the proportional size distribution … Continue reading → [Read more...]

I have updated the age-length key related functions in FSA and the age-length key vignette.  The details are below.   Let me know if you have questions or suggestions. FSA Changes All code that used ageKey(), ageKeyPrep(), and ageKeyPlot() should … Continue reading → [Read more...]

I mentioned previously, that I have been updating the Mark-Recapture vignettes.  That has morphed into a document that is an update of the Mark-Recapture Closed and Open vignettes and the depletion/removal vignettes and associated FSA functions.  Some of the changes … Continue reading → [Read more...]

As a follow-up to my post about major changes to FSA and that some of the “old” vignettes are now out-of-date, here is a brief summary of new material in the draft book chapters (linked to below) that replaced the … Continue reading → [Read more...]