Articles by dogle

fishR is moving

September 16, 2015 | dogle

I am in the process of moving the fishR website to 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...]

Bioenergetics in R

July 7, 2015 | dogle

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...]

IFAR Draft Submitted

July 4, 2015 | dogle

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...]

FSA Modifications

July 3, 2015 | dogle

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...]

Age & Growth with R (Portland, Oregon)

April 19, 2015 | dogle

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...]

New Packages for Reading Data into R

April 15, 2015 | dogle

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...]

Recruitment Chapter for IFAR

April 2, 2015 | dogle

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...]

Changes to Von B Growth Modeling in FSA

March 17, 2015 | dogle

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...]

Mortality & Age Comparisons Chapters

March 13, 2015 | dogle

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...]

Weight-Length & Condition Chapters Updated

March 7, 2015 | dogle

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...]

Data Wrangling Webinar and IFAR Chapter Update

January 22, 2015 | dogle

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...]

Plotting Fundamentals Chapter

December 24, 2014 | dogle

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...]

Introduction to R Chapter for IFSWR Book

December 19, 2014 | dogle

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...]

2 New (Draft) Chapters for Intro Fish Science with R

November 16, 2014 | dogle

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...]

Updated dplyr Examples

September 28, 2014 | dogle

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...]

Changes to FSA — Size Structure

September 16, 2014 | dogle

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...]

Age-Length Keys in FSA

August 30, 2014 | dogle

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...]

Changes to FSA — Estimating Abundance

August 17, 2014 | dogle

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...]

“Vignettes” Update

July 14, 2014 | dogle

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...]
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