A user of my Introductory Fisheries Analyses with R book recently asked me how to compute standard errors (SE) for the various PSD indices by using the usual equation for the SE of a proportion (square root of p times (1-p) divided by n). B... [Read more...]

I recently published a technical note in Fisheries Research that described an algorithm for implementing the “seasonal cessation in growth model” of @Paulyetal1992. Describing an algorithm for a growth model does not seem like a useful... [Read more...]

A colleague recently questioned whether the loge(2)/K, where K is the Brody growth coefficient in the typical parameterization of the von Bertalanffy growth function, represents the “amount of time it takes for a fish to grow from any length to a length halfway between the initial length and the ... [Read more...]

A new minor version (0.8.7) of the FSA (Fisheries Stock Assessment) package was recently released and is now on CRAN. A full description of changes is here. Three major changes are described below. Removed the dynamicPlot=TRUE option fr... [Read more...]

The Problem – Binning for Length Frequency Histograms Fisheries scientists often make histograms of fish lengths. For example, the code below uses hist() (actually hist.formula()) from the FSA package to construct a histogram of total lengths for Chinook Salmon from Argentinian waters.

<span>library</span><span>(</span><span>FSA</span><span>)</span>
<span>data</span><span>(</span><span>ChinookArg</span><span>)</span>
<span>hist</span><span>(</span><span>~</span><span>tl</span><span>,</span><span>data</span><span>=</span><span>ChinookArg</span><span>,</span><span>xlab</span><span>=</span><span>"Total Length (cm)"</span><span>)</span>

The default bins for these histograms are ... [Read more...]

A new minor version (0.8.5) of the FSA (Fisheries Stock Assessment) package was recently released and is now on CRAN. A full description of changes is here. Major changes are: agePrecision(): Fixed bug related to computations of percent agreement when NA values were present. There was an inconsistency between when what="... [Read more...]

A preview of the Introductory Fisheries Analyses with R book is available here on Google Books. The preview is only of the Table of Contents and Chapter 1. However, you can search within the book, though pages returned by the search are not... [Read more...]

I am pleased to announce that my Introductory Fisheries Analyses with R (IFAR) book has been published, almost two weeks ahead of schedule. Details about the book (and companion website) are here and it can be purchased from CRC Press (at a ... [Read more...]

I just noticed that there will be an Introduction to R workshop at the Society for Freshwater Science Annual Meeting in Sacramento on 20-May-20-16. Here is a link to the announcement. [Read more...]

It was just brought to my attention that there will be a workshop at the upcoming Midwest Fish and Wildlife Conference (Grand Rapids, MI) on the Bioenergetics 4.0 shiny app. The announcement from here (where there is a registration link) is ... [Read more...]

A large number of small data sets are available in the FSA and FSAdata packages. These data sets may be useful for demonstrating typical fisheries science analyses in an undergraduate or early graduate fisheries science and management course or if one is self-teaching how to perform these analyses. Indeed, several ... [Read more...]

I am pleased to announce that the FSA (Fish Stock Assessment) package has been released on CRAN. This package has been in development for several years, but this is the initial release on CRAN and coincides with the forthcoming Introductory ... [Read more...]

The Problem I have been attempting to use RMarkdown rather than LaTeX to produce R examples. One issue that has slowed my conversion has been my struggles with how to reference figures and tables. The examples below illustrate how I have been using captioner to solve this problem. The Solution ... [Read more...]

In fisheries analysis it is fairly common to compute the cumulative sum of values in a vector – i.e., all values before and including the current position in the vector. For example, the third value in the cumulative sum would be the sum of the first, second, and third values ... [Read more...]

A FSA user recently asked me if there was a way to see and work with the age comparison results for individual fish. In particular, this user wanted to identify each fish for which the individual CV values from comparing two independent age estimates was greater than 10. It turns out ... [Read more...]