Category Archives: Fisheries Science

Posts that are related to the analysis of typical fisheries science data (e.g., growth, mortality, abundance).

Changes to FSA — Estimating Abundance

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

Posted in Administration, Fisheries Science, R | Tagged , , , , , , | 4 Comments

Modified lencat() — Increased Flexibility with dplyr

One of the first functions in the FSA package was lencat(), which served me well over the years. However, I have been bothered by the use of a formula and data= to identify a single column to be “transformed” and … Continue reading

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dplyr Example #1

Hadley Wickam released the dplyr package in January 2014. Since then I have been itching to give it a try as it has been suggested to speed up some data manipulations and, more important to me, provide a singular framework … Continue reading

Posted in Fisheries Science, R | Tagged , , | 7 Comments

Visualizing Age-Length Keys — More

I recently posted on the addition of ageKeyPlot() to the FSA package for visualizing age-length keys. Since that post, I have added one more type of plot as illustrated below. This post should be considered as an extension of the … Continue reading

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Visualizing Age-Length Keys

Lately, I have been interested in methods related to age-length keys. One aspect of this interest has been in visualizing age-length keys. I had seen various visualizations in publications and wanted to be able to reproduce those relatively efficiently. To … Continue reading

Posted in Fisheries Science, R | Tagged , , , , | 4 Comments

Videos of Simple Fisheries Analyses in R (for Teaching) I

I am teaching my Fisheries Science and Management course at Northland College this semester.  The science portion of the course is a fairly traditional treatment of population dynamic parameter estimation methods (using R with the FSA package, of course).  This semester … Continue reading

Posted in Fisheries Science, R | Tagged , , , | 7 Comments

Age Precision and Bias — Changes to FSA

Last week I taught part of a workshop for the Minnesota Chapter of the American Fisheries Society on “Analyzing Age Data in R” (materials are here). I like doing these workshops because they give me ideas for improving the FSA … Continue reading

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Weisberg Growth Model

A fishR user asked me if I had Weisberg Linear Growth Model (LGM) vignette.  In the past, the Weisberg LGM referred to the fixed-effects models described in Weisberg (1993) and implemented in software that was written in XLISP-STAT and distributed … Continue reading

Posted in Fisheries Science, R, Statistics | Tagged , ,

Comparison Among Groups with Francis Parameterization

In my last post, I suggested that the Francis parameterization of the von Bertalanffy growth model may be used in cases where the typical parameterization did not converge (likely due to issues related to highly correlated parameters and data with … Continue reading

Posted in Fisheries Science, R | Tagged , , | 2 Comments

A Problem Fitting the von Bertalanffy Growth Model with nls()

Recently, a fishR user asked me the following (modified) question: I have successfully fit the typical von Bertalanffy growth model to all of my fish. However, when I subset the data by sex and attempt to fit the model separately … Continue reading

Posted in Fisheries Science, R | Tagged , , | 6 Comments