Blog Archives

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

January 11, 2014
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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 →

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Age Precision and Bias — Changes to FSA

December 12, 2013
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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

November 28, 2013
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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 →

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Reproducible Reporting Example

November 23, 2013
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Reproducible Reporting Example

I began playing with the screenr software this evening and my first attempt was to create a short video that demonstrates reproducible report writing in RStudio using knitr and LaTeX.  You can see the example at my screenr page (hit Play … Continue reading →

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Comparison Among Groups with Francis Parameterization

November 21, 2013
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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 →

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

November 19, 2013
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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 →

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Merge Relational Dataframes

November 11, 2013
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Merge Relational Dataframes

A Question Recently, a student, working on her Senior Thesis at Northland College, asked me the following question: Attached is an Excel file with three “important to R” worksheets. The only thing that connects all 3 worksheets is the Lift.ID … Continue reading →

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Multiple Removal Estimates at Once

October 30, 2013
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Multiple Removal Estimates at Once

A Question Recently, a fishR user asked me the following question: I have recently used the FSA package to calculate Zippin depletion population estimates resulting from 3 pass removals on smaller trout streams. I have currently been doing this the … Continue reading →

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R-Squared for a VBGM

August 9, 2013
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R-Squared for a VBGM

Recently, a fishR user asked me the following question: After fitting the age-length data into VBGM, I overviewed the results. But I can’t find the coefficient of determination () for the VBGM fitting. Because some reviewer want the the coefficient … Continue reading →

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Creating Catch Data from Individual Length Measurements II

July 26, 2013
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Creating Catch Data from Individual Length Measurements II

Note that this is largely a repeat of a previous post (except that I have added a few plots at the bottom) as I am experimenting with being able to write posts here directly from R using the knit2wp() function … Continue reading →

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