Publications by dogle
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 package and fishR. One of several things that came out of this workshop was a realization that the measures of precis...
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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 I am trying to use most of my lecture time to discuss the background, inte...
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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 do this, I have created ageKeyPlot() in the latest version of FSA. Below are examples of th...
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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 previous post. The FSA package is loaded and the same example age-length key is constructed with the following. librar...
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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 for a variety of common data manipulations. Recently, I gave it a try with some simple common manipulations for fisheries wor...
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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 that an “automatic” determination of startcat= was not coded. Additionally, lencat() did not work well with dplyr, which I rece...
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“Vignettes” Update
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 vignettes. Age Comparisons – Major changes are the addition of two more tests of symmetry (McNemar’s and Evans-Hoenigs), chan...
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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 are cosmetic, others are more important. I attempt to highlight the changes b...
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Age-Length Keys in FSA
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 be updated!! See below. ageKey() — DEPRECATED (will be removed by v1.0.0). See alkIndivAge()...
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Changes to FSA — Size Structure
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 (PSD) related functions in the FSA package — psdVals(), psdCalc(), psdDataPrep(), tictactoe(...
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