Publications by fishR Blog
Stock-Recruitment Graphing Questions
A fishR user recently asked me In the book that you published, I frequently use the stock-recruit curve code. The interface that shows both the Ricker/Beverton-Holt figure with the recruit per spawner to spawner figure (i.e., the dynamic plot for srStarts()) has not been working for quite some time. Additionally, I can get the recruits versus sp...
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Collapsing Categories or Values
Introduction I have received a few queries recently that can be categorized as “How do I collapse a list of categories or values into a shorter list of category or values?” For example, one user wanted to collapse species of fish into their respective families. Another user wanted to collapse years into decades. Data munging such as this is c...
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Adding Zero Catches
Introduction Much of my work is with undergraduates who are first learning to analyze fisheries data. A common “learning opportunity” occurs when students are asked to compute the mean catch (or CPE), along with a standard deviation (SD), across multiple gear sets for each species. The learning opportunity occurs because some species will inv...
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Testers for RFishBC
Back-calculating lengths of fish at previous ages from measurements made on calcified structures (scales, otoliths, etc.) is fairly common practice within some fisheries agencies and institutions. The FishBC software distributed by the American Fisheries Society is used by some of these agencies to facilitate gathering the required information fr...
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New FSA Authors
It was always my hope that the Fisheries Stock Assessment (FSA) R package would become a community endeavor. With the recent release on CRAN of v0.8.21 that hope has finally come to fruition. This version has two new co-authors. Alexis Dinno is the author of the dunn.test package. The dunnTest() function in FSA is simply a wrapper for dunn.test()...
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RFishBC CRAN Release
I am pleased to announce that the RFishBC package has been released to CRAN. This package is intended to help fisheries scientists gather age and measurement data from digital images of calcified structures and, possibly, back-calculate previous length from that data. RFishBC is intended to replace the FishBC software that has long been available...
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(Fish) Length Frequency Histograms in ggplot2
Introduction library(FSAdata) # for data library(ggplot2) I am finally learning ggplot2 for elegant graphics. One of the first plots that I wanted to make was a length frequency histogram. As it turns out, there are a few “tricks” to make the histogram appear as I expect most fisheries folks would want it to appear – primarily, left-inclus...
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von Bertalanffy Growth Plots I
Introduction library(FSAdata) # for data library(FSA) # for vbFuns(), vbStarts(), confint.bootCase() library(car) # for Boot() library(dplyr) # for filter(), mutate() library(ggplot2) I am continuing to learn ggplot2 for elegant graphics. I often make a plot to illustrate the fit of a von Bertalanffy growth function to data. In general,...
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von Bertalanffy Growth Plots II
Introduction library(FSAdata) # for data library(FSA) # for vbFuns(), vbStarts(), confint.bootCase() library(car) # for Boot() library(dplyr) # for filter(), mutate() library(ggplot2) In a previous post I demonstrated how to make a plot that illustrated the fit of a von Bertalanffy growth function (VBGF) to data. In this post, I will de...
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Age Bias Plots Using ggplot
Guest Post Note Please note that this is a guest post to fishR by Michael Lant, who at the time of this writing is a Senior at Northland College. Thanks, Michael, for the contribution to fishR. Introduction My objective is to demonstrate how to create the age bias plots using ggplot2 rather than functions in FSA. Graphs produced in ggplot2 are m...
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