Blog Archives

Age Bias Plot Changes in FSA

April 25, 2017
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Age Bias Plot Changes in FSA

In the last two weeks, I have posted twice about modifying age bias plots and Bland-Altman-like plots for comparing age estimates. From those posts, I have decided that I prefer to plot differences between the ages on the y-axis (as com...

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Bland-Altman Plot for Age Comparisons?

April 19, 2017
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Bland-Altman Plot for Age Comparisons?

Last week I posted about a modified age bias plot. In this post I began looking more deeply at an alternative plot called the Bland-Altman plot. Below, I describe this plot, demonstrate how to construct it in R, give a mild critique of its ...

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Modified Age Bias Plot

April 13, 2017
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Modified Age Bias Plot

Original Age Bias Plot Campana et al. (1995) introduced the “age bias plot” to visually assess potential differences in paired age estimates (e.g., between two structures such as scales and otoliths, between two readers, or between one ...

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Computing SE for PSD indices

December 9, 2016
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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...

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Pauly et al. (1992) Seasonal Cessation in Growth Model

October 10, 2016
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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...

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Exploring the Half-Life Property of K

June 11, 2016
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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 asymptotic mean length (Linf)”. This phenomenon is briefly illustrated...

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FSA v0.8.7 Released

May 7, 2016
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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...

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Histograms by Just Defining Bin Width

March 10, 2016
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Histograms by Just Defining Bin Width

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. library(FSA) data(ChinookArg) hist(~tl,data=ChinookArg,xlab="Total Length (cm)") The default bins for these histograms are rarely what the...

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FSA v0.8.5 Released

February 17, 2016
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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="precision" and what="difference" was used in...

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IFAR Preview in Google Books

December 22, 2015
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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...

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