Publications by fishR Blog
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,xla...
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FSA v0.8.7 Released
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 from vbStarts() and srStarts(). This functionality has been moved to vbStartsDP() and srStartsDP(), respective...
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Exploring the Half-Life Property of K
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 phenomeno...
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Pauly et al. (1992) Seasonal Cessation in Growth Model
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 contribution to the literature, as fitting growth models is pretty standard fare for fisheries scientists. ...
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Computing SE for PSD indices
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). Below is my response using the Inch Lake data from the book. Load required packages. library(FSA) library(m...
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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 reader at two times). One set of age estimates serve as “reference” ages in the age bias plot. The refer...
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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 use for compare fish age estimates, and develop an alternative that is mean to correct what I see as some of...
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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 compared to the nonreference ages), plot overlapping points with a transparent color that becomes darker as more p...
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Joy Plot of Length Frequencies
There has been a bit of a buzz recently about so-called “joyplots.” Wilke described joyplots as “partially overlapping line plots that create the impression of a mountain range.” I would describe them as partially overlapping density plots (akin to a smoothed histogram). Examples of joyplots are here, here, and here (from among many). I t...
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Plots of Back-Calculated Lengths-At-Age I
Last spring, I posted about my version of a modified age-bias plot. One reader commented on that post via Twitter – “Now that you solved the age-bias plot, how about the ‘best’ display of back-calculated length-at-age data, with VonB growth curve overlay?”. In addition, I recently received a question related to the non-convergence of a ...
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