Introduction We are deprecating residPlot() from the next version of FSA (v0.9.0). It will likely be removed at the end of the year 2001. We are taking this action to make FSA more focused on fisheries applications and to eliminate “black b... [Read more...]

We are deprecating filterD() from the next version of FSA (v0.9.0). It will likely be removed by the start of 2022. filterD() was an attempt to streamline the process of using filter() (from dplyr) followed by droplevels() to remove levels ... [Read more...]

Introduction We are deprecating fitPlot() from the next version of FSA (v0.9.0). It will likely be removed at the end of the year 2001. We are taking this action to make FSA more focused on fisheries applications and to eliminate “black box... [Read more...]

Introduction The compIntercepts() function in FSA (prior to v0.9.0) was used to statistically compare intercepts for all pairs of groups with the same slope in an indicator/dummy variable regression (I/DVR). However, the excellent emmeans()... [Read more...]

Introduction The compSlopes() function in FSA (prior to v0.9.0) was used to statistically compare slopes for all pairs of groups in an indicator/dummy variable regression (I/DVR). However, the excellent emtrends() function in the emmmeans p... [Read more...]

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 ... [Read more...]

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, ... [Read more...]

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 ... [Read more...]

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... [Read more...]

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 p... [Read more...]

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 Din... [Read more...]

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 Amer... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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 Von... [Read more...]

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 densit... [Read more...]

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... [Read more...]

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 ... [Read more...]

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 ... [Read more...]