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 … Continue reading → [Read more...]

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 … Continue reading → [Read 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 … Continue reading → [Read more...]

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 … Continue reading → [Read more...]

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 … Continue reading → [Read more...]

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 … Continue reading → [Read more...]

A fishR user asked me if I had Weisberg Linear Growth Model (LGM) vignette.  In the past, the Weisberg LGM referred to the fixed-effects models described in Weisberg (1993) and implemented in software that was written in XLISP-STAT and distributed … Continue reading → [Read more...]

I began playing with the screenr software this evening and my first attempt was to create a short video that demonstrates reproducible report writing in RStudio using knitr and LaTeX.  You can see the example at my screenr page (hit Play … Continue reading → [Read more...]

In my last post, I suggested that the Francis parameterization of the von Bertalanffy growth model may be used in cases where the typical parameterization did not converge (likely due to issues related to highly correlated parameters and data with … Continue reading → [Read more...]

Recently, a fishR user asked me the following (modified) question: I have successfully fit the typical von Bertalanffy growth model to all of my fish. However, when I subset the data by sex and attempt to fit the model separately … Continue reading → [Read more...]

A Question Recently, a student, working on her Senior Thesis at Northland College, asked me the following question: Attached is an Excel file with three “important to R” worksheets. The only thing that connects all 3 worksheets is the Lift.ID … Continue reading → [Read more...]

A Question Recently, a fishR user asked me the following question: I have recently used the FSA package to calculate Zippin depletion population estimates resulting from 3 pass removals on smaller trout streams. I have currently been doing this the … Continue reading → [Read more...]

Recently, a fishR user asked me the following question: After fitting the age-length data into VBGM, I overviewed the results. But I can’t find the coefficient of determination () for the VBGM fitting. Because some reviewer want the the coefficient … Continue reading → [Read more...]

Note that this is largely a repeat of a previous post (except that I have added a few plots at the bottom) as I am experimenting with being able to write posts here directly from R using the knit2wp() function … Continue reading → [Read more...]

This example has been updated in this post. I came across a “problem” today where I needed to create catch data for individual nets from length measurements made on individual fish in those nets.  In other words, I had data … Continue reading → [Read more...]

I am preparing for a workshop on mixed models and looked at the paper “Accounting for multilevel data structures in fisheries data using mixed models” by Wagner et al. (2006) (PDF available here).  Wagner et al. (2006) used two examples, with the … Continue reading → [Read more...]