Publications by dogle
Mixed Model Example — Wagner et al. (2006)
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 first being simulated fish density data from eight streams, four of which had a barrier and fo...
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Creating Catch Data from Individual Length Measurements
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 that showed three individual length measurements for Brook Trout, two measurements for Lake Trout, and two measurements...
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Creating Catch Data from Individual Length Measurements II
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 (in the knitR package) and the R markdown language. If successful this will allow my posts with R code to show the results produced, which...
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R-Squared for a VBGM
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 of determination, I have to show it. In general, the traditional “coefficient of determination�...
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Multiple Removal Estimates at Once
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 “long way”: ##GRYSUS2012 GRYSUS2012 <- c(31,23,9) a <- removal(GRYSUS2012) summary(a) confint(a...
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Merge Relational Dataframes
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 variable. Is there a way to tell R this so that I don’t have to paste all three worksheets onto one...
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A Problem Fitting the von Bertalanffy Growth Model with nls()
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 to males and females I receive an ‘infinity’ and ‘singular gradient’ error. Why does this happen and is there ...
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Comparison Among Groups with Francis Parameterization
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 lengths that are highly variable within ages and the full curvature of the model is not readily appa...
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Reproducible Reporting Example
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 and view as full screen). p.s., For those on the R police force, I know that I mistakingly called my FSA pac...
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Weisberg Growth Model
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 through Minnesota Sea Grant. [I do, actually, have a vignette that implements that technology in ...
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