fishRDemonstrations for using R for fisheries analyses.
http://derekogle.com/fishR
Mean Weights at Ages From Lengths
Introduction Recently I was tasked with estimating mean weights at age for data that contained no weights, but did contain lengths and ages (ages were from applying an age-length key). A weight-length relationship was available (derived from a smaller sample from the same population). A question arose about whether the...
Wed, 09 Aug 2017 00:00:00 -0500
http://derekogle.com/fishR/2017-08-09-MeanWeights
http://derekogle.com/fishR/2017-08-09-MeanWeightsJoy 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...
Fri, 28 Jul 2017 00:00:00 -0500
http://derekogle.com/fishR/2017-07-28-JoyPlot
http://derekogle.com/fishR/2017-07-28-JoyPlotAge 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...
Wed, 26 Apr 2017 00:00:00 -0500
http://derekogle.com/fishR/2017-04-26-AgeBias_inFSA
http://derekogle.com/fishR/2017-04-26-AgeBias_inFSABland-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,...
Thu, 20 Apr 2017 00:00:00 -0500
http://derekogle.com/fishR/2017-04-20-Modified_BlandAltmanPlot
http://derekogle.com/fishR/2017-04-20-Modified_BlandAltmanPlotModified 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...
Fri, 14 Apr 2017 00:00:00 -0500
http://derekogle.com/fishR/2017-04-14-Modified_AgeBiasPlot
http://derekogle.com/fishR/2017-04-14-Modified_AgeBiasPlotComputing 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...
Fri, 09 Dec 2016 00:00:00 -0600
http://derekogle.com/fishR/2016-12-09-PSD_SE
http://derekogle.com/fishR/2016-12-09-PSD_SEPauly et al. (1992) Seasonal Cessation in Growth Model
I recently published a technical note in Fisheries Research (Ogle 2017) that described an algorithm for implementing the “seasonal cessation in growth model” of Pauly et al. (1992). Describing an algorithm for a growth model does not seem like a useful contribution to the literature, as fitting growth models is...
Tue, 11 Oct 2016 00:00:00 -0500
http://derekogle.com/fishR/2016-10-11-Pauly-VBModel
http://derekogle.com/fishR/2016-10-11-Pauly-VBModelExploring 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...
Sun, 12 Jun 2016 00:00:00 -0500
http://derekogle.com/fishR/2016-06-12-Halflife-of-K
http://derekogle.com/fishR/2016-06-12-Halflife-of-KFSA 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(),...
Sun, 08 May 2016 00:00:00 -0500
http://derekogle.com/fishR/2016-05-08-FSA_0_8_7_Released
http://derekogle.com/fishR/2016-05-08-FSA_0_8_7_ReleasedHistograms 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...
Thu, 10 Mar 2016 00:00:00 -0600
http://derekogle.com/fishR/2016-03-10-Histograms-with-w
http://derekogle.com/fishR/2016-03-10-Histograms-with-wFSA v0.8.5 Released
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...
Wed, 17 Feb 2016 00:00:00 -0600
http://derekogle.com/fishR/2016-02-17-FSA_0_8_5_Released
http://derekogle.com/fishR/2016-02-17-FSA_0_8_5_ReleasedIFAR Preview in Google Books
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 shown in full. The book is available...
Tue, 22 Dec 2015 00:00:00 -0600
http://derekogle.com/fishR/2015-12-22-IFAR-Preview-in-Google-Books
http://derekogle.com/fishR/2015-12-22-IFAR-Preview-in-Google-BooksPublished -- Introductory Fisheries Analyses with R
I am pleased to announce that my Introductory Fisheries Analyses with R (IFAR) book has been published, almost two weeks ahead of schedule. Details about the book (and companion website) are here and it can be purchased from CRC Press (at a 20% discount through the end of the year)....
Sun, 06 Dec 2015 00:00:00 -0600
http://derekogle.com/fishR/2015-12-06-IFAR-published
http://derekogle.com/fishR/2015-12-06-IFAR-publishedR Workshop at SFS Meeting
I just noticed that there will be an Introduction to R workshop at the Society for Freshwater Science Annual Meeting in Sacramento on 20-May-20-16. Here is a link to the announcement.
Mon, 23 Nov 2015 00:00:00 -0600
http://derekogle.com/fishR/2015-11-23-R-Workshop-at-SFS-Meeting
http://derekogle.com/fishR/2015-11-23-R-Workshop-at-SFS-MeetingBioenergetics in R Workshop
It was just brought to my attention that there will be a workshop at the upcoming Midwest Fish and Wildlife Conference (Grand Rapids, MI) on the Bioenergetics 4.0 shiny app. The announcement from here (where there is a registration link) is below (I added the links): Instructors: Dr. David Deslauriers,...
Sun, 15 Nov 2015 00:00:00 -0600
http://derekogle.com/fishR/2015-11-15-Bioenergetics_in-R-Workshop
http://derekogle.com/fishR/2015-11-15-Bioenergetics_in-R-WorkshopFisheries Data Sets
A large number of small data sets are available in the FSA and FSAdata packages. These data sets may be useful for demonstrating typical fisheries science analyses in an undergraduate or early graduate fisheries science and management course or if one is self-teaching how to perform these analyses. Indeed, several...
Thu, 22 Oct 2015 00:00:00 -0500
http://derekogle.com/fishR/2015-10-22-Fisheries-Data-Sets
http://derekogle.com/fishR/2015-10-22-Fisheries-Data-SetsFSA Released
I am pleased to announce that the FSA (Fish Stock Assessment) package has been released on CRAN. This package has been in development for several years, but this is the initial release on CRAN and coincides with the forthcoming Introductory Fisheries Analysis with R book. The companion FSAdata package, which...
Sun, 11 Oct 2015 00:00:00 -0500
http://derekogle.com/fishR/2015-10-11-FSA-released
http://derekogle.com/fishR/2015-10-11-FSA-releasedFigure and Table Captions in Markdown
The Problem I have been attempting to use RMarkdown rather than LaTeX to produce R examples. One issue that has slowed my conversion has been my struggles with how to reference figures and tables. The examples below illustrate how I have been using captioner to solve this problem. The Solution...
Thu, 17 Sep 2015 00:00:00 -0500
http://derekogle.com/fishR/2015-09-17-Figure-Table-Captions-in-Markdown
http://derekogle.com/fishR/2015-09-17-Figure-Table-Captions-in-MarkdownTwo New Cumulative Sum Functions
In fisheries analysis it is fairly common to compute the cumulative sum of values in a vector – i.e., all values before and including the current position in the vector. For example, the third value in the cumulative sum would be the sum of the first, second, and third values...
Sun, 06 Sep 2015 00:00:00 -0500
http://derekogle.com/fishR/2015-09-06-Two-New-Cumulative-Sums
http://derekogle.com/fishR/2015-09-06-Two-New-Cumulative-SumsAge Comparison Results for Individual Fish
A FSA user recently asked me if there was a way to see and work with the age comparison results for individual fish. In particular, this user wanted to identify each fish for which the individual CV values from comparing two independent age estimates was greater than 10. It turns...
Sat, 05 Sep 2015 00:00:00 -0500
http://derekogle.com/fishR/2015-09-05-Age-Comparison-Results-for-Individual-Fish
http://derekogle.com/fishR/2015-09-05-Age-Comparison-Results-for-Individual-Fish