R for Fisheries Analyses and Tasks

See r-bloggers where these and other R-related blog posts are aggregated.

Bayesian LVB II - rstan
16 min
Tutorial on how to estimate parameters of the LVB model with Bayesian inference and rstan
Jason Doll
Feb 6, 2024

Feb 5, 2024

Bayesian LVB I - brms
9 min
Tutorial on how to estimate parameters of the LVB model with Bayesian inference and brms
Jason Doll
Feb 5, 2024

Feb 4, 2024

Working with Multiple Catch Curves
14 min
Computing mortality from catch curves for multiple groups.
Derek H. Ogle
Apr 24, 2023

Apr 24, 2023

Working with Multiple Age-Length Keys
11 min
Computing and applying age-length keys at once for multiple groups.
Derek H. Ogle
Apr 23, 2023

Apr 24, 2023

Murphy et al. (2021) Model Comparison Plots
36 min
Using ggplot2 to recreate the model comparison plots of Murphy et al. (2021).
Derek H. Ogle
Apr 11, 2023

Apr 11, 2023

O’Malley et al. (2021) Regression Plots
13 min
Using ggplot2 to recreate the regresion plots of O’Malley et al. (2021).
Derek H. Ogle
Apr 6, 2023

Apr 7, 2023

Vasquez et al. (2022) Kuskal-Wallis Results
9 min
Using ggplot2 to display results from Kruskal-Wallis test.
Derek H. Ogle
Apr 5, 2023

Apr 4, 2023

How Does Size Work in ggplot2
19 min
Demonstration of size= and linewidth= in ggplot2 objects.
Derek H. Ogle
Apr 3, 2023

Apr 3, 2023

Miller et al. (2022) Catch Curve Plot
8 min
Using ggplot2 to recreate the catch curve plot in Miller et al. (2022).
Derek H. Ogle
Apr 1, 2023

Apr 1, 2023

Miller et al. (2022) Size Plots
12 min
Using ggplot2 to recreate the length frequency histogram and weight-length relationships plots in Miller et al. (2022).
Derek H. Ogle
Mar 31, 2023

Mar 30, 2023

Nested X-Axis Labels
20 min
Creating nested labels for the x-axis in ggplot2.
Derek H. Ogle
Mar 30, 2023

Mar 29, 2023

Miller et al. (2022) CPE Plot
10 min
Using ggplot2 to recreate the CPE times series plot for two reservoirs in Miller et al. (2022).
Derek H. Ogle
Mar 29, 2023

Mar 28, 2023

McCarrick et al. (2022) Back-Calculated TL Plots
11 min
Using ggplot2 to recreate the boxplot and bar chart of back-calculated lengths at age in McCarrick et al. (2022).
Derek H. Ogle
Mar 28, 2023

Mar 27, 2023

McCarrick et al. (2022) Age Composition Plot
11 min
Using ggplot2 to recreate the age composition by year figure in McCarrick et al. (2022).
Derek H. Ogle
Mar 27, 2023

Mar 25, 2023

McCarrick et al. (2022) Wr Plot
8 min
Using ggplot2 to recreate the relative weight (wr) by year figure in McCarrick et al. (2022).
Derek H. Ogle
Mar 26, 2023

Mar 24, 2023

McCarrick et al. (2022) PSD Plot
12 min
Using ggplot2 to recreate the PSD by year figure in McCarrick et al. (2022). Extended it to include CIs.
Derek H. Ogle
Mar 25, 2023

Mar 23, 2023

McCarrick et al. (2022) CPE Plot
15 min
Using ggplot2 to recreate the cpe by species, year, and length category figure in McCarrick et al. (2022).
Derek H. Ogle
Mar 22, 2023

Mar 21, 2023

Rook et al. (2022) Estimated Cisco Stocking Densities
14 min
Using ggplot2 to recreate the figure of estimated Cisco stocking densities in Rook et al. (2022).
Derek H. Ogle
Mar 20, 2023

Mar 19, 2023

Rook et al. (2022) Cisco Harvest Figure
14 min
Using ggplot2 to recreate the figure of Great Lakes Coregonid harvest in Rook et al. (2022).
Derek H. Ogle
Mar 17, 2023

Mar 19, 2023

Axis Magic
25 min
Some tricks with respect to axes in ggplot2.
Derek H. Ogle
Mar 15, 2023

Mar 29, 2023

Using vjust= and hjust=
11 min
Explaining the use of vjust= and hjust= to position objects in ggplots.
Derek H. Ogle
Mar 10, 2023

Mar 19, 2023

Clemens (2022) Temperature Figure
10 min
Using ggplot2 to recreate the temperature figure in Clemens (2022).
Derek H. Ogle
Mar 9, 2023

Mar 19, 2023

Mack and Cheatwood (2022) Cumulative Sums Figure
8 min
Using ggplot2 to recreate the cumulative sums figures in Mack and Cheatwood (2022).
Derek H. Ogle
Mar 8, 2023

Mar 19, 2023

Landry et al. (2022) Logistic Regression Figures
15 min
Using ggplot2 to recreate the logistic regression figures in Landry et al. (2022).
Derek H. Ogle
Mar 6, 2023

Mar 6, 2023

Ulaski et al. (2022) Growth-Maturity Figure
17 min
Using ggplot2 to recreate the growth and maturity figure in Ulaski et al. (2022).
Derek H. Ogle
Feb 16, 2023

Mar 19, 2023

Vaisvil et al. (2022) Hatching Date Figure
10 min
Using ggplot2 to recreate the bass hatching date figure in Vaisvil et al. (2022).
Derek H. Ogle
Feb 15, 2023

Mar 19, 2023

Quist et al. (2022) Back-Calculation Figure
7 min
Using ggplot2 to recreate the back-calculated length-at-age figure in Quist et al. (2022).
Derek H. Ogle
Feb 14, 2023

Feb 14, 2023

Quist et al. (2022) Age Comparison Figures
14 min
Using ggplot2 to recreate the age comparison figures in Quist et al. (2022).
Derek H. Ogle
Feb 13, 2023

Feb 13, 2023

AFS Style in ggplot2 Figures
17 min
Suggestions for the Glassic et al. (2019) process for modifying ggplot2 graphs to match the AFS Style Guide.
Derek H. Ogle
Dec 22, 2022

Feb 13, 2023

Replace residPlot() with ggplot
9 min
Using ggplot() as an alternative to residPlot() which was removed from FSA.
Derek H. Ogle
Jun 1, 2021

Dec 14, 2022

Replace filterD()
2 min
An alternative to filterD() which was removed from FSA.
Derek H. Ogle
May 26, 2021

Dec 19, 2022

Replace fitPlot() with ggplot
13 min
Using ggplot() as an alternative to fitPlot() which was removed from FSA.
Derek H. Ogle
May 25, 2021

Dec 27, 2022

Replace compIntercepts() with emmeans()
6 min
Using emmeans() from emmeans as an alternative to compIntercepts() which was removed from FSA.
Derek H. Ogle
May 12, 2021

Jan 1, 2023

Replace compSlopes() with emtrends()
6 min
Using emtrends() from emmeans as an alternative to compSlopes() which was removed from FSA.
Derek H. Ogle
May 11, 2021

Jan 1, 2023

Age Bias Plots in ggplot2
9 min
Flexibly construct age bias and age difference plots using ggplot2
Michael Lant
Mar 15, 2021

Dec 7, 2022

von Bertalanffy Growth Plots I
11 min
How to plot one von Bertalanffy growth model with data.
Derek H. Ogle
Dec 31, 2019

Jun 14, 2023

Length Frequency Histograms in ggplot2
6 min
Flexibly construct length frequency histograms using ggplot2
Derek H. Ogle
Dec 28, 2019

Mar 19, 2023

von Bertalanffy Growth Plots II
20 min
How to plot multiple von Bertalanffy growth models with data.
Derek H. Ogle
Jan 2, 2019

Feb 13, 2023

Collapsing Categories or Values
8 min
How to collapse categories or values into other categories
Derek H. Ogle
Mar 30, 2018

Dec 19, 2022

Stock-Recruitment Graphing Questions
8 min
A reply to a user’s questions with respect to stock-recruitment function graphics.
Derek H. Ogle
Dec 12, 2017

Dec 18, 2022

Plots of Back-Calculated Lengths-At-Age
9 min
Initial thoughts on displaying back-calculated lengths-at-age.
Derek H. Ogle
Nov 7, 2017

Feb 13, 2023

Mean Weights at Ages From Lengths
16 min
Demonstrates concerns and corrections with estimating mean weight from observed lengths and a weight-length relationship.
Derek H. Ogle
Aug 9, 2017

Feb 13, 2023

Ridgeline Length Frequency Plots
3 min
How to visualize multiple length frequencies as ridgline plots.
Derek H. Ogle
Jul 28, 2017

Feb 13, 2023

Bland-Altman Plot for Age Comparisons?
11 min
Explore the use of Bland-Altman plots for comparing paired age estimates.
Derek H. Ogle
Apr 20, 2017

Feb 13, 2023

Computing SE for PSD indices
2 min
Demonstrate how to compute SE for PSD indices.
Derek H. Ogle
Dec 9, 2016

Dec 19, 2022

Pauly et al. (1992) Seasonal Cessation Growth Model
3 min
Announcement of an algorithm to fit the Pauly et al. (1992) seasonal cessation growth model
Derek H. Ogle
Nov 11, 2016

Feb 13, 2023

Two New Cumulative Sum Functions
2 min
Introducing the missing current and reverse cumulative sum functions.
Derek H. Ogle
Sep 6, 2015

Dec 19, 2022

Age Comparison Results for Individual Fish
2 min
Demonstrates how to extract age comparison results for individual fish from the object returned by ageComparisons().
Derek H. Ogle
Sep 5, 2015

Dec 7, 2022
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