Introductory Fisheries Analyses with R: 1st Edition (Hardback) book cover

Introductory Fisheries Analyses with R

1st Edition

By Derek H. Ogle

Chapman and Hall/CRC

317 pages | 76 B/W Illus.

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pub: 2015-11-24
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Description

A How-To Guide for Conducting Common Fisheries-Related Analyses in R

Introductory Fisheries Analyses with R provides detailed instructions on performing basic fisheries stock assessment analyses in the R environment. Accessible to practicing fisheries scientists as well as advanced undergraduate and graduate students, the book demonstrates the flexibility and power of R, offers insight into the reproducibility of script-based analyses, and shows how the use of R leads to more efficient and productive work in fisheries science.

The first three chapters present a minimal introduction to the R environment that builds a foundation for the fisheries-specific analyses in the remainder of the book. These chapters help you become familiar with R for basic fisheries analyses and graphics.

Subsequent chapters focus on methods to analyze age comparisons, age-length keys, size structure, weight-length relationships, condition, abundance (from capture-recapture and depletion data), mortality rates, individual growth, and the stock-recruit relationship. The fundamental statistical methods of linear regression, analysis of variance (ANOVA), and nonlinear regression are demonstrated within the contexts of these common fisheries analyses. For each analysis, the author completely explains the R functions and provides sufficient background information so that you can confidently implement each method.

Web Resource

The author’s website at http://derekogle.com/IFAR/ includes the data files and R code for each chapter, enabling you to reproduce the results in the book as well as create your own scripts. The site also offers supplemental code for more advanced analyses and practice exercises for every chapter.

Table of Contents

(Very Brief) Introduction to R Basics

Why R for Fisheries Scientists?

Installing R and RStudio

Packages

Prompts, Expressions, and Comments

Objects

Functions

Data Storage

More with Functions

Looping

Saving Results

Getting Help

Loading Data and Basic Manipulations

Loading Data into R

Basic Data Manipulations

Joining Data.Frames

Re-Arranging Data.Frames

New Data.Frame from Aggregation

Exporting Data.Frames to External Data Files

Further Considerations

Plotting Fundamentals

Scatterplots

Line Plots

Histograms

Bar Plots

Fitted Model Plots

Some Finer Control of Plots

Saving or Exporting Plots

Age Comparisons

Data Requirements

Age-Bias Plot

Bias Metrics

Precision Metrics

Further Considerations

Age-Length Keys

Foundational Background

Constructing an Age-Length Key

Visualizing the Age-Length Key

Apply an Age-Length Key

Statistically Compare Age-Length Keys

Further Considerations

Size Structure

Data Requirements

Length Frequency

Proportional Size Distribution (PSD)

Among-Group Statistical Comparisons

Further Considerations

Weight-Length Relationships

Data Requirements

Weight-Length Model

Fitting Linear Regressions

Among-Group Statistical Comparisons

Further Considerations

Condition

Data Requirements

Condition Metrics

Among Group Statistical Comparisons

Further Considerations

Abundance from Capture-Recapture Data

Data Requirements

Closed Population, Single Recapture

Closed Population, Multiple Recaptures

Open Populations

Further Considerations

Abundance from Depletion Data

Leslie and DeLury Methods

K-Pass Removal Methods

Mortality Rates

Total Mortality Definitions

Total Mortality from Catch Curve Data

Total Mortality from Capture-Recapture Data

Mortality Components

Further Considerations

Individual Growth

Data Requirements

Growth Functions

Fitting Nonlinear Regressions

Among-Group Statistical Comparisons

Typical Model Fitting Problems

Further Considerations

Recruitment

Stock-Recruitment Relationships

Spawning Potential Ratio

Year-Class Strength

Further Considerations

References

Subject Index

R Functions (Demonstrated) Index

R Functions (Mentioned) Index

Scientific Names

About the Author

Derek H. Ogle is a professor of mathematical sciences and natural resources at Northland College, where he teaches statistics and fisheries science courses and has received awards for teaching, scholarly work, service, and assessment activities. Dr. Ogle maintains the fishR website, which is dedicated to sharing information on how to perform fisheries analyses in R. He earned a PhD in fisheries science from the University of Minnesota. His research interests include the population dynamics of invasive species and little-studied native species.

About the Series

Chapman & Hall/CRC The R Series

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Subject Categories

BISAC Subject Codes/Headings:
MAT029000
MATHEMATICS / Probability & Statistics / General
NAT011000
NATURE / Environmental Conservation & Protection
SCI039000
SCIENCE / Life Sciences / Biology / Marine Biology