(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
Biography
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.
