Introductory Fisheries Analyses with R

• Main Author: Ogle, Derek H.
• Format: eBook Book
• Language: English
• Published: Boca Raton CRC Press 2016; CRC Press LLC; Chapman & Hall
• Edition: 1
• Series: Chapman & Hall/CRC The R Series
• Subjects: ANOVA; BIOSCIENCEnetBASE; Ecology - Environment Studies; ENVIROnetBASE; ENVIRONMENTALSCIENCEnetBASE; Fisheries > Computer programs; Fisheries > Statistics; fisheries data; fisheries science; fisheries stock assessment; fisheries stock assessment analyses; fisheries-specific analyses; Fishery management; Fishery sciences > Computer programs; Fishery sciences > Statistics; Handbooks, manuals, etc; LIFESCIENCEnetBASE; linear regression; Marine & Aquatic Science; metrics to assess fish populations; nonlinear regression; population dynamics; R (Computer program language); R for fisheries analyses and graphics; R functions; SCI-TECHnetBASE; script-based analyses; Statistics for the Biological Sciences; STATSnetBASE; STMnetBASE; stock-recruit relationship; Alk; Creek Chubs; Negative Log Likelihood Values; Quantile Regression; White Cells; Catch Curve; Bull Trout; Dummy Variable; Fulton’s Condition Factor; ANOVA Table; Von Bertalanffy Growth Func Tion; Weight Length Relationship; CSV File; Relative Condition Factor; NA NA NA NA NA; Cutthroat Trout; Black Crappie; Largemouth Bass; Beverton Holt Function; Descending Limb; Length Interval; Fork Length; NA NA NA NA; Homoscedasticity Assumption
• ISBN: 9781482235203; 148223520X
• DOI: 10.1201/9781315371986

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...

Table of Contents:

• 9.2 Closed Population, Single Recapture -- 9.3 Closed Population, Multiple Recaptures -- 9.4 Open Populations -- 9.5 Further Considerations -- 10 Abundance from Depletion Data -- 10.1 Leslie and DeLury Methods -- 10.2 K-Pass Removal Methods -- 11 Mortality Rates -- 11.1 Total Mortality Definitions -- 11.2 Total Mortality from Catch Curve Data -- 11.3 Total Mortality from Capture-Recapture Data -- 11.4 Mortality Components -- 11.5 Further Considerations -- 12 Individual Growth -- 12.1 Data Requirements -- 12.2 Growth Functions -- 12.3 Fitting Nonlinear Regressions -- 12.4 Among Group Statistical Comparisons -- 12.5 Typical Model Fitting Problems -- 12.6 Further Considerations -- 13 Recruitment -- 13.1 Stock-Recruitment Relationships -- 13.2 Spawning Potential Ratio -- 13.3 Year-Class Strength -- 13.4 Further Considerations -- References -- Subject Index -- R Functions (Demonstrated) Index -- R Functions (Mentioned) Index -- Scientific Names
• Cover -- Half Title -- Title Page -- Copyright Page -- Dedication -- Table of Contents -- Preface -- Author -- 1 (Very Brief) Introduction to R Basics -- 1.1 Why R for Fisheries Scientists? -- 1.2 Installing R and RStudio -- 1.3 Packages -- 1.4 Prompts, Expressions, and Comments -- 1.5 Objects -- 1.6 Functions -- 1.7 Data Storage -- 1.8 More with Functions -- 1.9 Looping -- 1.10 Saving Results -- 1.11 Getting Help -- 2 Loading Data and Basic Manipulations -- 2.1 Loading Data into R -- 2.2 Basic Data Manipulations -- 2.3 Joining Data.Frames -- 2.4 Rearranging Data.Frames -- 2.5 New Data.frame from Aggregation -- 2.6 Exporting Data.Frames to External Data Files -- 2.7 Further Considerations -- 3 Plotting Fundamentals -- 3.1 Scatterplots -- 3.2 Line Plots -- 3.3 Histograms -- 3.4 Bar Plots -- 3.5 Fitted Model Plots -- 3.6 Some Finer Control of Plots -- 3.7 Saving or Exporting Plots -- 4 Age Comparisons -- 4.1 Data Requirements -- 4.2 Age Bias Plot -- 4.3 Bias Metrics -- 4.4 Precision Metrics -- 4.5 Further Considerations -- 5 Age-Length Keys -- 5.1 Foundational Background -- 5.2 Constructing an Age-Length Key -- 5.3 Visualizing an Age-Length Key -- 5.4 Apply an Age-Length Key -- 5.5 Among Group Statistical Comparisons -- 5.6 Further Considerations -- 6 Size Structure -- 6.1 Data Requirements -- 6.2 Length Frequency -- 6.3 Proportional Size Distribution (PSD) -- 6.4 Among Group Statistical Comparisons -- 6.5 Further Considerations -- 7 Weight-Length Relationships -- 7.1 Data Requirements -- 7.2 Weight-Length Model -- 7.3 Fitting Linear Regressions -- 7.4 Among Group Statistical Comparisons -- 7.5 Further Considerations -- 8 Condition -- 8.1 Data Requirements -- 8.2 Condition Metrics -- 8.3 Among Group Statistical Comparisons -- 8.4 Further Considerations -- 9 Abundance from Capture-Recapture Data -- 9.1 Data Requirements