Functions to support simple fisheries stock assessment methods.

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Documentation for package ‘FSA’ version 0.4.0

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A B C D E F G H K L M O P R S T V W

FSA-package Fisheries stock assessment methods and data.

-- A --

addRadCap Add a total radius-at-capture variable to a data frame that contains one-fish-per-line increments data.
addZeroCatch Adds zero catch values for sampling events and species that were not captured.
ageComp Results for comparing paired sets of ages.
ageKey Applies an age-length key to individuals in a length-sample.
anova.catchCurve Mortality estimates from the descending limb of a catch curve.
anova.depletion Computes the Leslie or Delury population estimate from catch and effort data.
anova.emplm Computes the standard weight equation using the emperical-percentile method.
anova.empq Methods to assess length-bias in a proposed standard weight equation.
anova.rlp Computes the standard weight equation using the regression-line-percentile method.

-- B --

bcFuns Creates a function for a specific back-calculation model.
binCI Confidence intervals for binomial probability of success.
BluegillJL Capture histories (2 samples) of bluegill from Jackson Lake.
BluegillLM Length and weight of bluegill from Lake Mary, MN.
BrookTroutTH Catch-at-age for Tobin Harbor, Isle Royale brook trout.

-- C --

capFirst Capitalizes ONLY the first letter in a string.
capHistConvert Converts between different capture history recording types.
capHistSum Summarize individual fish capture histories.
catchCurve Mortality estimates from the descending limb of a catch curve.
catchCurve.default Mortality estimates from the descending limb of a catch curve.
catchCurve.formula Mortality estimates from the descending limb of a catch curve.
catchCurveSim Dynamics plots to explore catch-curve models.
chapmanPlot Constructs Ford-Walford and Chapman plots for mean length-at-age data.
chapmanPlot.default Constructs Ford-Walford and Chapman plots for mean length-at-age data.
chapmanPlot.formula Constructs Ford-Walford and Chapman plots for mean length-at-age data.
chapmanRobson Computes Chapman-Robson estimates of S and Z.
chapmanRobson.default Computes Chapman-Robson estimates of S and Z.
chapmanRobson.formula Computes Chapman-Robson estimates of S and Z.
chooseColors Allows user to create a list of colors from among a variety of color palettes.
CodNorwegian Stock and recruitment data for Norwegian cod,1937-1960.
coef.catchCurve Mortality estimates from the descending limb of a catch curve.
coef.depletion Computes the Leslie or Delury population estimate from catch and effort data.
coef.emp Computes the standard weight equation using the emperical-percentile method.
coef.empq Methods to assess length-bias in a proposed standard weight equation.
coef.FroeseWs Computes the standard weight equation using the methods described in Froese (2006).
coef.rlp Computes the standard weight equation using the regression-line-percentile method.
cohortSim Dynamics plots to explore numbers in a cohort over time.
confint.bootCase Associated S3 methods for bootCase from car.
confint.catchCurve Mortality estimates from the descending limb of a catch curve.
confint.chapmanRobson Computes Chapman-Robson estimates of S and Z.
confint.depletion Computes the Leslie or Delury population estimate from catch and effort data.
confint.mrClosed Estimate initial population size for single or multiple census mark-recapture data.
confint.mrOpen Estimate initial population size for multiple census mark-recapture data from an open population.
confint.nlsBoot Construct a confidence interval from nlsBoot results.
confint.nlsboot Construct a confidence interval from nlsBoot results.
confint.removal Computes population estimates for k-, 3-, or 2-pass removal data.
CutthroatAL Capture histories (3 samples) of cutthroat trout from Auke Lake.

-- D --

depletion Computes the Leslie or Delury population estimate from catch and effort data.
dietOverlap Computes indices of diet overlap between two species.

-- E --

Ecoli Population growth of Escherchia coli.
emp Computes the standard weight equation using the emperical-percentile method.

-- F --

fact2num Converts "numeric" factor levels to numeric values.
fishR Opens web pages associated with the fishR site.
fitPlot Fitted model plot for an lm, glm, or nls object.
fitPlot.emplm Computes the standard weight equation using the emperical-percentile method.
fitPlot.empq Methods to assess length-bias in a proposed standard weight equation.
fitPlot.emprq Computes the standard weight equation using the emperical-percentile method.
fitPlot.glm Fitted model plot for an lm, glm, or nls object.
fitPlot.IVR Fitted model plot for an lm, glm, or nls object.
fitPlot.lm Fitted model plot for an lm, glm, or nls object.
fitPlot.logreg Fitted model plot for an lm, glm, or nls object.
fitPlot.nls Fitted model plot for an lm, glm, or nls object.
fitPlot.ONEWAY Fitted model plot for an lm, glm, or nls object.
fitPlot.POLY Fitted model plot for an lm, glm, or nls object.
fitPlot.rlp Computes the standard weight equation using the regression-line-percentile method.
fitPlot.SLR Fitted model plot for an lm, glm, or nls object.
fitPlot.TWOWAY Fitted model plot for an lm, glm, or nls object.
FroeseWs Computes the standard weight equation using the methods described in Froese (2006).
FSA Fisheries stock assessment methods and data.
FSANews Read news and changes in the 'FSA' package.
fsaNews Read news and changes in the 'FSA' package.

-- G --

gConvert Converts between growth measurement data types.
gReshape Reshapes a one-fish-per-line data frame to a one-measurement-per-line data frame.
growthModels Show the growth model formulas implemented in the FSA package.
growthModelSim Dynamics plots to explore typical fisheries growth models.
growthRadPlot Constructs skeleton plots of radial or proportional radial measurements made at annuli on fish calcified structures.

-- H --

hist.bootCase Associated S3 methods for bootCase from car.
hist.formula Creates separate histograms by levels.
histStack Stacked histogram.
histStack.default Stacked histogram.
histStack.formula Stacked histogram.
hoCoef Performs a hypothesis test that a parameter in a linear model is equal to some specific value.
htest Constructs a p-value for a bootstrapped hypothesis test using nlsBoot.
htest.bootCase Associated S3 methods for bootCase from car.
htest.nlsBoot Constructs a p-value for a bootstrapped hypothesis test using nlsBoot.
hyperCI Confidence interval for population size (N) in hypergeometric distribution.

-- K --

ks2d Computes the D test statistic for the two-sample two-dimensional Kolmogrov-Smirnov test.
ks2dp A permutation test to compute a p-value for the D test statistic for the two-sample two-dimensional Kolmogrov-Smirnov test.
KS2D_NR Data from Figure 14.7.1 of Numerical Recipes
ksTest Kolmogorov-Smirnov Tests.
ksTest.default Kolmogorov-Smirnov Tests.
ksTest.formula Kolmogorov-Smirnov Tests.

-- L --

lagratio Ratio of lagged observations.
lencat Constructs length class/category variable.
lenFreqExpand Expands a length frequency based on a subsample.
leslieSim Dynamic plots to explore the Leslie depletion model.
LMBassWs Length-weight regression results for computing Ws for largemouth bass.
lwModelSim Dynamics plots to explore length-weight power function models.
lwPredsComp Constructs plots of predicted weights at given lengths among different groups.

-- M --

Mirex Mirex concentration, weight, capture year, and species of Lake Ontario salmon.
mrClosed Estimate initial population size for single or multiple census mark-recapture data.
mrClosed1Sim Dynamics plots to explore single-census mark-recapture models.
mrOpen Estimate initial population size for multiple census mark-recapture data from an open population.

-- O --

odd Determines if a number is odd.

-- P --

paletteChoices Provides a vector of possible color palettes.
PikeNY Summarized multiple mark-recapture data for all northern pike from Buckthorn Marsh.
PikeNYPartial1 Capture histories (4 samples), in capture history format, of a subset of northern pike from Buckthorn Marsh.
plot.ageComp Results for comparing paired sets of ages.
plot.bootCase Associated S3 methods for bootCase from car.
plot.catchCurve Mortality estimates from the descending limb of a catch curve.
plot.chapmanRobson Computes Chapman-Robson estimates of S and Z.
plot.depletion Computes the Leslie or Delury population estimate from catch and effort data.
plot.emplm Computes the standard weight equation using the emperical-percentile method.
plot.empq Methods to assess length-bias in a proposed standard weight equation.
plot.FroeseWs Computes the standard weight equation using the methods described in Froese (2006).
plot.ks2d Computes the D test statistic for the two-sample two-dimensional Kolmogrov-Smirnov test.
plot.ks2dp A permutation test to compute a p-value for the D test statistic for the two-sample two-dimensional Kolmogrov-Smirnov test.
plot.mrClosed Estimate initial population size for single or multiple census mark-recapture data.
plot.rlp Computes the standard weight equation using the regression-line-percentile method.
plotBinResp Plots a binary response variable versus a quantitative explanatory variable.
plotBinResp.default Plots a binary response variable versus a quantitative explanatory variable.
plotBinResp.formula Plots a binary response variable versus a quantitative explanatory variable.
plotH Scatterplot with histogram-like bars.
plotH.default Scatterplot with histogram-like bars.
plotH.formula Scatterplot with histogram-like bars.
poiCI Confidence interval for Poisson rate parameter.
popSizesPlot Constructs a plot of population size versus time from the projection of Leslie matrix.
pos2adj Convert a "directional" position to "adj" values for labeling a point.
predict.bootCase Associated S3 methods for bootCase from car.
predict.emp Computes the standard weight equation using the emperical-percentile method.
predict.empq Methods to assess length-bias in a proposed standard weight equation.
predict.nlsBoot Constructs a prediction and confidence interval from nlsBoot results.
predict.nlsboot Constructs a prediction and confidence interval from nlsBoot results.
predict.rlp Computes the standard weight equation using the regression-line-percentile method.
print.dietOverlap Computes indices of diet overlap between two species.
print.ks2d Computes the D test statistic for the two-sample two-dimensional Kolmogrov-Smirnov test.
print.ks2dp A permutation test to compute a p-value for the D test statistic for the two-sample two-dimensional Kolmogrov-Smirnov test.
print.willis Methods to assess length-bias in a proposed standard weight equation.
psdVal Finds Gabelhouse five-cell length categories (for PSS) for a particular species.
pssCalc Convenience function for caculating PSS-X values.
pssDataPrep Add five-cell length categories specific to a species to an entire data frame.
PSSlit Gabelhouse five-cell length categories for various species.
pssPlot Length-frequency histogram with PSS-X categories highlighted.
pssVal Finds Gabelhouse five-cell length categories (for PSS) for a particular species.

-- R --

rcumsum Computes the reverse cumulative sum of a vector.
recodeSpecies Recodes species names according to user choice or to have capitalization only for the first word in the name.
removal Computes population estimates for k-, 3-, or 2-pass removal data.
residPlot Construct a residual plot from lm or nls objects.
residPlot.emplm Computes the standard weight equation using the emperical-percentile method.
residPlot.IVR Construct a residual plot from lm or nls objects.
residPlot.lm Construct a residual plot from lm or nls objects.
residPlot.nls Construct a residual plot from lm or nls objects.
residPlot.ONEWAY Construct a residual plot from lm or nls objects.
residPlot.POLY Construct a residual plot from lm or nls objects.
residPlot.rlp Computes the standard weight equation using the regression-line-percentile method.
residPlot.SLR Construct a residual plot from lm or nls objects.
residPlot.TWOWAY Construct a residual plot from lm or nls objects.
residualPlot Construct a residual plot from lm or nls objects.
rlp Computes the standard weight equation using the regression-line-percentile method.
rsdVal Finds Gabelhouse five-cell length categories (for PSS) for a particular species.
RuffeWs Raw Length-weight data that can be used to compute the Ws for ruffe.

-- S --

simAgeBias Simulate an age bias and simulate the ages of fish using the age bias.
simAges Simulate an age structure.
simApplyAgeBias Simulate an age bias and simulate the ages of fish using the age bias.
simLenFromAge Simulate fish length from given ages.
simLenSelectM Simulate sampling fish based on length selectivity.
simLenSelectP Simulate sampling fish based on length selectivity.
SMBassLS Catch-effort data for Little Silver Lake smallmouth bass.
SMBassWB Growth increment data for West Bearskin Lake smallmouth bass.
SpotVA1 Age and length of spot.
srCobWeb Plots typical fisheries stock-recruitment models with cobwebbing traces.
srFuns Creates a function for a specific stock-recruitment model parameterization.
srModels Show the stock-recruitment model formulas implemented in FSA.
srSim Dynamic plots to explore typical fisheries stock-recruitment models.
srStarts Finds reasonable starting values for the parameters in a specific stock-recruitment model parameterization.
srStarts.default Finds reasonable starting values for the parameters in a specific stock-recruitment model parameterization.
srStarts.formula Finds reasonable starting values for the parameters in a specific stock-recruitment model parameterization.
StripedBass1 Age of striped bass assigned from scales and otoliths.
Subset Subsets a data frame and drops the unused levels.
Subset.data.frame Subsets a data frame and drops the unused levels.
Summarize Summary statistics for a numeric or factor variable.
Summarize.default Summary statistics for a numeric or factor variable.
Summarize.formula Summary statistics for a numeric or factor variable.
summary.ageComp Results for comparing paired sets of ages.
summary.catchCurve Mortality estimates from the descending limb of a catch curve.
summary.chapmanRobson Computes Chapman-Robson estimates of S and Z.
summary.depletion Computes the Leslie or Delury population estimate from catch and effort data.
summary.dietOverlap Computes indices of diet overlap between two species.
summary.emp Computes the standard weight equation using the emperical-percentile method.
summary.empq Methods to assess length-bias in a proposed standard weight equation.
summary.mrClosed Estimate initial population size for single or multiple census mark-recapture data.
summary.mrOpen Estimate initial population size for multiple census mark-recapture data from an open population.
summary.removal Computes population estimates for k-, 3-, or 2-pass removal data.
summary.rlp Computes the standard weight equation using the regression-line-percentile method.
summary.willis Methods to assess length-bias in a proposed standard weight equation.
swvANOVA Specific utilities for use in a Sweave/knitr document.
swvCode Specific utilities for use in a Sweave/knitr document.
swvCounts Specific utilities for use in a Sweave/knitr document.
swvFinish Specific utilities for use in a Sweave/knitr document.
swvGLHT Specific utilities for use in a Sweave/knitr document.
swvHtest Specific utilities for use in a Sweave/knitr document.
swvPvalue Specific utilities for use in a Sweave/knitr document.
swvREG Specific utilities for use in a Sweave/knitr document.

-- T --

tictactoe Constructs the base tic-tac-toe graph for presenting predator-prey PSS values.
tictactoeAdd Adds point and confidence intervals for observed preator-prey PSS to tic-tac-toe graph.
TroutDietSL Size and diet data for lake and bull trout from Swan Lake, Montana.
typeoflm Identify specific model type from lm object.

-- V --

vbComp Evaluates and plots the traditional von Bertalanffy growth model for several sets of parameter choices.
vbDataGen Randomly create a von Bertalanffy data set.
vbFuns Creates a function for a specific von Bertalanffy parameterization.
VBGMlit Von Bertalanffy parameter estimates from the literature.
vbModels Show the growth model formulas implemented in the FSA package.
vbStarts Finds reasonable starting values for the parameters in a specific von Bertalanffy model parameterization.
vbStarts.default Finds reasonable starting values for the parameters in a specific von Bertalanffy model parameterization.
vbStarts.formula Finds reasonable starting values for the parameters in a specific von Bertalanffy model parameterization.
view Shows a random selection of rows from a data frame or matrix.

-- W --

walfordPlot Constructs Ford-Walford and Chapman plots for mean length-at-age data.
walfordPlot.default Constructs Ford-Walford and Chapman plots for mean length-at-age data.
walfordPlot.formula Constructs Ford-Walford and Chapman plots for mean length-at-age data.
WalleyeGerowLW Raw length-weight data that can be used to compute the Ws for walleye as performed in Gerow (2005).
WR79 Age and length for a hypothetical sample from Westerheim and Ricker (1979).
wrAdd Appends standard weight and relative weight variables to a data frame.
wrDataPrep Add standard and relative weights specific to a species to an entire data frame.
WSlit Standard weight equations for various species.
wsVal Finds standard weight equation coefficients for a particular species.
wsValidate Methods to assess length-bias in a proposed standard weight equation.