Simple Fisheries Stock Assessment Methods


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Documentation for package ‘FSA’ version 0.8.13

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A B C D E F G H I J K L M N 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 zeros for catches of species not collected in some sampling events.
ageBias Compute and view possible differnces between paired sets of ages.
agePrecision Compute measures of precision among sets of ages.
alkAgeDist Proportions-at-age from an Age-Length Key
alkIndivAge Use an age-length key to assign age to individuals in the unaged sample.
alkMeanVar Mean Values-at-age from an Age-Length Key
alkPlot Plots to visualize age-length keys.
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.

-- 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 Jewett Lake, MI.
bootstrap Associated S3 methods for bootCase from car.
BrookTroutTH Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.

-- C --

capFirst Capitalizes the first letter of first or all words in a string.
capHistConvert Convert between capture history data.frame formats.
capHistSum Summarize capture histories in individual fish format.
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.
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.
ChinookArg Lengths and weights for Chinook Salmon from three locations in Argentina.
chooseColors 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.chapmanRobson Computes Chapman-Robson estimates of S and Z.
coef.depletion Computes the Leslie or DeLury population estimate from catch and effort data.
col2rgbt Converts an R color to RGB (red/green/blue) including a transparency (alpha channel).
compIntercepts Tests for significant differences among all pairs of intercepts in a dummy variable regression.
compSlopes Tests for significant differences among all pairs of slopes in a dummy variable regression (DVR).
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.mrClosed1 Estimate initial population size for single or multiple census mark-recapture data.
confint.mrClosed2 Estimate initial population size for single or multiple census mark-recapture data.
confint.mrOpen Jolly-Seber analysis from multiple mark-recapture events from an open population.
confint.nlsBoot Associated S3 methods for nlsBoot from nlstools.
confint.nlsboot Associated S3 methods for nlsBoot from nlstools.
confint.removal Population estimates for k-, 3-, or 2-pass removal data.
CutthroatAL Capture histories (9 samples) of Cutthroat Trout from Auke Lake.

-- D --

depletion Computes the Leslie or DeLury population estimate from catch and effort data.
diags Extract diagonals from a matrix.
dunnTest Dunn's Kruskal-Wallis Multiple Comparisons.
dunnTest.default Dunn's Kruskal-Wallis Multiple Comparisons.
dunnTest.formula Dunn's Kruskal-Wallis Multiple Comparisons.

-- E --

Ecoli Population growth of Escherichia coli.
expandCounts Repeat individual fish data (including lengths) from tallied counts.
expandLenFreq Expands a length frequency based on a subsample.
extraSS Likelihood ratio and extra sum-of-squares tests.
extraTests Likelihood ratio and extra sum-of-squares tests.

-- F --

fact2num Converts "numeric" factor levels to numeric values.
filterD Subsets/filters a data frame and drops the unused levels.
fishR Opens web pages associated with the fishR website.
fitPlot Fitted model plot for an lm, glm, or nls object.
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.SLR Fitted model plot for an lm, glm, or nls object.
fitPlot.TWOWAY Fitted model plot for an lm, glm, or nls object.
FSA Fisheries stock assessment methods and data.
FSANews Read news and changes for the 'FSA' package.
fsaNews Read news and changes for the 'FSA' package.
FSAUtils Capitalizes the first letter of first or all words in a string.

-- G --

gConvert Converts between types of measurements from calcified structures.
geomean Calculates the geometric mean or geometric standard deviation.
geosd Calculates the geometric mean or geometric standard deviation.
GompertzFuns Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
growthFunShow Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
growthModels Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.

-- H --

headtail Shows rows from the head and tail of a data frame or matrix.
hist.bootCase Associated S3 methods for bootCase from car.
hist.formula Creates separate histograms by levels.
histFromSum Create a histogram from a frequency table.
histFromSum.default Create a histogram from a frequency table.
histFromSum.formula Create a histogram from a frequency table.
histFromSum.table Create a histogram from a frequency table.
hoCoef Performs a hypothesis test that a linear model parameter is equal to a specific value.
htest Associated S3 methods for nlsBoot from nlstools.
htest.bootCase Associated S3 methods for bootCase from car.
htest.nlsBoot Associated S3 methods for nlsBoot from nlstools.
hyperCI Confidence interval for population size (N) in hypergeometric distribution.

-- I --

is.CapHist Summarize capture histories in individual fish format.
is.even Determine if a number is odd or even.
is.odd Determine if a number is odd or even.

-- J --

jolly Jolly-Seber analysis from multiple mark-recapture events from an open population.

-- K --

kCounts Specific utilities for use in a knitr document.
kPvalue Specific utilities for use in a knitr document.
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.
lencat.default Constructs length class/category variable.
lencat.formula Constructs length class/category variable.
logbtcf Constructs the correction-factor used when back-transforming log-transformed values.
logisticFuns Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
lrt Likelihood ratio and extra sum-of-squares tests.
lwCompPreds Constructs plots of predicted weights at given lengths among different groups.

-- M --

mapvalues Replace specified values in a vector or factor with new values.
metaM Estimate natural mortality from a variety of empirical methods.
Mirex Mirex concentration, weight, capture year, and species of Lake Ontario salmon.
Mmethods Estimate natural mortality from a variety of empirical methods.
mrClosed Estimate initial population size for single or multiple census mark-recapture data.
mrOpen Jolly-Seber analysis from multiple mark-recapture events from an open population.

-- N --

nlsTracePlot Adds model fits from nls iterations to active plot.

-- O --

oddeven Determine if a number is odd or even.

-- P --

paletteChoices Create a list of colors from among a variety of color palettes.
pcumsum Computes the prior to or reverse cumulative sum of a vector.
perc Computes the percentage of values in a vector less than or greater than (and equal to) some value.
PikeNY Summarized multiple mark-recapture data for all Northern Pike from Buckthorn Marsh, NY.
PikeNYPartial1 Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckthorn Marsh, NY.
plot.ageBias Compute and view possible differnces between paired sets of ages.
plot.agePrec Compute measures of precision among sets of ages.
plot.bootCase Associated S3 methods for bootCase from car.
plot.CapHist Summarize capture histories in individual fish format.
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.mrClosed2 Estimate initial population size for single or multiple census mark-recapture data.
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.
poiCI Confidence interval for Poisson counts.
predict.bootCase Associated S3 methods for bootCase from car.
predict.nlsBoot Associated S3 methods for nlsBoot from nlstools.
print.compIntercepts Tests for significant differences among all pairs of intercepts in a dummy variable regression.
print.compSlopes Tests for significant differences among all pairs of slopes in a dummy variable regression (DVR).
print.dunnTest Dunn's Kruskal-Wallis Multiple Comparisons.
print.extraTest Likelihood ratio and extra sum-of-squares tests.
print.metaM Estimate natural mortality from a variety of empirical methods.
psdAdd Creates a vector of Gabelhouse lengths for each species in an entire data frame.
psdAdd.default Creates a vector of Gabelhouse lengths for each species in an entire data frame.
psdAdd.formula Creates a vector of Gabelhouse lengths for each species in an entire data frame.
psdCalc Convenience function for calculating PSD-X and PSD X-Y values.
psdCI Compute confidence intervals for PSD-X and PSD X-Y values.
PSDlit Gabelhouse five-cell length categories for various species.
psdPlot Length-frequency histogram with Gabelhouse lengths highlighted.
psdVal Finds Gabelhouse lengths (for PSD calculations) for a species.
purl2 Specific utilities for use in a knitr document.

-- R --

rcumsum Computes the prior to or reverse cumulative sum of a vector.
removal Population estimates for k-, 3-, or 2-pass removal data.
reproInfo Specific utilities for use in a knitr document.
residPlot Construct a residual plot from lm or nls objects.
residPlot.IVR Construct a residual plot from lm or nls objects.
residPlot.lm Construct a residual plot from lm or nls objects.
residPlot.nlme 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.SLR Construct a residual plot from lm or nls objects.
residPlot.TWOWAY Construct a residual plot from lm or nls objects.
RichardsFuns Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.

-- S --

Schnute The four-parameter growth function from Schnute (1981).
se Computes standard error of the mean.
SMBassLS Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
SMBassWB Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.
SpotVA1 Age and length of spot.
srFuns Creates a function for a specific parameterization of a common stock-recruitment function .
srFunShow Creates a function for a specific parameterization of a common stock-recruitment function .
srStarts Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models.
stockRecruitment Creates a function for a specific parameterization of a common stock-recruitment function .
Subset Subsets/filters a data frame and drops the unused levels.
Summarize Summary statistics for a numeric variable.
Summarize.default Summary statistics for a numeric variable.
Summarize.formula Summary statistics for a numeric variable.
summary.ageBias Compute and view possible differnces between paired sets of ages.
summary.agePrec Compute measures of precision among 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.mrClosed1 Estimate initial population size for single or multiple census mark-recapture data.
summary.mrClosed2 Estimate initial population size for single or multiple census mark-recapture data.
summary.mrOpen Jolly-Seber analysis from multiple mark-recapture events from an open population.
summary.removal Population estimates for k-, 3-, or 2-pass removal data.
sumTable Creates a one- or two-way table of summary statistics.
sumTable.formula Creates a one- or two-way table of summary statistics.

-- T --

tictactoe Construct a base tic-tac-toe plot for presenting predator-prey PSD values.

-- V --

validn Finds the number of valid (non-NA) values in a vector.
vbFuns Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
vbStarts Find reasonable starting values for a von Bertalanffy growth function.

-- W --

WhitefishLC Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.
WR79 Ages and lengths for a hypothetical sample from Westerheim and Ricker (1979).
wrAdd Computes a vector of relative weights specific to a species in an entire data frame.
wrAdd.default Computes a vector of relative weights specific to a species in an entire data frame.
wrAdd.formula Computes a vector of relative weights specific to a species in an entire data frame.
WSlit All known standard weight equations.
wsVal Finds standard weight equation coefficients for a particular species.