Simple Fisheries Stock Assessment Methods

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Documentation for package ‘FSA’ version 0.10.0

• DESCRIPTION file.
• Package NEWS.

Help Pages

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

-- A --

addZeroCatch	Adds zeros for catches of species not collected in some sampling events.
ageBias	Compute and view possible differences 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 --

binCI	Confidence intervals for binomial probability of success.
BluegillJL	Capture histories (2 samples) of Bluegill from Jewett Lake, MI.
boot	Associated S3 methods for bootstrap results from car::Boot.
bootCase	DEFUNCT functions.
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	DEFUNCT functions.
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.
coef.removal	Population estimates for k-, 3-, or 2-pass removal data.
col2rgbt	Converts an R color to RGB (red/green/blue) including a transparency (alpha channel).
compIntercepts	DEFUNCT functions.
compSlopes	DEFUNCT functions.
confint.boot	Associated S3 methods for bootstrap results from car::Boot.
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.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.
depletion.default	Computes the Leslie or DeLury population estimate from catch and effort data.
depletion.formula	Computes the Leslie or DeLury population estimate from catch and effort data.
diags	DEFUNCT functions.
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	DEFUNCT functions.
findGrowthStarts	Find reasonable starting values for common fish growth functions.
fishR	Opens web pages associated with the fishR website.
fitPlot	DEFUNCT functions.
FSA-defunct	DEFUNCT functions.
fsaNews	DEFUNCT functions.

-- G --

geomean	Calculates the geometric mean or geometric standard deviation.
geosd	Calculates the geometric mean or geometric standard deviation.
GompertzFuns	DEPRECATED (as of v0.10.0). Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
GrowthData1	Hypothetical growth data for testing
GrowthData2	Hypothetical growth data for testing seasonal age models.
GrowthData3	Hypothetical growth data for testing
growthFunShow	DEPRECATED (as of v0.10.0). Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
growthModels	DEPRECATED (as of v0.10.0). 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.boot	Associated S3 methods for bootstrap results from car::Boot.
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	DEFUNCT functions.
htest	Associated S3 methods for nlsBoot from nlstools.
htest.boot	Associated S3 methods for bootstrap results from car::Boot.
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	DEPRECATED (as of v0.10.0). 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 --

makeGrowthFun	Creates a function for a specific parameterization of the von Bertalanffy and other common growth functions.
mapvalues	DEFUNCT functions.
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 --

nlsBoot	Associated S3 methods for nlsBoot from nlstools.
nlsTracePlot	Adds model fits from nls iterations to active plot.

-- P --

pcumsum	Computes the prior to or reverse cumulative sum of a vector.
peek	Peek into (show a subset of) a data frame or matrix.
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 Buckhorn Marsh, NY.
PikeNYPartial1	Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckhorn Marsh, NY.
plot.ageBias	Compute and view possible differences between paired sets of ages.
plot.agePrec	Compute measures of precision among sets of ages.
plot.boot	Associated S3 methods for bootstrap results from car::Boot.
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.
plotAB	Construct traditional (Campana-like) age-bias plots.
plotBinResp	DEFUNCT functions.
poiCI	Confidence interval for Poisson counts.
predict.boot	Associated S3 methods for bootstrap results from car::Boot.
predict.nlsBoot	Associated S3 methods for nlsBoot from nlstools.
print.dunnTest	Dunn's Kruskal-Wallis Multiple Comparisons.
print.extraTest	Likelihood ratio and extra sum-of-squares tests.
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.
removal.default	Population estimates for k-, 3-, or 2-pass removal data.
removal.formula	Population estimates for k-, 3-, or 2-pass removal data.
repeatedRows2Keep	Find non-repeated consecutive rows in a data.frame.
reproInfo	Specific utilities for use in a knitr document.
residPlot	DEFUNCT functions.
RichardsFuns	DEPRECATED (as of v0.10.0). Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
rSquared	Extract the coefficient of determination from a linear model object.
rSquared.catchCurve	Mortality estimates from the descending limb of a catch curve.
rSquared.default	Extract the coefficient of determination from a linear model object.
rSquared.depletion	Computes the Leslie or DeLury population estimate from catch and effort data.
rSquared.lm	Extract the coefficient of determination from a linear model object.

-- S --

Schnute	DEFUNCT functions.
se	Computes standard error of the mean.
showGrowthFun	Creates a string or an expression for a specific growth function.
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.
Subset	DEFUNCT functions.
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 differences 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	DEPRECATED (as of v0.10.0). 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.