# Simple Fisheries Stock Assessment Methods

## Documentation for package ‘FSA’ version 0.8.30

- DESCRIPTION file.

## Help Pages

A B C D E F G H I J K L M N O 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.
bootCase | Case bootstrapping and associated S3 methods.
bootstrap | Case bootstrapping and associated S3 methods.
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 | Case bootstrapping and associated S3 methods.
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 --

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 | Case bootstrapping and associated S3 methods.
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 | Case bootstrapping and associated S3 methods.
htest.nlsBoot | Associated S3 methods for nlsBoot from nlstools.
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.
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.bootCase | Case bootstrapping and associated S3 methods.
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 | 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 | Case bootstrapping and associated S3 methods.
predict.nlsbooot | Associated S3 methods for nlsBoot from nlstools.
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.
repeatedRows2Keep | Find non-repeated consecutive rows in a data.frame.
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.
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 | The four-parameter growth function from Schnute (1981).
SchnuteRichards | The five-parameter growth function from Schnute and Richards (1990).
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 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 | 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.