Functions for Simple Fisheries Stock Assessment Methods

Documentation for package ‘FSA’ version 0.8.5

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A B C D E F G H I J 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 zeroes for catches of species not collected in some sampling events.
ageBias	Compute and view possible biases between paired sets of ages.
ageKey	Use an age-length key to assign age to individuals in the unaged sample.
ageKeyPlot	Plots to visualize age-length keys.
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.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.
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.
GompertzModels	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.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.
lenFreqExpand	Expands a length frequency based on a subsample.
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.
logisticModels	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.

-- 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 biases 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 rate parameter.
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	Create vector of Gabelhouse lengths for each species from an entire data frame.
psdAdd.default	Create vector of Gabelhouse lengths for each species from an entire data frame.
psdAdd.formula	Create vector of Gabelhouse lengths for each species from 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 lengthshighlighted.
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.
RichardsModels	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).
SchnuteModels	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 model .
srModels	Creates a function for a specific parameterization of a common stock-recruitment model .
srStarts	Finds reasonable starting values for parameters in specific paramaterizations of common stock-recruitment models.
stockRecruitment	Creates a function for a specific parameterization of a common stock-recruitment model .
Subset	Subsets/filters 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.ageBias	Compute and view possible biases 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.
vbModels	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.