Functions to support Fish Stock Assessment book.

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Documentation for package ‘FSA’

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A B C D E F G L M P R S T V W Y

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FSA-package Functions to support the Fish Stock Assessment textbook.

-- A --

add.radcap Adds a total radius-at-capture column to a one-fish-per-line increments data frame.
add.zerocatch Adds zero catch values for sampling events and species that were not captured.
age.comp Computes results comparing two sets of ages to the same animals.
age.key Applies an age-length key to individuals in a length-sample.
alias.WLGM Performs the scale increment model of Weisberg's Linear Growth Models.
anova.CC 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.
anova.SR Fits a stock-recruitment curve for spawning stock and recruitment vectors.
anova.WLGM Performs the scale increment model of Weisberg's Linear Growth Models.

-- B --

boxcox.WLGM Performs the scale increment model of Weisberg's Linear Growth Models.

-- C --

caphist.convert Converts between different capture history recording types.
caphist.sum Summarize individual fish capture histories.
catch.curve Mortality estimates from the descending limb of a catch curve.
cc.sim Plots a catch curve (log catch vs age) for a hypothetical population exploited by a hypothetical fishery with slider bars to alter model parameters.
chapman.robson Computes Chapman-Robson estimates of S and Z.
coef.CC 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.FROESE 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.
coef.SR Fits a stock-recruitment curve for spawning stock and recruitment vectors.
coef.WLGM Performs the scale increment model of Weisberg's Linear Growth Models.
coefplot Constructs the coefficient plots for Weisberg's Linear Growth Model analyses.
cohort.sim Constructs a plot of the hypothetical number of individuals in a cohort over time.
confint.CC Mortality estimates from the descending limb of a catch curve.
confint.CR Computes Chapman-Robson estimates of S and Z.
confint.Depletion Computes the Leslie or Delury population estimate from catch and effort data.
confint.MRC Estimate initial population size for single or multiple census mark-recapture data.
confint.MRO Estimate initial population size for multiple census mark-recapture data from an open population.
confint.Removal Computes population estimates for k-, 3-, or 2-pass removal data.
confint.WLGM Performs the scale increment model of Weisberg's Linear Growth Models.

-- D --

depletion Computes the Leslie or Delury population estimate from catch and effort data.

-- E --

emp Computes the standard weight equation using the emperical-percentile method.

-- F --

fit.plot.EMPlm Computes the standard weight equation using the emperical-percentile method.
fit.plot.EMPQ Methods to assess length-bias in a proposed standard weight equation.
fit.plot.EMPrq Computes the standard weight equation using the emperical-percentile method.
fit.plot.RLP Computes the standard weight equation using the regression-line-percentile method.
fit.plot.WLGM Performs the scale increment model of Weisberg's Linear Growth Models.
FroeseWs Computes the standard weight equation using the methods described in Froese (2006).
FSA Functions to support the Fish Stock Assessment textbook.
FSAsims Creates a menu to give access to all simulations in the FSA package.

-- G --

g.convert Converts between growth measurement data types.
g.reshape Reshapes a one-fish-per-line data frame to a one-measurement-per-line data frame.
growmodel.sim Plots hypothetical size-at-age for several types of fisheries growth models with slider bars to alter model parameters.

-- L --

lencat Constructs length class/category variable.
lenfreq.expand Expands a length frequency based on a subsample.
leslie.sim Plots catch-per-unit-effort versus total catch (i.e., a Leslie model) for a hypothetical depletion fishery with slider bars to change parameter values.
leslie.sim2 Monte Carlo simulations for exploring Leslie model estimates of initial population size and catchability.
limnoprofile.plot Constructs a plot of depth versus limnological measure.
lwmodel.sim Plots a length-weight power function evaluated at a vector of lengths with slider bars to change parameter values.

-- M --

mr.closed Estimate initial population size for single or multiple census mark-recapture data.
mr.closed1.sim Monte Carlo simulations of single census mark-recapture data.
mr.open Estimate initial population size for multiple census mark-recapture data from an open population.

-- P --

plot.AgeComp Computes results comparing two sets of ages to the same animals.
plot.CC Mortality estimates from the descending limb of a catch curve.
plot.CR 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.FROESE Computes the standard weight equation using the methods described in Froese (2006).
plot.MRC2 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.
plot.SR Fits a stock-recruitment curve for spawning stock and recruitment vectors.
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.RLP Computes the standard weight equation using the regression-line-percentile method.
print.WILLIS Methods to assess length-bias in a proposed standard weight equation.
PSDval Finds five-cell or two-cell length categories (for RSD/PSD) for a particular species.

-- R --

rcumsum Computes the reverse cumulative sum of a vector.
removal Computes population estimates for k-, 3-, or 2-pass removal data.
residual.plot.EMPlm Computes the standard weight equation using the emperical-percentile method.
residual.plot.RLP Computes the standard weight equation using the regression-line-percentile method.
rlp Computes the standard weight equation using the regression-line-percentile method.
RSDval Finds five-cell or two-cell length categories (for RSD/PSD) for a particular species.

-- S --

stock.recruit Fits a stock-recruitment curve for spawning stock and recruitment vectors.
stock.recruit.sim Plots hypothetical number of recruits versus stock size for Beverton-Holt and Ricker stock-recruit models with slider bars to alter model parameters.
summary.AgeComp Computes results comparing two sets of ages to the same animals.
summary.CC Mortality estimates from the descending limb of a catch curve.
summary.CR Computes Chapman-Robson estimates of S and Z.
summary.Depletion Computes the Leslie or Delury population estimate from catch and effort data.
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.MRC Estimate initial population size for single or multiple census mark-recapture data.
summary.MRO 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.SR Fits a stock-recruitment curve for spawning stock and recruitment vectors.
summary.WILLIS Methods to assess length-bias in a proposed standard weight equation.
summary.WLGM Performs the scale increment model of Weisberg's Linear Growth Models.

-- T --

tictactoe Constructs the base tic-tac-toe graph for presenting predator-prey PSD values.
tictactoe.add Adds point and confidence intervals for observed preator-prey PSD to tic-tac-toe graph.

-- V --

validateWs Methods to assess length-bias in a proposed standard weight equation.
vb.comp Evaluates and plots the traditional von Bertalanffy growth model for several sets of parameter choices.

-- W --

wlgm Performs the scale increment model of Weisberg's Linear Growth Models.
WRval Finds standard weight equation coefficients for a particular species.
WSval Finds standard weight equation coefficients for a particular species.

-- Y --

ycplot Constructs the year-class (interaction) plots for Weisberg's Linear Growth Model analyses.