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FSA (version 0.10.0)

Simple Fisheries Stock Assessment Methods

Description

A variety of simple fish stock assessment methods.

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Version

Install

install.packages('FSA')

Monthly Downloads

20,996

Version

0.10.0

License

GPL (>= 2)

Maintainer

Derek Ogle

Last Published

May 6th, 2025

Functions in FSA (0.10.0)

alkPlot

Plots to visualize age-length keys.
alkMeanVar

Mean Values-at-age from an age-length key
WR79

Ages and lengths for a hypothetical sample from Westerheim and Ricker (1979).
WSlit

All known standard weight equations.
alkAgeDist

Proportions-at-age from an age-length key
WhitefishLC

Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.
alkIndivAge

Use an age-length key to assign age to individuals in the unaged sample.
addZeroCatch

Adds zeros for catches of species not collected in some sampling events.
agePrecision

Compute measures of precision among sets of ages.
ageBias

Compute and view possible differences between paired sets of ages.
col2rgbt

Converts an R color to RGB (red/green/blue) including a transparency (alpha channel).
dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.
capHistSum

Summarize capture histories in individual fish format.
capFirst

Capitalizes the first letter of first or all words in a string.
binCI

Confidence intervals for binomial probability of success.
confint.boot

Associated S3 methods for bootstrap results from car::Boot.
capHistConvert

Convert between capture history data.frame formats.
chapmanRobson

Computes Chapman-Robson estimates of S and Z.
catchCurve

Mortality estimates from the descending limb of a catch curve.
depletion

Computes the Leslie or DeLury population estimate from catch and effort data.
expandCounts

Repeat individual fish data (including lengths) from tallied counts.
geomean

Calculates the geometric mean or geometric standard deviation.
extraTests

Likelihood ratio and extra sum-of-squares tests.
findGrowthStarts

Find reasonable starting values for common fish growth functions.
fact2num

Converts "numeric" factor levels to numeric values.
hist.formula

Creates separate histograms by levels.
expandLenFreq

Expands a length frequency based on a subsample.
headtail

Shows rows from the head and tail of a data frame or matrix.
growthModels

DEPRECATED (as of v0.10.0). Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
fishR

Opens web pages associated with the fishR website.
ksTest

Kolmogorov-Smirnov Tests.
histFromSum

Create a histogram from a frequency table.
logbtcf

Constructs the correction-factor used when back-transforming log-transformed values.
hyperCI

Confidence interval for population size (N) in hypergeometric distribution.
lwCompPreds

Constructs plots of predicted weights at given lengths among different groups.
is.odd

Determine if a number is odd or even.
lencat

Constructs length class/category variable.
lagratio

Ratio of lagged observations.
kCounts

Specific utilities for use in a knitr document.
makeGrowthFun

Creates a function for a specific parameterization of the von Bertalanffy and other common growth functions.
peek

Peek into (show a subset of) a data frame or matrix.
poiCI

Confidence interval for Poisson counts.
jolly

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

Creates a vector of Gabelhouse lengths for each species in an entire data frame.
Mmethods

Estimate natural mortality from a variety of empirical methods.
nlsTracePlot

Adds model fits from nls iterations to active plot.
nlsBoot

Associated S3 methods for nlsBoot from nlstools.
perc

Computes the percentage of values in a vector less than or greater than (and equal to) some value.
mrClosed

Estimate initial population size for single or multiple census mark-recapture data.
plotAB

Construct traditional (Campana-like) age-bias plots.
rSquared

Extract the coefficient of determination from a linear model object.
showGrowthFun

Creates a string or an expression for a specific growth function.
psdVal

Finds Gabelhouse lengths (for PSD calculations) for a species.
psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.
psdCI

Compute confidence intervals for PSD-X and PSD X-Y values.
repeatedRows2Keep

Find non-repeated consecutive rows in a data.frame.
psdCalc

Convenience function for calculating PSD-X and PSD X-Y values.
rcumsum

Computes the prior to or reverse cumulative sum of a vector.
removal

Population estimates for k-, 3-, or 2-pass removal data.
se

Computes standard error of the mean.
srFuns

Creates a function for a specific parameterization of a common stock-recruitment function .
vbStarts

Find reasonable starting values for a von Bertalanffy growth function.
wsVal

Finds standard weight equation coefficients for a particular species.
wrAdd

Computes a vector of relative weights specific to a species in an entire data frame.
validn

Finds the number of valid (non-NA) values in a vector.
sumTable

Creates a one- or two-way table of summary statistics.
tictactoe

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

Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models.
Ecoli

Population growth of Escherichia coli.
FSA-defunct

DEFUNCT functions.
CutthroatAL

Capture histories (9 samples) of Cutthroat Trout from Auke Lake.
CodNorwegian

Stock and recruitment data for Norwegian cod, 1937-1960.
.onAttach

Internal functions.
BrookTroutTH

Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.
FSA

Fisheries stock assessment methods and data.
ChinookArg

Lengths and weights for Chinook Salmon from three locations in Argentina.
BluegillJL

Capture histories (2 samples) of Bluegill from Jewett Lake, MI.
GrowthData1

Hypothetical growth data for testing
PikeNY

Summarized multiple mark-recapture data for all Northern Pike from Buckhorn Marsh, NY.
PSDlit

Gabelhouse five-cell length categories for various species.
GrowthData3

Hypothetical growth data for testing
SMBassLS

Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
Summarize

Summary statistics for a numeric variable.
SMBassWB

Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.
GrowthData2

Hypothetical growth data for testing seasonal age models.
Mirex

Mirex concentration, weight, capture year, and species of Lake Ontario salmon.
PikeNYPartial1

Capture histories (4 samples), in capture history format, of a subset of Northern Pike from Buckhorn Marsh, NY.
SpotVA1

Age and length of spot.