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FSA (version 0.9.6)

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

12,252

Version

0.9.6

License

GPL (>= 2)

Maintainer

Derek Ogle

Last Published

January 7th, 2025

Functions in FSA (0.9.6)

Summarize

Summary statistics for a numeric variable.
SpotVA1

Age and length of spot.
PikeNYPartial1

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

The five-parameter growth function from Schnute and Richards (1990).
SMBassWB

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

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

The four-parameter growth function from Schnute (1981).
PSDlit

Gabelhouse five-cell length categories for various species.
WR79

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

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

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

Confidence intervals for binomial probability of success.
WSlit

All known standard weight equations.
alkMeanVar

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

Compute measures of precision among sets of ages.
alkIndivAge

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

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

Plots to visualize age-length keys.
addZeroCatch

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

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

Dunn's Kruskal-Wallis Multiple Comparisons.
capFirst

Capitalizes the first letter of first or all words in a string.
col2rgbt

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

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

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

Summarize capture histories in individual fish format.
capHistConvert

Convert between capture history data.frame formats.
depletion

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

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

Computes Chapman-Robson estimates of S and Z.
headtail

Shows rows from the head and tail of a data frame or matrix.
fact2num

Converts "numeric" factor levels to numeric values.
fishR

Opens web pages associated with the fishR website.
expandLenFreq

Expands a length frequency based on a subsample.
histFromSum

Create a histogram from a frequency table.
geomean

Calculates the geometric mean or geometric standard deviation.
hist.formula

Creates separate histograms by levels.
extraTests

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

Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
hyperCI

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

Determine if a number is odd or even.
lwCompPreds

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

Kolmogorov-Smirnov Tests.
mrClosed

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

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

Estimate natural mortality from a variety of empirical methods.
kCounts

Specific utilities for use in a knitr document.
lagratio

Ratio of lagged observations.
jolly

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

Constructs length class/category variable.
plotAB

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

Associated S3 methods for nlsBoot from nlstools.
psdCalc

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

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

Adds model fits from nls iterations to active plot.
perc

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

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

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

Length-frequency histogram with Gabelhouse lengths highlighted.
poiCI

Confidence interval for Poisson counts.
repeatedRows2Keep

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

Computes standard error of the mean.
srFuns

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

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

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

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

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

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

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

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

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

Finds standard weight equation coefficients for a particular species.
vbStarts

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

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

Lengths and weights for Chinook Salmon from three locations in Argentina.
FSA-defunct

DEFUNCT functions.
Ecoli

Population growth of Escherichia coli.
.onAttach

Internal functions.
Mirex

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

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

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

Fisheries stock assessment methods and data.
CodNorwegian

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

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