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FSA (version 0.9.5)

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

15,054

Version

0.9.5

License

GPL (>= 2)

Maintainer

Derek Ogle

Last Published

August 26th, 2023

Functions in FSA (0.9.5)

Mirex

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

Summary statistics for a numeric variable.
SchnuteRichards

The five-parameter growth function from Schnute and Richards (1990).
WR79

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

Population growth of Escherichia coli.
SMBassWB

Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.
PikeNYPartial1

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

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

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

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

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

Gabelhouse five-cell length categories for various species.
SpotVA1

Age and length of spot.
alkPlot

Plots to visualize age-length keys.
addZeroCatch

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

All known standard weight equations.
binCI

Confidence intervals for binomial probability of success.
WhitefishLC

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

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

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

Compute measures of precision among sets of ages.
alkMeanVar

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

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

Summarize capture histories in individual fish format.
dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.
confint.boot

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

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

Convert between capture history data.frame formats.
col2rgbt

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

Computes Chapman-Robson estimates of S and Z.
depletion

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

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

Capitalizes the first letter of first or all words in a string.
fact2num

Converts "numeric" factor levels to numeric values.
expandLenFreq

Expands a length frequency based on a subsample.
headtail

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

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

Creates separate histograms by levels.
growthModels

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.
extraTests

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

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

Create a histogram from a frequency table.
is.odd

Determine if a number is odd or even.
ksTest

Kolmogorov-Smirnov Tests.
lagratio

Ratio of lagged observations.
kCounts

Specific utilities for use in a knitr document.
mrClosed

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

Constructs length class/category variable.
lwCompPreds

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

Estimate natural mortality from a variety of empirical methods.
jolly

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

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

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

Confidence interval for Poisson counts.
peek

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

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

Length-frequency histogram with Gabelhouse lengths highlighted.
nlsTracePlot

Adds model fits from nls iterations to active plot.
psdCI

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

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

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

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

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

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

Construct a base tic-tac-toe plot for presenting predator-prey PSD values.
repeatedRows2Keep

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

Computes standard error of the mean.
wsVal

Finds standard weight equation coefficients for a particular species.
rSquared

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

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

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

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

Capture histories (9 samples) of Cutthroat Trout from Auke Lake.
FSA-defunct

DEFUNCT functions.
FSA

Fisheries stock assessment methods and data.
BluegillJL

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

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

Internal functions.
ChinookArg

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