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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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Install
install.packages('FSA')
Monthly Downloads
10,956
Version
0.9.5
License
GPL (>= 2)
Maintainer
Derek Ogle
Last Published
August 26th, 2023
Functions in FSA (0.9.5)
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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.