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FSA (version 0.9.0)

Simple Fisheries Stock Assessment Methods

Description

A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website .

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Version

Install

install.packages('FSA')

Monthly Downloads

19,856

Version

0.9.0

License

GPL (>= 2)

Issues

3

Pull Requests

0

Stars

71

Forks

23

Maintainer

Derek Ogle

Last Published

June 9th, 2021

Functions in FSA (0.9.0)

.onAttach

Internal functions.
FSA-defunct

DEFUNCT functions.
FSA

Fisheries stock assessment methods and data.
Ecoli

Population growth of Escherichia coli.
CutthroatAL

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

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

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

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

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

Plots to visualize age-length keys.
SchnuteRichards

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

Confidence intervals for binomial probability of success.
Mirex

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

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

Summary statistics for a numeric variable.
WR79

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

Adds zeros for catches of species not collected in some sampling events.
SpotVA1

Age and length of spot.
col2rgbt

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

Computes Chapman-Robson estimates of S and Z.
ageBias

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

Gabelhouse five-cell length categories for various species.
WSlit

All known standard weight equations.
Schnute

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

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

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

Opens web pages associated with the fishR website.
alkIndivAge

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

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

DEPRECATED -- Fitted model plot for an lm, glm, or nls object.
WhitefishLC

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

Kolmogorov-Smirnov Tests.
confint.boot

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

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

Specific utilities for use in a knitr document.
headtail

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

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

Compute measures of precision among sets of ages.
nlsTracePlot

Adds model fits from nls iterations to active plot.
psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.
fact2num

Converts "numeric" factor levels to numeric values.
psdVal

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

Dunn's Kruskal-Wallis Multiple Comparisons.
plotAB

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

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

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

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

DEPRECATED -- Construct a residual plot from lm or nls objects.
filterD-deprecated

DEPRECATED - Subsets/filters a data frame and drops the unused levels.
hist.formula

Creates separate histograms by levels.
histFromSum

Create a histogram from a frequency table.
expandCounts

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

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

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

Convert between capture history data.frame formats.
nlsBoot

Associated S3 methods for nlsBoot from nlstools.
se

Computes standard error of the mean.
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.
wsVal

Finds standard weight equation coefficients for a particular species.
lagratio

Ratio of lagged observations.
lencat

Constructs length class/category variable.
vbStarts

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

Calculates the geometric mean or geometric standard deviation.
capFirst

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

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

Estimate natural mortality from a variety of empirical methods.
fsaNews

Read news and changes for the 'FSA' package.
is.odd

Determine if a number is odd or even.
poiCI

Confidence interval for Poisson counts.
mrClosed

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

Summarize capture histories in individual fish format.
repeatedRows2Keep

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

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

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

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

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

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

Expands a length frequency based on a subsample.
psdAdd

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

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

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

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