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FSA (version 0.9.1)

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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Install

install.packages('FSA')

Monthly Downloads

19,856

Version

0.9.1

License

GPL (>= 2)

Issues

3

Pull Requests

0

Stars

71

Forks

23

Maintainer

Derek Ogle

Last Published

July 17th, 2021

Functions in FSA (0.9.1)

FSA

Fisheries stock assessment methods and data.
BluegillJL

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

DEFUNCT functions.
CutthroatAL

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

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

Population growth of Escherichia coli.
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.
BrookTroutTH

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

Summary statistics for a numeric variable.
SMBassWB

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

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

Gabelhouse five-cell length categories for various species.
PikeNY

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

Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
PikeNYPartial1

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

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

All known standard weight equations.
alkIndivAge

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

Compute measures of precision among sets of ages.
SchnuteRichards

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

Proportions-at-age from an age-length key
SpotVA1

Age and length of spot.
alkMeanVar

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

Plots to visualize age-length keys.
ageBias

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

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

Confidence intervals for binomial probability of success.
chapmanRobson

Computes Chapman-Robson estimates of S and Z.
col2rgbt

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

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

Summarize capture histories in individual fish format.
capHistConvert

Convert between capture history data.frame formats.
dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.
expandCounts

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

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

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

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

Expands a length frequency based on a subsample.
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.
fact2num

Converts "numeric" factor levels to numeric values.
filterD-deprecated

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

Ratio of lagged observations.
lencat

Constructs length class/category variable.
is.odd

Determine if a number is odd or even.
hyperCI

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

Specific utilities for use in a knitr document.
ksTest

Kolmogorov-Smirnov Tests.
hist.formula

Creates separate histograms by levels.
fishR

Opens web pages associated with the fishR website.
histFromSum

Create a histogram from a frequency table.
fitPlot

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

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

Confidence interval for Poisson counts.
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.
fsaNews

Read news and changes for the 'FSA' package.
jolly

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

Adds model fits from nls iterations to active plot.
Mmethods

Estimate natural mortality from a variety of empirical methods.
mrClosed

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

Calculates the geometric mean or geometric standard deviation.
nlsBoot

Associated S3 methods for nlsBoot from nlstools.
residPlot

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

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

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

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

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

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

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

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

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

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

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

Length-frequency histogram with Gabelhouse lengths highlighted.
validn

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

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

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

Computes standard error of the mean.
tictactoe

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

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

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

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

Finds standard weight equation coefficients for a particular species.