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FSA (version 0.9.2)

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

0.9.2

License

GPL (>= 2)

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Repository

https://github.com/droglenc/FSA

Maintainer

Derek Ogle

Last Published

February 12th, 2022

Functions in FSA (0.9.2)

BluegillJL

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

CutthroatAL

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

Schnute

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

Ecoli

Population growth of Escherichia coli.

SMBassWB

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

SchnuteRichards

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

depletion

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

mrClosed

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

lwCompPreds

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

FSA-defunct

DEFUNCT functions.

plotAB

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

CodNorwegian

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

expandCounts

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

SpotVA1

Age and length of spot.

ChinookArg

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

col2rgbt

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

nlsTracePlot

Adds model fits from nls iterations to active plot.

capFirst

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

BrookTroutTH

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

PSDlit

Gabelhouse five-cell length categories for various species.

catchCurve

Mortality estimates from the descending limb of a catch curve.

.onAttach

Internal functions.

vbStarts

Find reasonable starting values for a von Bertalanffy growth function.

binCI

Confidence intervals for binomial probability of success.

WSlit

All known standard weight equations.

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.

nlsBoot

Associated S3 methods for nlsBoot from nlstools.

confint.boot

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

SMBassLS

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

jolly

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

FSA

Fisheries stock assessment methods and data.

hist.formula

Creates separate histograms by levels.

headtail

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

Computes standard error of the mean.

Mirex

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

rcumsum

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

repeatedRows2Keep

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

agePrecision

Compute measures of precision among sets of ages.

Mmethods

Estimate natural mortality from a variety of empirical methods.

alkPlot

Plots to visualize age-length keys.

alkAgeDist

Proportions-at-age from an age-length key

srFuns

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

poiCI

Confidence interval for Poisson counts.

WR79

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

srStarts

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

Summarize

Summary statistics for a numeric variable.

rSquared

Extract the coefficient of determination from a linear model object.

PikeNY

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

peek

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

chapmanRobson

Computes Chapman-Robson estimates of S and Z.

expandLenFreq

Expands a length frequency based on a subsample.

psdAdd

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

dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.

fishR

Opens web pages associated with the fishR website.

psdVal

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

fact2num

Converts "numeric" factor levels to numeric values.

perc

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

alkMeanVar

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

validn

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

histFromSum

Create a histogram from a frequency table.

psdCalc

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

addZeroCatch

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

extraTests

Likelihood ratio and extra sum-of-squares tests.

ageBias

Compute and view possible differences between paired sets of ages.

ksTest

Kolmogorov-Smirnov Tests.

psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.

lagratio

Ratio of lagged observations.

psdCI

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

removal

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

hyperCI

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

alkIndivAge

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

kCounts

Specific utilities for use in a knitr document.

capHistSum

Summarize capture histories in individual fish format.

logbtcf

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

lencat

Constructs length class/category variable.

geomean

Calculates the geometric mean or geometric standard deviation.

sumTable

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

is.odd

Determine if a number is odd or even.

capHistConvert

Convert between capture history data.frame formats.

wrAdd

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

growthModels

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

tictactoe

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

wsVal

Finds standard weight equation coefficients for a particular species.