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FSA (version 0.9.4)

Simple Fisheries Stock Assessment Methods

Description

A variety of simple fish stock assessment methods.

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Install

install.packages('FSA')

Monthly Downloads

20,921

Version

0.9.4

License

GPL (>= 2)

Maintainer

Derek Ogle

Last Published

February 1st, 2023

Functions in FSA (0.9.4)

FSA

Fisheries stock assessment methods and data.

BrookTroutTH

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

Mirex

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

BluegillJL

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

PikeNY

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

Ecoli

Population growth of Escherichia coli.

PSDlit

Gabelhouse five-cell length categories for various species.

FSA-defunct

DEFUNCT functions.

SMBassWB

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

Summarize

Summary statistics for a numeric variable.

.onAttach

Internal functions.

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).

WR79

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

alkIndivAge

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

SpotVA1

Age and length of spot.

SchnuteRichards

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

alkMeanVar

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

confint.boot

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

alkAgeDist

Proportions-at-age from an age-length key

agePrecision

Compute measures of precision among sets of ages.

WhitefishLC

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

chapmanRobson

Computes Chapman-Robson estimates of S and Z.

WSlit

All known standard weight equations.

capFirst

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

ageBias

Compute and view possible differences between paired sets of ages.

catchCurve

Mortality estimates from the descending limb of a catch curve.

addZeroCatch

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

extraTests

Likelihood ratio and extra sum-of-squares tests.

expandLenFreq

Expands a length frequency based on a subsample.

dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.

expandCounts

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

histFromSum

Create a histogram from a frequency table.

hyperCI

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

capHistConvert

Convert between capture history data.frame formats.

capHistSum

Summarize capture histories in individual fish format.

headtail

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

nlsBoot

Associated S3 methods for nlsBoot from nlstools.

hist.formula

Creates separate histograms by levels.

nlsTracePlot

Adds model fits from nls iterations to active plot.

lencat

Constructs length class/category variable.

is.odd

Determine if a number is odd or even.

alkPlot

Plots to visualize age-length keys.

Mmethods

Estimate natural mortality from a variety of empirical methods.

plotAB

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

lwCompPreds

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

poiCI

Confidence interval for Poisson counts.

repeatedRows2Keep

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

srFuns

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

peek

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

kCounts

Specific utilities for use in a knitr document.

srStarts

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

psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.

psdCalc

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

growthModels

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

binCI

Confidence intervals for binomial probability of success.

perc

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

rcumsum

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

geomean

Calculates the geometric mean or geometric standard deviation.

logbtcf

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

rSquared

Extract the coefficient of determination from a linear model object.

jolly

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

mrClosed

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

psdVal

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

psdCI

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

psdAdd

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

Computes standard error of the mean.

vbStarts

Find reasonable starting values for a von Bertalanffy growth function.

validn

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

fact2num

Converts "numeric" factor levels to numeric values.

fishR

Opens web pages associated with the fishR website.

ksTest

Kolmogorov-Smirnov Tests.

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.

tictactoe

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

sumTable

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

wsVal

Finds standard weight equation coefficients for a particular species.

wrAdd

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

lagratio

Ratio of lagged observations.

removal

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

CutthroatAL

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

ChinookArg

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

CodNorwegian

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