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FSA (version 0.8.31)

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.packages('FSA')

Monthly Downloads

25,045

Version

0.8.31

License

GPL (>= 2)

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Repository

https://github.com/droglenc/FSA

Maintainer

Derek Ogle

Last Published

November 8th, 2020

Functions in FSA (0.8.31)

SMBassWB

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

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.

Subset

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

Summarize

Summary statistics for a numeric variable.

FSA

Fisheries stock assessment methods and data.

alkAgeDist

Proportions-at-age from an age-length key

alkIndivAge

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

PikeNY

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

SchnuteRichards

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

PSDlit

Gabelhouse five-cell length categories for various species.

alkPlot

Plots to visualize age-length keys.

WR79

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

WSlit

All known standard weight equations.

Schnute

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

alkMeanVar

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

WhitefishLC

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

SpotVA1

Age and length of spot.

addZeroCatch

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

catchCurve

Mortality estimates from the descending limb of a catch curve.

binCI

Confidence intervals for binomial probability of success.

bootstrap

Case bootstrapping and associated S3 methods.

agePrecision

Compute measures of precision among sets of ages.

dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.

ageBias

Compute and view possible differences between paired sets of ages.

compSlopes

Tests for significant differences among all pairs of slopes in a dummy variable regression (DVR).

diags

Extract diagonals from a matrix.

growthModels

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

compIntercepts

Tests for significant differences among all pairs of intercepts in a dummy variable regression.

depletion

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

geomean

Calculates the geometric mean or geometric standard deviation.

capHistConvert

Convert between capture history data.frame formats.

fact2num

Converts "numeric" factor levels to numeric values.

fishR

Opens web pages associated with the fishR website.

chapmanRobson

Computes Chapman-Robson estimates of S and Z.

fitPlot

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

expandLenFreq

Expands a length frequency based on a subsample.

extraTests

Likelihood ratio and extra sum-of-squares tests.

lwCompPreds

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

capHistSum

Summarize capture histories in individual fish format.

mapvalues

Replace specified values in a vector or factor with new values.

logbtcf

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

kCounts

Specific utilities for use in a knitr document.

hyperCI

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

lencat

Constructs length class/category variable.

fsaNews

Read news and changes for the 'FSA' package.

psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.

histFromSum

Create a histogram from a frequency table.

expandCounts

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

hoCoef

Performs a hypothesis test that a linear model parameter is equal to a specific value.

jolly

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

chooseColors

Create a list of colors from among a variety of color palettes.

col2rgbt

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

psdVal

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

lagratio

Ratio of lagged observations.

mrClosed

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

ksTest

Kolmogorov-Smirnov Tests.

Mmethods

Estimate natural mortality from a variety of empirical methods.

sumTable

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

hist.formula

Creates separate histograms by levels.

headtail

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

residPlot

Construct a residual plot from lm or nls objects.

plotAB

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

plotBinResp

Plots a binary response variable versus a quantitative explanatory variable.

nlsTracePlot

Adds model fits from nls iterations to active plot.

tictactoe

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

perc

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

rSquared

Extract the coefficient of determination from a linear model object.

peek

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

rcumsum

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

confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.

srStarts

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

poiCI

Confidence interval for Poisson counts.

psdAdd

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

Computes standard error of the mean.

removal

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

validn

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

vbStarts

Find reasonable starting values for a von Bertalanffy growth function.

stockRecruitment

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

oddeven

Determine if a number is odd or even.

wrAdd

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

psdCI

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

psdCalc

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

wsVal

Finds standard weight equation coefficients for a particular species.

repeatedRows2Keep

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

BluegillJL

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

Ecoli

Population growth of Escherichia coli.

CutthroatAL

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

FSAUtils

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

ChinookArg

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

.onAttach

Internal functions.

CodNorwegian

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

BrookTroutTH

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

Mirex

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