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FSA (version 0.8.30)

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

16,224

Version

0.8.30

License

GPL (>= 2)

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Repository

https://github.com/droglenc/FSA

Maintainer

Derek Ogle

Last Published

March 9th, 2020

Functions in FSA (0.8.30)

CodNorwegian

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

FSAUtils

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

PSDlit

Gabelhouse five-cell length categories for various species.

BrookTroutTH

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

WhitefishLC

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

PikeNY

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

addZeroCatch

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

Mirex

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

PikeNYPartial1

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

.onAttach

Internal functions.

FSA

Fisheries stock assessment methods and data.

SMBassWB

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

SMBassLS

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

Schnute

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

compIntercepts

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

compSlopes

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

ageBias

Compute and view possible differences between paired sets of ages.

agePrecision

Compute measures of precision among sets of ages.

alkMeanVar

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

alkPlot

Plots to visualize age-length keys.

dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.

expandCounts

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

binCI

Confidence intervals for binomial probability of success.

bootstrap

Case bootstrapping and associated S3 methods.

SchnuteRichards

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

SpotVA1

Age and length of spot.

catchCurve

Mortality estimates from the descending limb of a catch curve.

confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.

jolly

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

hyperCI

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

kCounts

Specific utilities for use in a knitr document.

chapmanRobson

Computes Chapman-Robson estimates of S and Z.

plotAB

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

Summarize

Summary statistics for a numeric variable.

Subset

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

alkAgeDist

Proportions-at-age from an age-length key

plotBinResp

Plots a binary response variable versus a quantitative explanatory variable.

residPlot

Construct a residual plot from lm or nls objects.

alkIndivAge

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

expandLenFreq

Expands a length frequency based on a subsample.

Computes standard error of the mean.

depletion

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

extraTests

Likelihood ratio and extra sum-of-squares tests.

wsVal

Finds standard weight equation coefficients for a particular species.

WSlit

All known standard weight equations.

diags

Extract diagonals from a matrix.

WR79

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

wrAdd

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

capHistConvert

Convert between capture history data.frame formats.

capHistSum

Summarize capture histories in individual fish format.

chooseColors

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

histFromSum

Create a histogram from a frequency table.

col2rgbt

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

hoCoef

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

nlsTracePlot

Adds model fits from nls iterations to active plot.

oddeven

Determine if a number is odd or even.

poiCI

Confidence interval for Poisson counts.

psdAdd

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

sumTable

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

fact2num

Converts "numeric" factor levels to numeric values.

fitPlot

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

tictactoe

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

fishR

Opens web pages associated with the fishR website.

fsaNews

Read news and changes for the 'FSA' package.

ksTest

Kolmogorov-Smirnov Tests.

headtail

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

mapvalues

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

geomean

Calculates the geometric mean or geometric standard deviation.

lagratio

Ratio of lagged observations.

lencat

Constructs length class/category variable.

peek

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

perc

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

lwCompPreds

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

Mmethods

Estimate natural mortality from a variety of empirical methods.

growthModels

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

mrClosed

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

rSquared

Extract the coefficient of determination from a linear model object.

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.

psdVal

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

hist.formula

Creates separate histograms by levels.

logbtcf

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

psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.

stockRecruitment

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

psdCI

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

vbStarts

Find reasonable starting values for a von Bertalanffy growth function.

rcumsum

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

removal

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

repeatedRows2Keep

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

validn

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

ChinookArg

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

Ecoli

Population growth of Escherichia coli.

CutthroatAL

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

BluegillJL

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