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FSA (version 0.8.27)

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

9,602

Version

0.8.27

License

GPL (>= 2)

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Repository

https://github.com/droglenc/FSA

Maintainer

Derek Ogle

Last Published

February 3rd, 2020

Functions in FSA (0.8.27)

FSAUtils

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

FSA

Fisheries stock assessment methods and data.

CodNorwegian

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

Mirex

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

ChinookArg

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

PSDlit

Gabelhouse five-cell length categories for various species.

CutthroatAL

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

Ecoli

Population growth of Escherichia coli.

.onAttach

Internal functions.

BluegillJL

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

Summarize

Summary statistics for a numeric variable.

WR79

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

SpotVA1

Age and length of spot.

BrookTroutTH

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

ageBias

Compute and view possible differences between paired sets of ages.

SchnuteRichards

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

SMBassWB

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

Subset

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

PikeNYPartial1

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

agePrecision

Compute measures of precision among sets of ages.

binCI

Confidence intervals for binomial probability of success.

dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.

catchCurve

Mortality estimates from the descending limb of a catch curve.

SMBassLS

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

WSlit

All known standard weight equations.

alkPlot

Plots to visualize age-length keys.

capHistConvert

Convert between capture history data.frame formats.

Schnute

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

col2rgbt

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

alkAgeDist

Proportions-at-age from an age-length key

alkIndivAge

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

expandCounts

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

capHistSum

Summarize capture histories in individual fish format.

addZeroCatch

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

chapmanRobson

Computes Chapman-Robson estimates of S and Z.

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.

chooseColors

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

bootstrap

Case bootstrapping and associated S3 methods.

fitPlot

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

PikeNY

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

depletion

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

kCounts

Specific utilities for use in a knitr document.

compSlopes

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

fact2num

Converts "numeric" factor levels to numeric values.

hyperCI

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

Mmethods

Estimate natural mortality from a variety of empirical methods.

histFromSum

Create a histogram from a frequency table.

diags

Extract diagonals from a matrix.

compIntercepts

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

ksTest

Kolmogorov-Smirnov Tests.

psdAdd

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

poiCI

Confidence interval for Poisson counts.

fsaNews

Read news and changes for the 'FSA' package.

expandLenFreq

Expands a length frequency based on a subsample.

mrClosed

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

srStarts

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

extraTests

Likelihood ratio and extra sum-of-squares tests.

geomean

Calculates the geometric mean or geometric standard deviation.

fishR

Opens web pages associated with the fishR website.

growthModels

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

headtail

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

jolly

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

hist.formula

Creates separate histograms by levels.

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.

mapvalues

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

lagratio

Ratio of lagged observations.

psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.

lencat

Constructs length class/category variable.

stockRecruitment

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.

oddeven

Determine if a number is odd or even.

logbtcf

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

rcumsum

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

wrAdd

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

psdVal

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

peek

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

psdCI

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

psdCalc

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

removal

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

rSquared

Extract the coefficient of determination from a linear model object.

confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.

wsVal

Finds standard weight equation coefficients for a particular species.

residPlot

Construct a residual plot from lm or nls objects.

repeatedRows2Keep

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

Computes standard error of the mean.

perc

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

plotAB

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

plotBinResp

Plots a binary response variable versus a quantitative explanatory variable.

sumTable

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

tictactoe

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

validn

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

vbStarts

Find reasonable starting values for a von Bertalanffy growth function.