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FSA (version 0.8.19)

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

16,224

Version

0.8.19

License

GPL (>= 2)

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Repository

https://github.com/droglenc/FSA

Maintainer

Derek Ogle

Last Published

April 8th, 2018

Functions in FSA (0.8.19)

alkAgeDist

Proportions-at-age from an Age-Length Key

addZeroCatch

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

addRadCap

Add a total radius-at-capture variable to a data.frame that contains one-fish-per-line increments data.

mapvalues

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

WR79

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

col2rgbt

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

compIntercepts

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

extraTests

Likelihood ratio and extra sum-of-squares tests.

alkMeanVar

Mean Values-at-age from an Age-Length Key

fact2num

Converts "numeric" factor levels to numeric values.

fsaNews

Read news and changes for the 'FSA' package.

alkPlot

Plots to visualize age-length keys.

lwCompPreds

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

chooseColors

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

compSlopes

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

hoCoef

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

histFromSum

Create a histogram from a frequency table.

agePrecision

Compute measures of precision among sets of ages.

chapmanRobson

Computes Chapman-Robson estimates of S and Z.

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.

poiCI

Confidence interval for Poisson counts.

gConvert

Converts between types of measurements from calcified structures.

logbtcf

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

binCI

Confidence intervals for binomial probability of success.

bcFuns

Creates a function for a specific back-calculation model.

lencat

Constructs length class/category variable.

psdAdd

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

WhitefishLC

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

WSlit

All known standard weight equations.

alkIndivAge

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

bootstrap

Case bootstrapping and associated S3 methods.

fishR

Opens web pages associated with the fishR website.

removal

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

capHistSum

Summarize capture histories in individual fish format.

catchCurve

Mortality estimates from the descending limb of a catch curve.

fitPlot

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

geomean

Calculates the geometric mean or geometric standard deviation.

perc

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

plotBinResp

Plots a binary response variable versus a quantitative explanatory variable.

jolly

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

expandCounts

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

expandLenFreq

Expands a length frequency based on a subsample.

hyperCI

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

kCounts

Specific utilities for use in a knitr document.

Computes standard error of the mean.

growthModels

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

srStarts

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

wsVal

Finds standard weight equation coefficients for a particular species.

confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.

capHistConvert

Convert between capture history data.frame formats.

psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.

dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.

hist.formula

Creates separate histograms by levels.

diags

Extract diagonals from a matrix.

headtail

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

mrClosed

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

Mmethods

Estimate natural mortality from a variety of empirical methods.

psdCI

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

ksTest

Kolmogorov-Smirnov Tests.

lagratio

Ratio of lagged observations.

psdCalc

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

rSquared

Extract the coefficient of determination from a linear model object.

rcumsum

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

residPlot

Construct a residual plot from lm or nls objects.

nlsTracePlot

Adds model fits from nls iterations to active plot.

vbStarts

Find reasonable starting values for a von Bertalanffy growth 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.

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.

psdVal

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

stockRecruitment

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

sumTable

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

BluegillJL

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

BrookTroutTH

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

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.

ageBias

Compute and view possible differences between paired sets of ages.

FSAUtils

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

CutthroatAL

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

Ecoli

Population growth of Escherichia coli.

.onAttach

Internal functions.

Mirex

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

ChinookArg

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

CodNorwegian

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

FSA

Fisheries stock assessment methods and data.

SMBassWB

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

Schnute

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

SpotVA1

Age and length of spot.

Subset

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

Summarize

Summary statistics for a numeric variable.

PSDlit

Gabelhouse five-cell length categories for various species.