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FSA (version 0.8.11)

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

0.8.11

License

GPL (>= 2)

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Repository

https://github.com/droglenc/FSA

Maintainer

Derek Ogle

Last Published

December 13th, 2016

Functions in FSA (0.8.11)

bcFuns

Creates a function for a specific back-calculation model.

addZeroCatch

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

alkPlot

Plots to visualize age-length keys.

addRadCap

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

binCI

Confidence intervals for binomial probability of success.

agePrecision

Compute measures of precision among sets of ages.

alkMeanVar

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

alkIndivAge

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

ageBias

Compute and view possible biases between paired sets of ages.

alkAgeDist

Proportions-at-age from an Age-Length Key

capHistSum

Summarize capture histories in individual fish format.

BluegillJL

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

CodNorwegian

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

capHistConvert

Convert between capture history data.frame formats.

ChinookArg

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

bootstrap

Associated S3 methods for bootCase from car.

catchCurve

Mortality estimates from the descending limb of a catch curve.

chapmanRobson

Computes Chapman-Robson estimates of S and Z.

chooseColors

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

BrookTroutTH

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

compSlopes

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

compIntercepts

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

col2rgbt

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

Ecoli

Population growth of Escherichia coli.

expandLenFreq

Expands a length frequency based on a subsample.

CutthroatAL

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

depletion

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

dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.

expandCounts

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

diags

Extract diagonals from a matrix.

fsaNews

Read news and changes for the 'FSA' package.

FSAUtils

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

.onAttach

Internal functions.

FSA

Fisheries stock assessment methods and data.

geomean

Calculates the geometric mean or geometric standard deviation.

extraTests

Likelihood ratio and extra sum-of-squares tests.

gConvert

Converts between types of measurements from calcified structures.

fishR

Opens web pages associated with the fishR website.

fact2num

Converts "numeric" factor levels to numeric values.

fitPlot

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

hyperCI

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

hoCoef

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

histFromSum

Create a histogram from a frequency table.

hist.formula

Creates separate histograms by levels.

lagratio

Ratio of lagged observations.

ksTest

Kolmogorov-Smirnov Tests.

kCounts

Specific utilities for use in a knitr document.

lencat

Constructs length class/category variable.

headtail

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

growthModels

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

Mirex

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

mrClosed

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

lwCompPreds

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

logbtcf

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

mapvalues

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

Mmethods

Estimate natural mortality from a variety of empirical methods.

confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.

jolly

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

nlsTracePlot

Adds model fits from nls iterations to active plot.

oddeven

Determine if a number is odd or even.

PikeNY

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

poiCI

Confidence interval for Poisson counts.

psdCI

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

psdCalc

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

psdAdd

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

psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.

PSDlit

Gabelhouse five-cell length categories for various species.

plotBinResp

Plots a binary response variable versus a quantitative explanatory variable.

PikeNYPartial1

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

perc

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

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).

removal

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

Computes standard error of the mean.

SpotVA1

Age and length of spot.

residPlot

Construct a residual plot from lm or nls objects.

srStarts

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

psdVal

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

rcumsum

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

Summarize

Summary statistics for a numeric variable.

sumTable

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

stockRecruitment

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

vbStarts

Find reasonable starting values for a von Bertalanffy growth function.

WSlit

All known standard weight equations.

Subset

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

WhitefishLC

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

wrAdd

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

WR79

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

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.