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FSA (version 0.8.4)

Functions for Simple Fisheries Stock Assessment Methods

Description

Functions to perform a variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website listed below.

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Install

install.packages('FSA')

Monthly Downloads

14,249

Version

0.8.4

License

GPL (>= 2)

Issues

3

Pull Requests

0

Stars

70

Forks

24

Maintainer

Derek Ogle

Last Published

December 21st, 2015

Functions in FSA (0.8.4)

alkMeanVar

Mean Values-at-age from an Age-Length Key
PikeNYPartial1

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

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

Compute and view possible biases between paired sets of ages.
CutthroatAL

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

Mortality estimates from the descending limb of a catch curve.
fishR

Opens web pages associated with the fishR website.
SMBassLS

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

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

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

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

Gabelhouse five-cell length categories for various species.
FSA

Fisheries stock assessment methods and data.
psdVal

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

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

Population growth of Escherichia coli.
lenFreqExpand

Expands a length frequency based on a subsample.
headtail

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

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

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

Convert between capture history data.frame formats.
fitPlot

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

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

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

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

All known standard weight equations.
BrookTroutTH

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

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

Summary statistics for a numeric or factor variable.
alkAgeDist

Proportions-at-age from an Age-Length Key
lagratio

Ratio of lagged observations.
ageKeyPlot

Plots to visualize age-length keys.
SMBassWB

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

Plots a binary response variable versus a quantitative explanatory variable.
depletion

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

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

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

Estimate natural mortality from a variety of empirical methods.
lencat

Constructs length class/category variable.
wrAdd

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

Converts between types of measurements from calcified structures.
Mirex

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

Specific utilities for use in a knitr document.
tictactoe

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

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

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

Associated S3 methods for bootCase from car.
Schnute

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

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

Capitalizes the first letter of first or all words in a string.
fact2num

Converts "numeric" factor levels to numeric values.
binCI

Confidence intervals for binomial probability of success.
chapmanRobson

Computes Chapman-Robson estimates of S and Z.
psdCI

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

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

Calculates the geometric mean or geometric standard deviation.
hist.formula

Creates separate histograms by levels.
psdAdd

Create vector of Gabelhouse lengths for each species from an entire data frame.
growthModels

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

Find reasonable starting values for a von Bertalanffy growth function.
WR79

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

Length-frequency histogram with Gabelhouse lengthshighlighted.
compIntercepts

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

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

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

Determine if a number is odd or even.
agePrecision

Compute measures of precision among sets of ages.
SpotVA1

Age and length of spot.
ageKey

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

Computes standard error of the mean.
srStarts

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

Likelihood ratio and extra sum-of-squares tests.
.onAttach

Internal functions.
poiCI

Confidence interval for Poisson rate parameter.
bcFuns

Creates a function for a specific back-calculation model.
wsVal

Finds standard weight equation coefficients for a particular species.
ksTest

Kolmogorov-Smirnov Tests.
residPlot

Construct a residual plot from lm or nls objects.
fsaNews

Read news and changes for the 'FSA' package.
perc

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

Associated S3 methods for nlsBoot from nlstools.
addRadCap

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

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

Summarize capture histories in individual fish format.
dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.
col2rgbt

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

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