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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
11,140
Version
0.8.19
License
GPL (>= 2)
Issues
3
Pull Requests
0
Stars
65
Forks
20
Repository
https://github.com/droglenc/FSA
Maintainer
Derek Ogle
Last Published
April 8th, 2018
Functions in FSA (0.8.19)
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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.
se
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.