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FSA (version 0.8.17)
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
10,956
Version
0.8.17
License
GPL (>= 2)
Issues
3
Pull Requests
0
Stars
63
Forks
20
Repository
https://github.com/droglenc/FSA
Maintainer
Derek Ogle
Last Published
October 29th, 2017
Functions in FSA (0.8.17)
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.onAttach
Internal functions.
PSDlit
Gabelhouse five-cell length categories for various species.
PikeNY
Summarized multiple mark-recapture data for all Northern Pike from Buckthorn Marsh, NY.
alkMeanVar
Mean Values-at-age from an Age-Length Key
alkPlot
Plots to visualize age-length keys.
FSA
Fisheries stock assessment methods and data.
capHistSum
Summarize capture histories in individual fish format.
catchCurve
Mortality estimates from the descending limb of a catch curve.
compSlopes
Tests for significant differences among all pairs of slopes in a dummy variable regression (DVR).
depletion
Computes the Leslie or DeLury population estimate from catch and effort data.
hyperCI
Confidence interval for population size (N) in hypergeometric distribution.
kCounts
Specific utilities for use in a knitr document.
lwCompPreds
Constructs plots of predicted weights at given lengths among different groups.
mapvalues
Replace specified values in a vector or factor with new values.
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.
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.
SpotVA1
Age and length of spot.
Subset
Subsets/filters a data frame and drops the unused levels.
ageBias
Compute and view possible differnces between paired sets of ages.
agePrecision
Compute measures of precision among sets of ages.
chapmanRobson
Computes Chapman-Robson estimates of S and Z.
chooseColors
Create a list of colors from among a variety of color palettes.
extraTests
Likelihood ratio and extra sum-of-squares tests.
fact2num
Converts "numeric" factor levels to numeric values.
geomean
Calculates the geometric mean or geometric standard deviation.
growthModels
Creates a function for a specific parameterization of the von Bertalanffy, Gompertz, Richards, and logistic growth functions.
jolly
Jolly-Seber analysis from multiple mark-recapture events from an open population.
confint.nlsBoot
Associated S3 methods for nlsBoot from nlstools.
psdCI
Compute confidence intervals for PSD-X and PSD X-Y values.
psdCalc
Convenience function for calculating PSD-X and PSD X-Y values.
FSAUtils
Capitalizes the first letter of first or all words in a string.
Mirex
Mirex concentration, weight, capture year, and species of Lake Ontario salmon.
Summarize
Summary statistics for a numeric variable.
WR79
Ages and lengths for a hypothetical sample from Westerheim and Ricker (1979).
addRadCap
Add a total radius-at-capture variable to a data.frame that contains one-fish-per-line increments data.
srStarts
Finds reasonable starting values for parameters in specific parameterizations of common stock-recruitment models.
stockRecruitment
Creates a function for a specific parameterization of a common stock-recruitment function .
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 Buckthorn Marsh, NY.
SMBassLS
Catch-effort data for Little Silver Lake (Ont) Smallmouth Bass.
alkAgeDist
Proportions-at-age from an Age-Length Key
addZeroCatch
Adds zeros for catches of species not collected in some sampling events.
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.
fsaNews
Read news and changes for the 'FSA' package.
gConvert
Converts between types of measurements from calcified structures.
psdPlot
Length-frequency histogram with Gabelhouse lengths highlighted.
psdVal
Finds Gabelhouse lengths (for PSD calculations) for a species.
rcumsum
Computes the prior to or reverse cumulative sum of a vector.
removal
Population estimates for k-, 3-, or 2-pass removal data.
alkIndivAge
Use an age-length key to assign age to individuals in the unaged sample.
bootstrap
Associated S3 methods for bootCase from car.
capHistConvert
Convert between capture history data.frame formats.
diags
Extract diagonals from a matrix.
dunnTest
Dunn's Kruskal-Wallis Multiple Comparisons.
headtail
Shows rows from the head and tail of a data frame or matrix.
hist.formula
Creates separate histograms by levels.
lencat
Constructs length class/category variable.
logbtcf
Constructs the correction-factor used when back-transforming log-transformed values.
ChinookArg
Lengths and weights for Chinook Salmon from three locations in Argentina.
CodNorwegian
Stock and recruitment data for Norwegian cod, 1937-1960.
bcFuns
Creates a function for a specific back-calculation model.
binCI
Confidence intervals for binomial probability of success.
fishR
Opens web pages associated with the fishR website.
residPlot
Construct a residual plot from lm or nls objects.
se
Computes standard error of the mean.
wrAdd
Computes a vector of relative weights specific to a species in an entire data frame.
wsVal
Finds standard weight equation coefficients for a particular species.
fitPlot
Fitted model plot for an lm, glm, or nls object.
CutthroatAL
Capture histories (9 samples) of Cutthroat Trout from Auke Lake.
Ecoli
Population growth of Escherichia coli.
SMBassWB
Growth increment data for West Bearskin Lake, MN, Smallmouth Bass.
Schnute
The four-parameter growth function from Schnute (1981).
WSlit
All known standard weight equations.
WhitefishLC
Assigned ages from two readers on three structures for Lake Whitefish from Lake Champlain.
expandCounts
Repeat individual fish data (including lengths) from tallied counts.
expandLenFreq
Expands a length frequency based on a subsample.
histFromSum
Create a histogram from a frequency table.
hoCoef
Performs a hypothesis test that a linear model parameter is equal to a specific value.
ksTest
Kolmogorov-Smirnov Tests.
lagratio
Ratio of lagged observations.
poiCI
Confidence interval for Poisson counts.
mrClosed
Estimate initial population size for single or multiple census mark-recapture data.
nlsTracePlot
Adds model fits from nls iterations to active plot.
oddeven
Determine if a number is odd or even.
validn
Finds the number of valid (non-NA) values in a vector.
vbStarts
Find reasonable starting values for a von Bertalanffy growth function.
Mmethods
Estimate natural mortality from a variety of empirical methods.
psdAdd
Creates a vector of Gabelhouse lengths for each species in an entire data frame.