⚠️There's a newer version (0.9.6) of this package.Take me there.

FSA (version 0.8.6)

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 .

Copy Link

Version

Install

install.packages('FSA')

Monthly Downloads

20,921

Version

0.8.6

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/droglenc/FSA

Maintainer

Derek Ogle

Last Published

March 24th, 2016

Functions in FSA (0.8.6)

addZeroCatch

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

expandCounts

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

dunnTest

Dunn's Kruskal-Wallis Multiple Comparisons.

CodNorwegian

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

perc

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

binCI

Confidence intervals for binomial probability of success.

ageKey

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

hyperCI

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

depletion

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

lagratio

Ratio of lagged observations.

PikeNYPartial1

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

fact2num

Converts "numeric" factor levels to numeric values.

WSlit

All known standard weight equations.

Ecoli

Population growth of Escherichia coli.

bootstrap

Associated S3 methods for bootCase from car.

SMBassLS

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

gConvert

Converts between types of measurements from calcified structures.

capHistConvert

Convert between capture history data.frame formats.

Subset

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

CutthroatAL

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

alkMeanVar

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

oddeven

Determine if a number is odd or even.

catchCurve

Mortality estimates from the descending limb of a catch curve.

logbtcf

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

Mirex

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

fsaNews

Read news and changes for the 'FSA' package.

agePrecision

Compute measures of precision among sets of ages.

BluegillJL

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

chapmanRobson

Computes Chapman-Robson estimates of S and Z.

compSlopes

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

extraTests

Likelihood ratio and extra sum-of-squares tests.

chooseColors

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

headtail

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

jolly

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

SMBassWB

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

psdPlot

Length-frequency histogram with Gabelhouse lengths highlighted.

kCounts

Specific utilities for use in a knitr document.

histFromSum

Create a histogram from a frequency table.

removal

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

psdVal

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

alkAgeDist

Proportions-at-age from an Age-Length Key

confint.nlsBoot

Associated S3 methods for nlsBoot from nlstools.

hist.formula

Creates separate histograms by levels.

lencat

Constructs length class/category variable.

psdCI

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

poiCI

Confidence interval for Poisson rate parameter.

Schnute

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

validn

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

tictactoe

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

ageKeyPlot

Plots to visualize age-length keys.

PSDlit

Gabelhouse five-cell length categories for various species.

FSAUtils

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

rcumsum

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

PikeNY

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

fishR

Opens web pages associated with the fishR website.

col2rgbt

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

plotBinResp

Plots a binary response variable versus a quantitative explanatory variable.

addRadCap

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

ksTest

Kolmogorov-Smirnov Tests.

lenFreqExpand

Expands a length frequency based on a subsample.

compIntercepts

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

vbStarts

Find reasonable starting values for a von Bertalanffy growth function.

ageBias

Compute and view possible biases between paired sets of ages.

lwCompPreds

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

geomean

Calculates the geometric mean or geometric standard deviation.

sumTable

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

WhitefishLC

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

ChinookArg

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

wrAdd

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

BrookTroutTH

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

mapvalues

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

SpotVA1

Age and length of spot.

wsVal

Finds standard weight equation coefficients for a particular species.

mrClosed

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

fitPlot

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

capHistSum

Summarize capture histories in individual fish format.

Summarize

Summary statistics for a numeric or factor variable.

WR79

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

growthModels

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

FSA

Fisheries stock assessment methods and data.

psdCalc

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

residPlot

Construct a residual plot from lm or nls objects.

stockRecruitment

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

Computes standard error of the mean.

bcFuns

Creates a function for a specific back-calculation model.

Mmethods

Estimate natural mortality from a variety of empirical methods.

srStarts

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

psdAdd

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

.onAttach

Internal functions.

hoCoef

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