Simple Fisheries Stock Assessment Methods

addZeroCatch | Adds zeros for catches of species not collected in some... |

ageBias | Compute and view possible differences between paired sets of... |

agePrecision | Compute measures of precision among sets of ages. |

ALKAgeDist | Proportions-at-age from an age-length key |

alkIndivAge | Use an age-length key to assign age to individuals in the... |

ALKMeanVar | Mean Values-at-age from an age-length key |

alkPlot | Plots to visualize age-length keys. |

binCI | Confidence intervals for binomial probability of success. |

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

bootCase | Case bootstrapping and associated S3 methods. |

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

capHistConvert | Convert between capture history data.frame formats. |

capHistSum | Summarize capture histories in individual fish format. |

catchCurve | Mortality estimates from the descending limb of a catch... |

chapmanRobson | Computes Chapman-Robson estimates of S and Z. |

ChinookArg | Lengths and weights for Chinook Salmon from three locations... |

chooseColors | Create a list of colors from among a variety of color... |

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

col2rgbt | Converts an R color to RGB (red/green/blue) including a... |

compIntercepts | Tests for significant differences among all pairs of... |

compSlopes | Tests for significant differences among all pairs of slopes... |

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

depletion | Computes the Leslie or DeLury population estimate from catch... |

diags | Extract diagonals from a matrix. |

dunnTest | Dunn's Kruskal-Wallis Multiple Comparisons. |

Ecoli | Population growth of Escherichia coli. |

expandCounts | Repeat individual fish data (including lengths) from tallied... |

expandLenFreq | Expands a length frequency based on a subsample. |

extraTests | Likelihood ratio and extra sum-of-squares tests. |

fact2num | Converts "numeric" factor levels to numeric values. |

fishR | Opens web pages associated with the fishR website. |

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

FSA | Fisheries stock assessment methods and data. |

FSA-internals | Internal functions. |

fsaNews | Read news and changes for the 'FSA' package. |

FSAUtils | Capitalizes the first letter of first or all words in a... |

geomean | Calculates the geometric mean or geometric standard... |

growthModels | Creates a function for a specific parameterization of the von... |

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

hist.formula | Creates separate histograms by levels. |

histFromSum | Create a histogram from a frequency table. |

hoCoef | Performs a hypothesis test that a linear model parameter is... |

hyperCI | Confidence interval for population size (N) in hypergeometric... |

knitUtil | Specific utilities for use in a knitr document. |

ksTest | Kolmogorov-Smirnov Tests. |

lagratio | Ratio of lagged observations. |

lencat | Constructs length class/category variable. |

logbtcf | Constructs the correction-factor used when back-transforming... |

lwCompPreds | Constructs plots of predicted weights at given lengths among... |

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

metaM | Estimate natural mortality from a variety of empirical... |

Mirex | Mirex concentration, weight, capture year, and species of... |

mrClosed | Estimate initial population size for single or multiple... |

mrOpen | Jolly-Seber analysis from multiple mark-recapture events from... |

nlsBoot | Associated S3 methods for nlsBoot from nlstools. |

nlsTracePlot | Adds model fits from nls iterations to active plot. |

oddeven | Determine if a number is odd or even. |

perc | Computes the percentage of values in a vector less than or... |

PikeNY | Summarized multiple mark-recapture data for all Northern Pike... |

PikeNYPartial1 | Capture histories (4 samples), in capture history format, of... |

plotAB | Construct traditional (Campana-like) age-bias plots. |

plotBinResp | Plots a binary response variable versus a quantitative... |

poiCI | Confidence interval for Poisson counts. |

psdAdd | Creates a vector of Gabelhouse lengths for each species in an... |

psdCalc | Convenience function for calculating PSD-X and PSD X-Y... |

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

PSDlit | Gabelhouse five-cell length categories for various species. |

psdPlot | Length-frequency histogram with Gabelhouse lengths... |

psdVal | Finds Gabelhouse lengths (for PSD calculations) for a... |

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

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

residPlot | Construct a residual plot from lm or nls objects. |

rSquared | Extract the coefficient of determination from a linear model... |

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

SchnuteRichards | The five-parameter growth function from Schnute and Richards... |

se | Computes standard error of the mean. |

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

SMBassWB | Growth increment data for West Bearskin Lake, MN, Smallmouth... |

SpotVA1 | Age and length of spot. |

srStarts | Finds reasonable starting values for parameters in specific... |

stockRecruitment | Creates a function for a specific parameterization of a... |

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

Summarize | Summary statistics for a numeric variable. |

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

tictactoe | Construct a base tic-tac-toe plot for presenting... |

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

vbStarts | Find reasonable starting values for a von Bertalanffy growth... |

WhitefishLC | Assigned ages from two readers on three structures for Lake... |

WR79 | Ages and lengths for a hypothetical sample from Westerheim... |

wrAdd | Computes a vector of relative weights specific to a species... |

WSlit | All known standard weight equations. |

wsVal | Finds standard weight equation coefficients for a particular... |

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