If parm='lm' then confidence intervals for the underlying linear model are returned. Not used if x is not a formula.Īn object saved from the catchCurve call (i.e., of class catchCurve).Ī numeric or string (of parameter names) vector that specifies which parameters are to be given confidence intervals. See details.Ī ame from which the variables in the x formula can be found. See details.Ī single non-negative numeric that will replace negative weights (defaults to 0). Not used if x is a formula.Ī numerical vector of ages that define the descending limb of the catch curve.Ī logical that indicates whether a weighted regression should be used. An object saved from catchCurve (i.e., of class catchCurve) when used in the methods.Ī numerical vector of catches or CPUEs for the ages in the catch curve. )Ī numerical vector of assigned ages in the catch curve or a formula of the form catch~age when used in catchCurve. RSquared(object, digits = getOption('digits'), percent = FALSE. A plot method highlights the descending limb, shows the linear model on the descending limb, and, optionally, prints the estimated Z and A. Method functions extract estimates of the instantaneous (Z) and total annual (A) mortality rates with associated standard errors and confidence intervals. Descriptionįits a linear model to the user-defined descending limb of a catch curve. Mortality estimates from the descending limb of a catch curve. nlsTracePlot: Adds model fits from nls iterations to active plot.nlsBoot: Associated S3 methods for nlsBoot from nlstools.mrOpen: Jolly-Seber analysis from multiple mark-recapture events from.mrClosed: Estimate initial population size for single or multiple.Mirex: Mirex concentration, weight, capture year, and species of.metaM: Estimate natural mortality from a variety of empirical.lwCompPreds: Constructs plots of predicted weights at given lengths among.logbtcf: Constructs the correction-factor used when back-transforming.lencat: Constructs length class/category variable.lagratio: Ratio of lagged observations.knitUtil: Specific utilities for use in a knitr document.is.odd: Determine if a number is odd or even.hyperCI: Confidence interval for population size (N) in hypergeometric.histFromSum: Create a histogram from a frequency table.hist.formula: Creates separate histograms by levels.headtail: Shows rows from the head and tail of a data frame or matrix.growthModels: Creates a function for a specific parameterization of the von.geomean: Calculates the geometric mean or geometric standard.FSA: Fisheries stock assessment methods and data.fishR: Opens web pages associated with the fishR website.fact2num: Converts 'numeric' factor levels to numeric values.extraTests: Likelihood ratio and extra sum-of-squares tests.expandLenFreq: Expands a length frequency based on a subsample.expandCounts: Repeat individual fish data (including lengths) from tallied.Ecoli: Population growth of Escherichia coli.dunnTest: Dunn's Kruskal-Wallis Multiple Comparisons.depletion: Computes the Leslie or DeLury population estimate from catch.CutthroatAL: Capture histories (9 samples) of Cutthroat Trout from Auke.col2rgbt: Converts an R color to RGB (red/green/blue) including a.CodNorwegian: Stock and recruitment data for Norwegian cod, 1937-1960.ChinookArg: Lengths and weights for Chinook Salmon from three locations.chapmanRobson: Computes Chapman-Robson estimates of S and Z.catchCurve: Mortality estimates from the descending limb of a catch.capHistSum: Summarize capture histories in individual fish format.capHistConvert: Convert between capture history ame formats.capFirst: Capitalizes the first letter of first or all words in a.BrookTroutTH: Catch-at-age for Tobin Harbor, Isle Royale Brook Trout.boot: Associated S3 methods for bootstrap results from car::Boot.BluegillJL: Capture histories (2 samples) of Bluegill from Jewett Lake.binCI: Confidence intervals for binomial probability of success.alkPlot: Plots to visualize age-length keys.alkMeanVar: Mean Values-at-age from an age-length key.alkIndivAge: Use an age-length key to assign age to individuals in the.alkAgeDist: Proportions-at-age from an age-length key.agePrecision: Compute measures of precision among sets of ages.ageBias: Compute and view possible differences between paired sets of.addZeroCatch: Adds zeros for catches of species not collected in some.

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