Modelling and Quantitative Methods in Fisheries

Documentation for package ‘MQMF’ version 0.1.5

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A B C D F G H I L M N O P Q R S T U V W misc

-- A --

abdat	abdat A list of fishery data for blacklip abalone
addcontours	addcontours simplifies adding contours to an xy plot of points
addlnorm	addlnorm estimates a log-normal distribution from output of hist
addnorm	addnorm adds a normal distribution to a histogram of a data set.
aicbic	aicbic returns the AIC and BIC for a given model
altnegLL	altnegLL calculate the Normal negative log-likelihood

-- B --

bce	bce Baranov catch equation
bh	bh represents one version of Beverton-Holt recruitment
blackisland	blackisland tagging data from a blacklip abalone population
bracket	bracket bounds a value on the x-axis and y-axis

-- C --

calcprior	calcprior return the sum of a vector of constant values as priors
chapter2	chapter2 The 15 R-code chunks from A Non-Introduction to R
chapter3	chapter3 The 27 R-code chunks from Simple Population Models
chapter4	chapter4 The 47 R-code chunks from Model Parameter Estimation
chapter5	chapter5 The 23 R-code chunks from Static Models
chapter6	chapter6 The 53 R-code chunks from On Uncertainty
chapter7	chapter7 The 67 R-code chunks from Surplus Production Models
countgtone	countgtone used in apply to count the number > 1 in a vector
countgtzero	countgtzero used in apply to count numbers > zero in a vector
countNAs	countNAs used in apply to count the number of NAs in a vector
countones	countones used in apply to count the number of ones in a vector
countzeros	countzeros used in apply to count the number of zeros in a vector

-- D --

dataspm	dataspm A data.frame of fisheries catch and cpue data
discretelogistic	discretelogistic example and figure 3.2 Discrete logistic model
domed	domed calculates domed selectivity curves
do_MCMC	do_MCMC conducts an MCMC using Gibbs within Metropolis

-- F --

fabens	fabens calculates predicted growth increment for tagging data
facttonum	facttonum converts a vector of numeric factors into numbers
fitSPM	fitSPM fits a surplus production model
freqMean	freqMean calculates the mean and stdev of count data

-- G --

getlag	getlag is used to look for the response of cpue to previous catches
getmax	getmax can be used to define the upper bound for a plot
getmin	getmin can be used to define the lower bound for a plot
getMSY	getMSY calculates the MSY for the Polacheck et al 1993 equation
getname	getname returns the name of a variable as character
getrmse	getrmse calculates the rmse of the input 'invar' series
getseed	getseed generates a random number seed
getsingle	getsingle extracts one number from an input line of characters
gettime	gettime calculates time in seconds passed each day
getvector	getvector extracts a vector of numbers from a line of characters
Gz	Gz calculates predicted Gompertz length-at-age growth curve

-- H --

halftable

halftable halves the height of a tall narrow data.frame for printing

-- I --

inthist	inthist a replacement for the hist function for use with integers
invl	invl calculates growth increments for the inverse logistic
iscol	incol is a utility to determine if a column is present in a matrix

-- L --

LatA	LatA Simulated length-at-age for 358 female fish
likeratio	likeratio conducts a likelihood ratio test
linter	linter finds a value in a series using its location in another
logist	logist Logistic selectivity function

-- M --

magnitude	magnitude returns the magnitude of numbers in base 10
makelabel	makelabel generates a label from text and values
mature	mature alternative logistic function commonly used for maturity
minnow	minnow contains weekly growth data for use with seasonal growth curves
mm	mm calculates the predicted Michaelis-Menton length-at-age
mnnegLL	mnnegLL generic multinomial negative log-likelihoods

-- N --

negLL	negLL calculate log-normal log-likelihoods
negLL1	negLL1 calculate log-normal log-likelihoods with a penalty
negLLM	negLLM -ve log-normal likelihoods for multiple index time-series
negLLP	negLLP -ve log-likelihood for normally distributed variables
negNLL	negNLL -ve log-likelihood for normally distributed variables
negnormL	negnormL an alternative -log-likelihood for normal errors
npf	npf fishery catch data from Northern Prawn Fishery 1970-1992

-- O --

outfit

outfit tidy print of output from optim, nlminb, or nlm

-- P --

panel.cor	panel.cor is a version of a function given in the help for pairs
parasympt	parasympt generates N vectors from a multi-variate normal
parset	parset alters the current base graphics par settings
parsyn	parsyn types the standard par command syntax to the console
penalty0	penalty0 enables the adding of a large penalty as one approaches 0.0
penalty1	penalty1 adds an increasingly large penalty as a value approaches 1.0
plot.dynpop	plot.dynpop an S3 method for plotting dynpop objects
plot1	plot1 a quick way to plot an xy line or point plot
plotfishM	plotfishM plots the catch and optionally the cpue
plotlag	plotlag plots the effect of a lag between two variables
plotprep	plotprep sets up a window and the par values for plotting
plotprofile	plotprofile simplifies plotting single likelihood profiles
plotproj	plotproj generate a plot of a matrix of biomass projections
plotspmdat	plotspmdat plots the fish data containing catches and cpue
plotspmmod	plotspmmod plots an spm model fit given parameters and data
predfreq	predfreq is used for modal analysis of count data
printV	printV returns a vector cbinded to 1:length(invect)
properties	properties - used to examine the properties of a data.frame
pttuna	pttuna is yellowfin tuna fishery data from Pella-Tomlinson 1969

-- Q --

quants

quants used in apply to estimate quantiles across a vector

-- R --

removeEmpty	removeEmpty removes empty strings from a vector of strings
ricker	ricker one version of the Ricker stock recruitment
robustSPM	robustSPM does a robustness test on quality of fit of an SPM

-- S --

schaef	schaef is yellowfin tuna fishery data from Schaefer 1957
setpalette	setpalette is a shortcut for altering the palette to R4
simpspm	simpspm calculates only the predicted log(CE) for an SPM
simpspmM	simpspmM calculates predicted CE when multiple indices are present
spm	spm calculates the dynamics of a Schaefer or Fox model
spmboot	spmboot conducts a bootstrap analysis on a spm model
spmCE	spmCE - calculates the dynamics for multiple cpue time-series
spmphaseplot	spmphaseplot - plots the phase plot of harvest rate vs biomass
spmproj	spmproj calculates biomass trajectories for replicate parameters
spmprojDet	spmprojDet conducts forward projections from known conditions
srug	srug is the Schnute and Richards Unified Growth Curve
ssq	ssq a generalized function for summing squared residuals
summspm	summspm extracts critical statistics from output of plotspmmod

-- T --

tasab	tasab is a matrix of abalone maturity-at-length data
tigers	tigers is tiger prawn recruitment data from Penn & Caputi 1986
twoindex	twoindex has orange roughy catches with hypothetical cpue

-- U --

uphist

uphist a histogram with an upper limit on the x-axis

-- V --

vB	vB calculates the predicted von Bertalanffy length at age

-- W --

which.closest

which.closest find a number in a vector closest to a given value

-- misc --

%ni%	'%ni%' identifies which element in x is NOT in y