R: Modelling and Quantitative Methods in Fisheries

# Modelling and Quantitative Methods in Fisheries

## Documentation for package ‘MQMF’ version 0.1.5

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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