Package: MQMF 0.1.5

MQMF: Modelling and Quantitative Methods in Fisheries

Complements the book "Using R for Modelling and Quantitative Methods in Fisheries" ISBN 9780367469894, published in 2021 by Chapman & Hall in their "Using R series". There are numerous functions and data-sets that are used in the book's many practical examples.

Authors:Malcolm Haddon [aut, cre]

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NEWS

# Install 'MQMF' in R:

install.packages('MQMF', repos = c('https://haddonm.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/haddonm/mqmf/issues

Datasets:

LatA - LatA Simulated length-at-age for 358 female fish
abdat - Abdat A list of fishery data for blacklip abalone
blackisland - Blackisland tagging data from a blacklip abalone population
dataspm - Dataspm A data.frame of fisheries catch and cpue data
minnow - Minnow contains weekly growth data for use with seasonal growth curves
npf - Npf fishery catch data from Northern Prawn Fishery 1970-1992
pttuna - Pttuna is yellowfin tuna fishery data from Pella-Tomlinson 1969
schaef - Schaef is yellowfin tuna fishery data from Schaefer 1957
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

On CRAN:

ecology fisheries haddon quantitative-methods uncertainty

4.12 score 11 stars 24 scripts 244 downloads 94 exports 2 dependencies

Last updated 1 years agofrom:f171966258. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 06 2024
R-4.5-win	OK	Nov 06 2024
R-4.5-linux	OK	Nov 06 2024
R-4.4-win	OK	Nov 06 2024
R-4.4-mac	OK	Nov 06 2024
R-4.3-win	OK	Nov 06 2024
R-4.3-mac	OK	Nov 06 2024

Exports:%ni%addcontours addlnorm addnorm aicbic altnegLL bce bh bracket calcprior chapter2 chapter3 chapter4 chapter5 chapter6 chapter7 countgtone countgtzero countNAs countones countzeros discretelogistic do_MCMC domed fabens facttonum fitSPM freqMean getlag getmax getmin getMSY getname getrmse getseed getsingle gettime getvector Gz halftable inthist invl iscol likeratio linter logist magnitude makelabel mature mm mnnegLL negLL negLL1 negLLM negLLP negNLL negnormL outfit panel.cor parasympt parset parsyn penalty0 penalty1 plot1 plotfishM plotlag plotprep plotprofile plotproj plotspmdat plotspmmod predfreq printV properties quants removeEmpty ricker robustSPM setpalette simpspm simpspmM spm spmboot spmCE spmphaseplot spmproj spmprojDet srug ssq summspm uphist vB which.closest

Dependencies:MASS mvtnorm

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'%ni%' identifies which element in x is NOT in y	%ni%
abdat A list of fishery data for blacklip abalone	abdat
addcontours simplifies adding contours to an xy plot of points	addcontours
addlnorm estimates a log-normal distribution from output of hist	addlnorm
addnorm adds a normal distribution to a histogram of a data set.	addnorm
aicbic returns the AIC and BIC for a given model	aicbic
altnegLL calculate the Normal negative log-likelihood	altnegLL
bce Baranov catch equation	bce
bh represents one version of Beverton-Holt recruitment	bh
blackisland tagging data from a blacklip abalone population	blackisland
bracket bounds a value on the x-axis and y-axis	bracket
calcprior return the sum of a vector of constant values as priors	calcprior
chapter2 The 15 R-code chunks from A Non-Introduction to R	chapter2
chapter3 The 27 R-code chunks from Simple Population Models	chapter3
chapter4 The 47 R-code chunks from Model Parameter Estimation	chapter4
chapter5 The 23 R-code chunks from Static Models	chapter5
chapter6 The 53 R-code chunks from On Uncertainty	chapter6
chapter7 The 67 R-code chunks from Surplus Production Models	chapter7
countgtone used in apply to count the number > 1 in a vector	countgtone
countgtzero used in apply to count numbers > zero in a vector	countgtzero
countNAs used in apply to count the number of NAs in a vector	countNAs
countones used in apply to count the number of ones in a vector	countones
countzeros used in apply to count the number of zeros in a vector	countzeros
dataspm A data.frame of fisheries catch and cpue data	dataspm
discretelogistic example and figure 3.2 Discrete logistic model	discretelogistic
do_MCMC conducts an MCMC using Gibbs within Metropolis	do_MCMC
domed calculates domed selectivity curves	domed
fabens calculates predicted growth increment for tagging data	fabens
facttonum converts a vector of numeric factors into numbers	facttonum
fitSPM fits a surplus production model	fitSPM
freqMean calculates the mean and stdev of count data	freqMean
getlag is used to look for the response of cpue to previous catches	getlag
getmax can be used to define the upper bound for a plot	getmax
getmin can be used to define the lower bound for a plot	getmin
getMSY calculates the MSY for the Polacheck et al 1993 equation	getMSY
getname returns the name of a variable as character	getname
getrmse calculates the rmse of the input 'invar' series	getrmse
getseed generates a random number seed	getseed
getsingle extracts one number from an input line of characters	getsingle
gettime calculates time in seconds passed each day	gettime
getvector extracts a vector of numbers from a line of characters	getvector
Gz calculates predicted Gompertz length-at-age growth curve	Gz
halftable halves the height of a tall narrow data.frame for printing	halftable
inthist a replacement for the hist function for use with integers	inthist
invl calculates growth increments for the inverse logistic	invl
incol is a utility to determine if a column is present in a matrix	iscol
LatA Simulated length-at-age for 358 female fish	LatA
likeratio conducts a likelihood ratio test	likeratio
linter finds a value in a series using its location in another	linter
logist Logistic selectivity function	logist
magnitude returns the magnitude of numbers in base 10	magnitude
makelabel generates a label from text and values	makelabel
mature alternative logistic function commonly used for maturity	mature
minnow contains weekly growth data for use with seasonal growth curves	minnow
mm calculates the predicted Michaelis-Menton length-at-age	mm
mnnegLL generic multinomial negative log-likelihoods	mnnegLL
negLL calculate log-normal log-likelihoods	negLL
negLL1 calculate log-normal log-likelihoods with a penalty	negLL1
negLLM -ve log-normal likelihoods for multiple index time-series	negLLM
negLLP -ve log-likelihood for normally distributed variables	negLLP
negNLL -ve log-likelihood for normally distributed variables	negNLL
negnormL an alternative -log-likelihood for normal errors	negnormL
npf fishery catch data from Northern Prawn Fishery 1970-1992	npf
outfit tidy print of output from optim, nlminb, or nlm	outfit
panel.cor is a version of a function given in the help for pairs	panel.cor
parasympt generates N vectors from a multi-variate normal	parasympt
parset alters the current base graphics par settings	parset
parsyn types the standard par command syntax to the console	parsyn
penalty0 enables the adding of a large penalty as one approaches 0.0	penalty0
penalty1 adds an increasingly large penalty as a value approaches 1.0	penalty1
plot.dynpop an S3 method for plotting dynpop objects	plot.dynpop
plot1 a quick way to plot an xy line or point plot	plot1
plotfishM plots the catch and optionally the cpue	plotfishM
plotlag plots the effect of a lag between two variables	plotlag
plotprep sets up a window and the par values for plotting	plotprep
plotprofile simplifies plotting single likelihood profiles	plotprofile
plotproj generate a plot of a matrix of biomass projections	plotproj
plotspmdat plots the fish data containing catches and cpue	plotspmdat
plotspmmod plots an spm model fit given parameters and data	plotspmmod
predfreq is used for modal analysis of count data	predfreq
printV returns a vector cbinded to 1:length(invect)	printV
properties - used to examine the properties of a data.frame	properties
pttuna is yellowfin tuna fishery data from Pella-Tomlinson 1969	pttuna
quants used in apply to estimate quantiles across a vector	quants
removeEmpty removes empty strings from a vector of strings	removeEmpty
ricker one version of the Ricker stock recruitment	ricker
robustSPM does a robustness test on quality of fit of an SPM	robustSPM
schaef is yellowfin tuna fishery data from Schaefer 1957	schaef
setpalette is a shortcut for altering the palette to R4	setpalette
simpspm calculates only the predicted log(CE) for an SPM	simpspm
simpspmM calculates predicted CE when multiple indices are present	simpspmM
spm calculates the dynamics of a Schaefer or Fox model	spm
spmboot conducts a bootstrap analysis on a spm model	spmboot
spmCE - calculates the dynamics for multiple cpue time-series	spmCE
spmphaseplot - plots the phase plot of harvest rate vs biomass	spmphaseplot
spmproj calculates biomass trajectories for replicate parameters	spmproj
spmprojDet conducts forward projections from known conditions	spmprojDet
srug is the Schnute and Richards Unified Growth Curve	srug
ssq a generalized function for summing squared residuals	ssq
summspm extracts critical statistics from output of plotspmmod	summspm
tasab is a matrix of abalone maturity-at-length data	tasab
tigers is tiger prawn recruitment data from Penn & Caputi 1986	tigers
twoindex has orange roughy catches with hypothetical cpue	twoindex
uphist a histogram with an upper limit on the x-axis	uphist
vB calculates the predicted von Bertalanffy length at age	vB
which.closest find a number in a vector closest to a given value	which.closest