MQMF0.1.5 package

addcontours simplifies adding contours to an xy plot of points

addlnorm estimates a log-normal distribution from output of hist

addnorm adds a normal distribution to a histogram of a data set.

aicbic returns the AIC and BIC for a given model

altnegLL calculate the Normal negative log-likelihood

bce Baranov catch equation

bh represents one version of Beverton-Holt recruitment

bracket bounds a value on the x-axis and y-axis

calcprior return the sum of a vector of constant values as priors

chapter2 The 15 R-code chunks from A Non-Introduction to R

chapter3 The 27 R-code chunks from Simple Population Models

chapter4 The 47 R-code chunks from Model Parameter Estimation

chapter5 The 23 R-code chunks from Static Models

chapter6 The 53 R-code chunks from On Uncertainty

chapter7 The 67 R-code chunks from Surplus Production Models

countgtone used in apply to count the number > 1 in a vector

countgtzero used in apply to count numbers > zero in a vector

countNAs used in apply to count the number of NAs in a vector

countones used in apply to count the number of ones in a vector

countzeros used in apply to count the number of zeros in a vector

discretelogistic example and figure 3.2 Discrete logistic model

do_MCMC conducts an MCMC using Gibbs within Metropolis

domed calculates domed selectivity curves

fabens calculates predicted growth increment for tagging data

facttonum converts a vector of numeric factors into numbers

fitSPM fits a surplus production model

freqMean calculates the mean and stdev of count data

getlag is used to look for the response of cpue to previous catches

getmax can be used to define the upper bound for a plot

getmin can be used to define the lower bound for a plot

getMSY calculates the MSY for the Polacheck et al 1993 equation

getname returns the name of a variable as character

getrmse calculates the rmse of the input 'invar' series

getseed generates a random number seed

getsingle extracts one number from an input line of characters

gettime calculates time in seconds passed each day

getvector extracts a vector of numbers from a line of characters

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

Gz calculates predicted Gompertz length-at-age growth curve

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

inthist a replacement for the hist function for use with integers

invl calculates growth increments for the inverse logistic

incol is a utility to determine if a column is present in a matrix

likeratio conducts a likelihood ratio test

linter finds a value in a series using its location in another

logist Logistic selectivity function

magnitude returns the magnitude of numbers in base 10

makelabel generates a label from text and values

mature alternative logistic function commonly used for maturity

mm calculates the predicted Michaelis-Menton length-at-age

mnnegLL generic multinomial negative log-likelihoods

MQMF functions for Using R for Modelling and Quantitative Methods in F...

negLL calculate log-normal log-likelihoods

negLL1 calculate log-normal log-likelihoods with a penalty

negLLM -ve log-normal likelihoods for multiple index time-series

negLLP -ve log-likelihood for normally distributed variables

negNLL -ve log-likelihood for normally distributed variables

negnormL an alternative -log-likelihood for normal errors

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

panel.cor is a version of a function given in the help for pairs

parasympt generates N vectors from a multi-variate normal

parset alters the current base graphics par settings

parsyn types the standard par command syntax to the console

penalty0 enables the adding of a large penalty as one approaches 0.0

penalty1 adds an increasingly large penalty as a value approaches 1.0

plot.dynpop an S3 method for plotting dynpop objects

plot1 a quick way to plot an xy line or point plot

plotfishM plots the catch and optionally the cpue

plotlag plots the effect of a lag between two variables

plotprep sets up a window and the par values for plotting

plotprofile simplifies plotting single likelihood profiles

plotproj generate a plot of a matrix of biomass projections

plotspmdat plots the fish data containing catches and cpue

plotspmmod plots an spm model fit given parameters and data

predfreq is used for modal analysis of count data

printV returns a vector cbinded to 1:length(invect)

properties - used to examine the properties of a data.frame

quants used in apply to estimate quantiles across a vector

removeEmpty removes empty strings from a vector of strings

ricker one version of the Ricker stock recruitment

robustSPM does a robustness test on quality of fit of an SPM

setpalette is a shortcut for altering the palette to R4

simpspm calculates only the predicted log(CE) for an SPM

simpspmM calculates predicted CE when multiple indices are present

spm calculates the dynamics of a Schaefer or Fox model

spmboot conducts a bootstrap analysis on a spm model

spmCE - calculates the dynamics for multiple cpue time-series

spmphaseplot - plots the phase plot of harvest rate vs biomass

spmproj calculates biomass trajectories for replicate parameters

spmprojDet conducts forward projections from known conditions

srug is the Schnute and Richards Unified Growth Curve

ssq a generalized function for summing squared residuals

summspm extracts critical statistics from output of plotspmmod

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

vB calculates the predicted von Bertalanffy length at age

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