Man pages for haddonm/datalowSA
A Package to Faciliate Application of Data poor Stock Assessments

addnormaddnorm - adds a normal distribution to a histogram of a data...
altnegLLaltnegLL calculate the normal negative log-likelihood
asmreductionasmreduction conducts an age-structured stock reduction
aspmLLaspmLL negative log-likelihood for the ASPM
aspmPENLLaspmPENLL penalized negative log-likelihood for the ASPM
aspmphaseplotaspmphaseplot - plots the phase plot of harvest rate vs...
aspmSSQaspmSSQ sum-of-squared residuals for the ASPM.
bhbh calculates the expected Beverton-Holt recruitment
bhCbh calculates the expected Beverton-Holt recruitment
bootASPMbootASPM boostraps on the results of fitting an ASPM
bootspmbootspm conducts a bootstrap analysis on a spm model
calcoutcalcout runs asmreduction across a vector of M values
calcrmsecalcrmse calcuates the root mean square error for two vectors
ccyearccyear plots a histogram of naa and plots log(naa) each year...
centralcentral generates three estimates of central tendency
checkdatacheckdata determines which methods match the input data
checkspmdatacheckspmdata ensures the input data contains the necessary...
classicCCclassicCC conducts a naive catch curve on the input data
cMSYphaseplotcMSYphaseplot plots the phase plot and catch and harvest rate...
compyearcompyear plots a histogram of a variable for each year...
countgtzerocountgtzero used in apply to count the number of zeros in a...
datalowSAdatalowSA a set of functions to assist with data-poor...
dataspmdataspm Three data objects suitable for use with datalowSA.
dataTemplatedataTemplate - generates a standard input datafile as a...
displayModeldisplayModel plots the model fit given the parameters and...
doconstCdoconstC calculates and plots projections under a constant...
doDepletiondoDepletion - depletes the stock to the declared initdep...
doprojectdoproject after running the cMSY analysis the plausible...
dynamicsdynamics describe the ASPM dynamics
ExBExB calculate exploitable biomass from numbers-at-age
ExBCExBC calculate exploitable biomass
facttonumfacttonum converts a vector of numeric factors into numbers
fillell2fillell2 runs the criteria of success on each SRA
fishdatfishdat Three data objects suitable for use with datalowSA.
fishNAACfishNAAC numbers-at-age dynamics using Rcpp.
fitASPMfitASPM fits an age-structured production model
fitSPMfitSPM fits a surplus production model
getB0getB0 calculates the B0 from biological properties and R0
getlaggetlag is used to look for the response of cpue to previous...
getLNCIgetLNCI gets the log-normal confidence intervals
getmaxygetmaxy generates the upper bound for a plot
getminygetminy generates the lower bound for a plot
getProductiongetProduction estimates MSY from output of ASPM
getProductionCgetProductionC estimates MSY from output of ASPM
getpropgetprop extract proportion of values between lim1 and lim2
getrmsegetrmse calculates the rmse of the input 'invar' series
getsinglegetsingle extracts a single number from an input line of...
gettrajectgettraject extracts the plausible biomass trajectories from...
getvectorgetvector extracts a vector of numbers from a line of...
greplowgreplow - uses tolower in the search for the pattern
halftablehalftable halves the height of a tall narrow data.frame
histyearhistyear plots a histogram of a variable for each year...
invertinvert data derived from a trawl caught invertebrate fishery.
iscolincol is a utility to determine is a column is present in a...
logistlogist Logistic selectivity function
MaAMaA an alternative logistic function commonly used for...
magnitudemagnitude returns the magnitude of numbers
makebiomCmakebiomC runs the surplus production model inside catch-MSY.
makecMSYdatmakecMSYdat generates a cMSY dataset out of other data files
makedatasetmakedataset combines year, catch, and optionally cpue into a...
makedepletmakedeplet converts the biomass trajectories into a depletion...
makespmdatamakespmdata puts together correctly formatted data for SPM...
multinomLLmultinomLL is the negative log-likelihood for multinomial...
multLLmultLL calculates the negative log-likelihood for the...
negLLnegLL -ve log-likelihood for normally distributed variables
orhdat1orhdat1 Three data objects suitable for use with asmreduct.
outoptimoutoptim provides a sucinct summary of the optim solution
parsynparsyn types the standard syntax for the par command to the...
penalty0penalty0 enables the adding of a large penalty as one...
penalty1penalty1 enables the adding of a large penalty as one...
plaiceplaice data derived from Beverton and Holt, 1957 for European...
plot1plot1 a simple way to plot an xy line plot
plotASPMplotASPM plots catch, CPUE, Spawning Biomass and Harvest Rate
plotceASPMplotceASPM plots just the fit of the ASPM model to the CPUE...
plotcMSY6plotcMSY6 plots out a summary of the Catch-MSY results in 6...
plotconstCplotconstC summarizes constant catch projections in catch-MSY
plotdepletionplotdepletion
plotfishplotfish plots the catch and optionally the cpue from fish
plotfisheryplotfishery plots the catch and optionally the cpue from fish
plotlagplotlag plots the effect of a lag between two variables
plotoutplotout
plotprepplotprep: sets up a window and the par values for a single...
plotreductionplotreduction generates a summary plot of a stock reduction
plot.spmdatplot.spmdat S3 method that plots an spmdat data set
plottrajectoryplottrajectory literally plots predicted trajectories
popNpopN calculates the proportional catch at age for catch...
prodASPMprodASPM summarizes ASPM statistics and plots the...
projstatsprojstats
pulloutStatspulloutStats summaries results from the Catch-MSY analysis
quantsquants used in apply to estimate quantiles across a vector
readdatareaddata reads in a standard format data file
removeEmptyremoveEmpty removes empty strings from a vector of strings
robustASPMrobustASPM conducts a robustness test on the quality of fit...
robustSPMrobustSPM conducts a robustness test on the quality of fit of...
run_cMSYrun_cMSY - sets up and runs the catch-MSY simulations
selectCCselectCC conducts a selectivity enhanced catch curve analysis
simpfoxsimpfox simply calculates the predicted CE for an SPM;...
simpspmsimpspm simply calculates the predicted CE for an SPM
SpBSpB - calculate spawning biomass from a vector of...
SpBCSpBC calculate spawning biomass from a vector of...
spmspm - calcuates the dynamics using a Schaefer or Fox model
spmMultspmMult - calculates the dynamics using a Schaefer or Fox...
spmphaseplotspmphaseplot - plots the phase plot of harvest rate vs...
sraMSYsraMSY sets up the input parameters and data for oneSRA
ssqssq a generalized function for summing squared residuals
summarycMSYsummarycMSY makes tables of msy,r,K,meanr,meanK,and all picks
summary.reductionsummary.reduction S3 summary method for a reduction object
summspmsummspm extracts critical statistics from output of...
toXLtoXL copies a data.frame or matrix to the clipboard
trendMSYtrendMSY calculates the mean MSY per K class
unfishedunfished generates the numbers at age for an unfished...
vBvB calculates the predicted von Bertalanffy length at age
which.closestwhich.closest find the number closest to a given value
haddonm/datalowSA documentation built on Aug. 21, 2019, 1:39 p.m.