addnorm | addnorm - adds a normal distribution to a histogram of a data... |
altnegLL | altnegLL calculate the normal negative log-likelihood |
asmreduction | asmreduction conducts an age-structured stock reduction |
aspmLL | aspmLL negative log-likelihood for the ASPM |
aspmPENLL | aspmPENLL penalized negative log-likelihood for the ASPM |
aspmphaseplot | aspmphaseplot - plots the phase plot of harvest rate vs... |
aspmSSQ | aspmSSQ sum-of-squared residuals for the ASPM. |
bh | bh calculates the expected Beverton-Holt recruitment |
bhC | bh calculates the expected Beverton-Holt recruitment |
bootASPM | bootASPM boostraps on the results of fitting an ASPM |
bootspm | bootspm conducts a bootstrap analysis on a spm model |
calcout | calcout runs asmreduction across a vector of M values |
calcrmse | calcrmse calcuates the root mean square error for two vectors |
ccyear | ccyear plots a histogram of naa and plots log(naa) each year... |
central | central generates three estimates of central tendency |
checkdata | checkdata determines which methods match the input data |
checkspmdata | checkspmdata ensures the input data contains the necessary... |
classicCC | classicCC conducts a naive catch curve on the input data |
cMSYphaseplot | cMSYphaseplot plots the phase plot and catch and harvest rate... |
compyear | compyear plots a histogram of a variable for each year... |
countgtzero | countgtzero used in apply to count the number of zeros in a... |
datalowSA | datalowSA a set of functions to assist with data-poor... |
dataspm | dataspm Three data objects suitable for use with datalowSA. |
dataTemplate | dataTemplate - generates a standard input datafile as a... |
displayModel | displayModel plots the model fit given the parameters and... |
doconstC | doconstC calculates and plots projections under a constant... |
doDepletion | doDepletion - depletes the stock to the declared initdep... |
doproject | doproject after running the cMSY analysis the plausible... |
dynamics | dynamics describe the ASPM dynamics |
ExB | ExB calculate exploitable biomass from numbers-at-age |
ExBC | ExBC calculate exploitable biomass |
facttonum | facttonum converts a vector of numeric factors into numbers |
fillell2 | fillell2 runs the criteria of success on each SRA |
fishdat | fishdat Three data objects suitable for use with datalowSA. |
fishNAAC | fishNAAC numbers-at-age dynamics using Rcpp. |
fitASPM | fitASPM fits an age-structured production model |
fitSPM | fitSPM fits a surplus production model |
getB0 | getB0 calculates the B0 from biological properties and R0 |
getlag | getlag is used to look for the response of cpue to previous... |
getLNCI | getLNCI gets the log-normal confidence intervals |
getmaxy | getmaxy generates the upper bound for a plot |
getminy | getminy generates the lower bound for a plot |
getProduction | getProduction estimates MSY from output of ASPM |
getProductionC | getProductionC estimates MSY from output of ASPM |
getprop | getprop extract proportion of values between lim1 and lim2 |
getrmse | getrmse calculates the rmse of the input 'invar' series |
getsingle | getsingle extracts a single number from an input line of... |
gettraject | gettraject extracts the plausible biomass trajectories from... |
getvector | getvector extracts a vector of numbers from a line of... |
greplow | greplow - uses tolower in the search for the pattern |
halftable | halftable halves the height of a tall narrow data.frame |
histyear | histyear plots a histogram of a variable for each year... |
invert | invert data derived from a trawl caught invertebrate fishery. |
iscol | incol is a utility to determine is a column is present in a... |
logist | logist Logistic selectivity function |
MaA | MaA an alternative logistic function commonly used for... |
magnitude | magnitude returns the magnitude of numbers |
makebiomC | makebiomC runs the surplus production model inside catch-MSY. |
makecMSYdat | makecMSYdat generates a cMSY dataset out of other data files |
makedataset | makedataset combines year, catch, and optionally cpue into a... |
makedeplet | makedeplet converts the biomass trajectories into a depletion... |
makespmdata | makespmdata puts together correctly formatted data for SPM... |
multinomLL | multinomLL is the negative log-likelihood for multinomial... |
multLL | multLL calculates the negative log-likelihood for the... |
negLL | negLL -ve log-likelihood for normally distributed variables |
orhdat1 | orhdat1 Three data objects suitable for use with asmreduct. |
outoptim | outoptim provides a sucinct summary of the optim solution |
parsyn | parsyn types the standard syntax for the par command to the... |
penalty0 | penalty0 enables the adding of a large penalty as one... |
penalty1 | penalty1 enables the adding of a large penalty as one... |
plaice | plaice data derived from Beverton and Holt, 1957 for European... |
plot1 | plot1 a simple way to plot an xy line plot |
plotASPM | plotASPM plots catch, CPUE, Spawning Biomass and Harvest Rate |
plotceASPM | plotceASPM plots just the fit of the ASPM model to the CPUE... |
plotcMSY6 | plotcMSY6 plots out a summary of the Catch-MSY results in 6... |
plotconstC | plotconstC summarizes constant catch projections in catch-MSY |
plotdepletion | plotdepletion |
plotfish | plotfish plots the catch and optionally the cpue from fish |
plotfishery | plotfishery plots the catch and optionally the cpue from fish |
plotlag | plotlag plots the effect of a lag between two variables |
plotout | plotout |
plotprep | plotprep: sets up a window and the par values for a single... |
plotreduction | plotreduction generates a summary plot of a stock reduction |
plot.spmdat | plot.spmdat S3 method that plots an spmdat data set |
plottrajectory | plottrajectory literally plots predicted trajectories |
popN | popN calculates the proportional catch at age for catch... |
prodASPM | prodASPM summarizes ASPM statistics and plots the... |
projstats | projstats |
pulloutStats | pulloutStats summaries results from the Catch-MSY analysis |
quants | quants used in apply to estimate quantiles across a vector |
readdata | readdata reads in a standard format data file |
removeEmpty | removeEmpty removes empty strings from a vector of strings |
robustASPM | robustASPM conducts a robustness test on the quality of fit... |
robustSPM | robustSPM conducts a robustness test on the quality of fit of... |
run_cMSY | run_cMSY - sets up and runs the catch-MSY simulations |
selectCC | selectCC conducts a selectivity enhanced catch curve analysis |
simpfox | simpfox simply calculates the predicted CE for an SPM;... |
simpspm | simpspm simply calculates the predicted CE for an SPM |
SpB | SpB - calculate spawning biomass from a vector of... |
SpBC | SpBC calculate spawning biomass from a vector of... |
spm | spm - calcuates the dynamics using a Schaefer or Fox model |
spmMult | spmMult - calculates the dynamics using a Schaefer or Fox... |
spmphaseplot | spmphaseplot - plots the phase plot of harvest rate vs... |
sraMSY | sraMSY sets up the input parameters and data for oneSRA |
ssq | ssq a generalized function for summing squared residuals |
summarycMSY | summarycMSY makes tables of msy,r,K,meanr,meanK,and all picks |
summary.reduction | summary.reduction S3 summary method for a reduction object |
summspm | summspm extracts critical statistics from output of... |
toXL | toXL copies a data.frame or matrix to the clipboard |
trendMSY | trendMSY calculates the mean MSY per K class |
unfished | unfished generates the numbers at age for an unfished... |
vB | vB calculates the predicted von Bertalanffy length at age |
which.closest | which.closest find the number closest to a given value |
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