| 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 |
