calcHarvest | Calculate harvest rate |
calcInitVals | Calculate initial values for MCMC. |
calculateHarvested | Calculate harvested recruits and escapement |
calculatePEandSmsy | Calculate process error and SMSY. |
centerProdCap | Center productivty and log capacity parameters |
conditionalcenterProdCap | Center productivty and log capacity parameters conditioned on... |
createBUGSdata | Create bugs data for model with or without age data. |
createPriors | Create a priors list. |
createRAVfile | Create rav file. |
DM | Shiny app to run DM and VRAP |
findOptimum | Optimization functions. |
getPostDraws | Get the simulations from a jags output list. |
info | Helper file for creating text for the reports. |
plotAgeComp | Create plots of age composition |
plotCapacity | Create plots of capacity posteriors |
plotCoefs | Create plots of covariate coefficients |
plotPriors | Create plots of priors for productivity and log capacity. |
plotProductivity | Create plots of productivity posteriors |
plotResults | Create plots from DM runs |
readData | This reads in the csv file saved from an A & P file and... |
runJAGS | Call JAGS to get the posterior draws. |
runModel | Run the DM model |
selectSR | Helper function that takes the name of SR function and... |
simplePlot | Create posterior credible interval plots from multiple DM... |
srfunctions | SR funcitons |
SSTfuncDM | Original dynamic model |
summarizeRuns | Summarize runs |
uncenterProdCap | Uncenter productivty and log capacity parameters |
writeBUGScode | write the model in BUGS language |
writeReport | Creates a report with plots. |
writeResultsToFile | Save DM output. |
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