Man pages for eeholmes/DM
Dynamic Model
| 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. |
