| additionalEggsProcessing | Processing for egg calculations |
| addStochList | Add stochasticity to a list |
| androscogginRiverModel | Androscoggin River Model |
| annualUpstream | Annual upstream migration parameters |
| arr.B | Arrival regression parameters for bucks |
| arr.R | Arrival regression parameters for roes |
| assignFishToPU | Assign fish to routes |
| assignFishToRoutes | Assign fish to routes |
| b.parms | von Bertalanffy growth parameters for bucks |
| b.parms_merrimack | von Bertalanffy growth parameters for roes |
| CI | Calculate 95 percent confidence intervals |
| connecticutRiverModel | Connecticut River Model |
| createPUMatrix | Create production unit matrix |
| ctr_proj45 | Projected daily river temperatures (RCP4.5) in CT River, USA |
| ctr_proj85 | Projected daily river temperatures (RCP8.5) in CT River, USA |
| defineHabitat | Production potential definition |
| defineHydroSystem | Definition of hydro system |
| defineOutputVectors | Define simulation output vectors and pre-allocate memory |
| definePassageRates | Assign upstream and downstream passage efficiencies |
| downstreamMigration | Downstream migration model |
| fillOutputVectors | Fill output vectors on loop completion |
| fish | Growth data for Connecticut River American shad |
| fwFishingMort | Assign freshwater fishing mortality |
| getMaturity | Get maturity schedule |
| getMaxAge | Get maximum age |
| getPhotoperiod | Get maturity schedule |
| get_rkm1 | Get rkm1 |
| hudson_blueback | Length and mass of Hudson River American shad |
| hudson_shad | Length and mass of Hudson River American shad |
| innerLoopSampling | Stochastic sampling of annual variables |
| invlogit | Inverse logit |
| kennebecRiverModel | Kennebec River Model |
| length_weight | Length-weight regression coefficients for American shad |
| merrimackRiverModel | Merrimack River Model |
| mohawkHudsonRiverModel | Mohawk-Hudson River Model |
| nextGeneration | Project population to the next year |
| penobscotRiverModel | Penobscot River Model |
| pnr_proj45 | Projected daily river temperatures (RCP4.5) in Penobscot... |
| pnr_proj85 | Projected daily river temperatures (RCP8.5) in Penobscot... |
| populationMatrices | Define in-river population matrices |
| postSpawnMortality | Define in-river population matrices |
| processCohorts | Process numbers of fish by age, sex, PU, and migration route |
| processPopulation | Process population |
| rcp45_sst | Projected sea surface temperatures RCP 4.5 |
| rcp85_sst | Projected sea surface temperatures RCP 4.5 |
| regions | Region-system key for von Bertalanffy growth estimates |
| r.parms | von Bertalanffy growth parameters for roes |
| r.parms_merrimack | von Bertalanffy growth parameters for roes |
| sacoRiverModel | Saco River Model |
| scalePop | Scale population to speed computations |
| setScalar | Set population scalar for small rivers |
| setUpTemperatureData | Set up data for simulations |
| shadia | shadia: American shad dam passage performance standard models... |
| simDailyTemperatures | Simulate (or retrieve) daily temperatures |
| simGrowth | Simulate growth parameters |
| simMarineS | Simulate marine survival |
| simStartingPop | Create starting population |
| simTemperature | Simulate daily temperatures |
| substrRight | Substring right |
| susquehannaRiverModel | Susquehanna River Model |
| tempD | Connecticut River temperatures, Stratford, NH, USA |
| tempData | Penobscot River temperatures, Eddington, ME, USA |
| tempData_androscoggin | Androscoggin River Temperatures |
| tempData_connecticut | Connecticut River temperatures, Turner's Falls, MA, USA. |
| tempData_hudson | Hudson River Temperatures |
| tempData_kennebec | Kennebec River Temperatures |
| tempData_merrimack | South Branch Piscataqoug River near Goffstown, NH, USA |
| tempData_saco | Saco River at River Street in Bartlett, NH |
| tempData_susquehanna | Susquehanna River at Danville, PA |
| upstreamMort | Assign upstream mortality during upstream passage of dams. |
| vbgf_agg | Sex-aggregate von Bertalanffy growth parameters for American... |
| vbgf_f | Female von Bertalanffy growth parameters for American shad |
| vbgf_hudson_agg | Sex-aggregate von Bertalanffy growth parameters for blueback... |
| vbgf_hudson_f | Female von Bertalanffy growth parameters for blueback herring... |
| vbgf_hudson_m | Female von Bertalanffy growth parameters for blueback herring... |
| vbgf_kennebec_bbh_agg | Sex-aggregate von Bertalanffy growth parameters for blueback... |
| vbgf_kennebec_bbh_f | Female von Bertalanffy growth parameters for blueback herring... |
| vbgf_kennebec_bbh_m | Female von Bertalanffy growth parameters for blueback herring... |
| vbgf_m | Male von Bertalanffy growth parameters for American shad |
| writeData | Write simulation results |
