Man pages for cttedwards/bdm
Bayesian biomass dynamics model
| as.bdm | Convert a 'stanfit' object into a 'bdm' object |
| as.kobe | Convert a 'bdm' object to a format suitable for the 'kobe'... |
| bdm-class | Class definition for 'bdm' object |
| bdmData-class | Class containing input data for model run |
| compiler | Compile stan model code in 'bdm' object |
| cumsumplot | Plot cumulative sum of MCMC chain |
| dynplot | Plot estimated dynamics from 'bdm' model fit |
| getcpp | Return C++ code generated by 'rstan' |
| getlogK | Extract an initial value for the carrying capacity |
| getparams | Return model parameters (including input data) |
| getr | Extract log-normal parameters for the prior on intrinsic... |
| getx | Estimate an initial vector of depletion values |
| ggtheme | Theme for dignostic plotting using 'ggplot2' |
| histplot | Plot posterior histograms |
| idxplot | Plot the 'bdm' model fit |
| optimr | Fit 'bdm' model using maxium penalised density |
| plot.bdmData | Plot index and harvest data |
| postplot | Plot posterior updates from 'bdm' model fit |
| project | Projection function |
| sampler | Fit 'bdm' model |
| shape | Access or assign shape of the production function |
| sigmao | Access or assign the observation error |
| sigmap | Access or assign the process error |
| status | Extract status and reference point estimates |
| traceplot-bdm-method | Traceplot for MCMC output |
| updatePrior | Update priors in 'bdm' model |
