Man pages for jameshay218/mcmcJH
Generic random walk MCMC algorithm for parameter inference
| condense.data | Condenses a table of data to provide mean and standard... |
| condense.data.simple | Condenses data from the same times points into mean values |
| create_polygons | Polygon for prediction intervals |
| fromUnitScale1 | fromUnitScale |
| generate_prediction_intervals_1.1 | Prediction interval generating function |
| generate_prediction_intervals_1.2 | Second tier function for generating prediction intervals from... |
| generate_prior_data | Generates data for prior density plots |
| likelihood_norm | Normally distributed errors likelihood function |
| likelihood_observation | Observation error only function |
| likelihood_poisson | Poisson distributed errors likelihood function |
| load_param_table | Parameter table loading function |
| logistic | Logistic function |
| logit | Logit function |
| mcmc_all_plots_multi | Plot all MCMC density and iteration plots |
| mcmc_all_plots_single | Plot all MCMC density and iteration plots with a single chain |
| mcmc_density_multi | Individual MCMC density plots with multiple chains |
| mcmc_density_single | Individual MCMC density plots for a single chain |
| mcmc_diagnostics | MCMC diagnostic tests |
| MCMC_fit_1.1 | First level wrapper function for the MCMC algorithm. |
| MCMC_fit_1.2 | Second level wrapper for the MCMC fitting procedure. HIGHEST,... |
| MCMC_fit_single | Bottom level MCMC wrapper function |
| mcmc_iter_multi | Individual MCMC iteration plots with multiple chains |
| mcmc_iter_single | Individual MCMC iter plots for a single chain |
| MCMC_main | Main MCMC wrapper function |
| mcmc_param_check | MCMC parameter table check |
| optifix | Fixed parameter optimisation |
| pad_lists | Pads lists of different sizes |
| param_check | Model parameter table check |
| plot_model_fits | Model plotting function |
| posterior1 | Posterior function |
| predict.titre.fast | Basic ferret model function |
| predict.titre.fast.bounded | Ferret model function with lower bounded titres |
| predict.titre.OLD | Old titre prediction function |
| predict_titre_universal_m | Ferret model function with a universal waning parameter, m |
| predict_titre_universal_m_2 | Ferret model function with lower bounded titres and a... |
| prior | Calculates and sums priors for posterior |
| prior_wrapper | Prior wrapper function |
| proposalfunction1 | MCMC proposal function |
| rand.params | Random parameter generator |
| remove_zero_data | Remove zero value groups |
| restrain_bounds | Restrains values in a data frame by the given bounds |
| run_metropolis_MCMC | Adaptive Metropolis-within-Gibbs Random Walk Algorithm. |
| scaletuning1 | Scale step sizes |
| titre_model | ODE for ferret model |
| toUnitScale1 | toUnitScale |
| transform_logistic | Custom logistic transformation |
| transform_logit | Custom logit transform |
| transform_params_logistic | Parameter logistic/exp transform function |
| transform_params_logisticOLD | OLD transform parameters to logistic |
| transform_params_logit | Parameter logit/log transform function |
| transform_params_logitOLD | OLD transform parameters to logit |
