Man pages for JMacDonaldPhD/Epidemics
Inference For Epidemics (one line, title case)
| adaptiveSIRfsMCMC7_blockedIS | Calculate the amount of blockSamples which need to be made To... |
| adaptiveSIR_PseudoMarginalMCMC | Adaptive Pseudo-Marginal MCMC for SIR Epidemic Panel Data |
| adaptiveSISfsMCMC | Adaptive fsMCMC MCMC for SIS Epidemic Panel Data |
| adaptiveSISfsMCMC7_blockedIS | Calculate the amount of blockSamples which need to be made To... |
| adaptiveSIS_PseudoMarginalMCMC | Adaptive Pseudo-Marginal MCMC for SIS Epidemic Panel Data |
| Contact_Kernel | Contact_Kernel Given a matrix containing information on... |
| dHyperGeom | dHyperGeom function |
| Epidemic_fsMCMC | Endemic (SIS) fsMCMC |
| epidemicImportanceSampler | Importance Sampling with known epidemic parameters Epidemic... |
| epidemic_loglikelihood | Computes the full epidemic likelihood |
| fsMCMC_SIS | Create Storage Matrix Proposal Acceptance Counter Propose new... |
| General_Epidemic_Process | The parameters and the rate structure together will determine... |
| heterogeneousSIR_Gillespie | Possible states and their respective logical representations.... |
| Homogeneous_Kernel | Kernels |
| homogeneousPanelDataSIR_Gillespie | |
| homogeneousPanelDataSIR_GillespieEU | Possible states and their respective logical representations. |
| homogeneousPanelDataSIS_Gillespie | ==== SIS Gillespie with Panel Data Output ==== Possible... |
| homogeneousPanelDataSIS_GillespieEU | ==== Non-Centered SIS Gillespie with Panel Data Output ====... |
| homogeneousSIR_Gillespie | SIR Gillespie *NEW* Split into seperate cases State is (X, Y,... |
| Homo_HighPop_HighR0 | Simulated Epidemic Dataset |
| Homo_HighPop_LowR0 | Simulated Epidemic Dataset |
| Homo_HighPop_MedR0 | Simulated Epidemic Dataset |
| Homo_LowPop_HighR0 | Simulated Epidemic Dataset |
| Homo_LowPop_LowR0 | DATA |
| Homo_LowPop_MedR0 | Simulated Epidemic Dataset |
| Homo_MedPop_HighR0 | Simulated Epidemic Dataset |
| Homo_MedPop_LowR0 | Simulated Epidemic Dataset |
| Homo_MedPop_MedR0 | Simulated Epidemic Dataset |
| individualHomogeneousSIR_Gillespie | Incorporate the ideas of the event matrix and a matrix of... |
| individualHomogeneousSIS_Gillespie | Possible states and their respective logical representations.... |
| Infectious_Disease_Gillespie | Infectious_Disease_Gillespie function |
| inf_time_proposal | PhD A Gibbs Sampler for a partially observed SIR epidemic. |
| interval_intersect | Relies on the period of time for which individual j exerts... |
| IP_t | fsMCMC for Epidemic Panel Data |
| log_likelihood_rem | Computes the Removal portion of an epidemic likelihood |
| MCMCplots | Functions for MCMC Output |
| NonCentered_MCMC | MCMC Sampler for a non-centered Bayesian Parameterisation of... |
| oneParticlePM_SIS | Create Storage Matrix Proposal Acceptance Counter Propose new... |
| oneParticlePM_SIS_beta | Create Storage Matrix Proposal Acceptance Counter Propose new... |
| panel_data_new.epidemics | Temporary Panel Data Generator |
| panelDataSIR_Gillespie | Possible states and their respective logical representations.... |
| pi_Y_given_X | Psuedo-Marginal MCMC For Inference on Epidemic Data |
| plot.epidemic | Function for plotting the evolution of epidemic |
| PM_MCMCexperiment | PM-MCMC Panel Experiment Sample Panel Data |
| PNC.Algorithm | PhD Partially Non-Centered Sampling Algorithm for Epidemics |
| possible_transitions | possible_transitions function |
| prod_part_inf | Infection component of Heterogeneous Likelihood Functions... |
| Pseudo_Marginal_MCMC | Variable List to Pass to Cores Intialise Missing Data by... |
| rates | General Epidemic Process |
| relevant_rates | Seems like drawing the time to next event and which event... |
| RWMSampler | (Multiplicative) Random-Walk Metropolis for Heterogeneous SIR... |
| SIR_fsMCMC_blockedIS | fsMCMC MCMC for SIR Epidemic Panel Data (with blocked... |
| SIRfsMCMCexperiment1 | Testing New blocked Independent Sampler fsMCMC for SIR (+... |
| SIR_Gillespie | SIR_Gillespie function |
| SIR_PM_MCMCexperiment1 | SIR Test Epidemic 1 PM-MCMC Experiment Test data |
| SIR_PseudoMarginalMCMC | SIR PM-MCMC Create Storage Matrix Proposal Acceptance Counter... |
| SIS_fsMCMC | Create Storage Matrix Proposal Acceptance Counter Folded... |
| SIS_fsMCMC_beta | Create Storage Matrix Proposal Acceptance Counter Folded... |
| SIS_fsMCMC_blockedIS | Calculate the amount of blockSamples which need to be made To... |
| SISfsMCMCexperiment | Variance of beta, gamma for varying number of panels. |
| SIS_fsMCMC_oneProposal | Create Storage Matrix Proposal Acceptance Counter Folded... |
| SIS_Gillespie | SIS_Gillespie function |
| SIS_PseudoMarginalMCMC | New Pseudo-Marginal SIS Create Storage Matrix Proposal... |
| SIS_y_soln | SIS Functions |
| start_state | Transition Panel Data for a General Epidemic Event Table |
| state | State Function |
| state_table | state_table function |
| time_to_next_event | time_to_next_event Draws the time to next event in the... |
| transitionData | Function which transforms panel data into Transition Data |
| which_event | which_event Decides which event will occur next in the... |
