Reconstruction of Transmission Chains from Surveillance Data
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Documentation for package ‘o2geosocial’ version 1.1.2
Help Pages
| create_config | Set and check parameter settings |
| create_param | Initializes outputs for outbreaker |
| custom_likelihoods | Customise likelihood functions for o2geosocial |
| custom_moves | Customise samplers for outbreaker |
| custom_priors | Customise priors for outbreaker |
| outbreaker | outbreaker: main function for reconstructing disease outbreaks |
| outbreaker_chains | Basic methods for processing outbreaker results |
| outbreaker_data | Process input data for outbreaker |
| outbreaker_param | Initializes outputs for outbreaker |
| outbreaker_store | Initializes outputs for outbreaker |
| plot.outbreaker_chains | Basic methods for processing outbreaker results |
| pre_clustering | Pre cluster cases in groups according using the genotypes and the arbitrary thresholds gamma (spatial) and delta (temporal). |
| print.custom_likelihoods | Customise likelihood functions for o2geosocial |
| print.custom_priors | Customise priors for outbreaker |
| print.outbreaker_chains | Basic methods for processing outbreaker results |
| summary.outbreaker_chains | Basic methods for processing outbreaker results |
| toy_outbreak_long | Simulated outbreaks |
| toy_outbreak_short | Simulated outbreaks |