Man pages for MJomaba/flu-evidence-synthesis
Flu Evidence Synthesis: Analysing Effectiveness of Vaccine Strategies
| adaptive.mcmc | Adaptive MCMC algorithm |
| adaptive.mcmc.cpp | Adaptive MCMC algorithm implemented in C++ |
| age_group_levels | Create age group level description based on passed upper... |
| age_group_limits | Extract upper age group limits from age group level... |
| age_group_mapping | Calculate a mapping from one sets of age groups to another... |
| age_sizes | Number of people of each age for the UK in 1999 |
| aggregateModel | Aggregate model results at different time points |
| as_age_group | Age as age group |
| as.age.group | Age as age group |
| as_R0 | Calculate R0 from transmission rate |
| as_transmission_rate | Calculate transmission rate from R0 |
| as_vaccination_calendar | Create a vaccination calendar object |
| as.vaccination.calendar | Create a vaccination calendar object |
| confirmed.samples | Number of confirmed positive samples per week |
| contact_matrix | Create a contact matrix based on polymod data. |
| contact.matrix | Create a contact matrix based on polymod data. |
| coverage | Data on vaccine coverage during the 2007-08 season |
| credible.interval.model | Calculate the (equal tailed) credible interval at different... |
| demography | Demography of the UK in 1999 |
| dmultinom.cpp | Probability density function for multinomial distribution |
| getTimeFromWeekYear | Convert given week in given year into an exact date... |
| ili | Number of Influenza-like illness cases per week |
| infectionODEs | Run the SEIR model for the given parameters |
| infectionODEs.cpp | Run the SEIR model for the given parameters |
| inference | MCMC based inference of the parameter values given the... |
| inference.results | MCMC Result produced by the inference function |
| log_likelihood_cases | Returns log likelihood of the predicted number of cases given... |
| mcmcsample | DEPRECATED: MCMC Result produced by the inference function |
| parameter_mapping | Mapping parameters to the model |
| polymod_uk | Polymod contact data for the UK |
| public_health_outcome | Calculate the number of public health relevant cases (e.g.... |
| read.legacy.vaccine.file | Function to read legacy file format for vaccine calendar |
| risk_group_mapping | Calculate a mapping from one sets of risk groups to another... |
| separate.into.age.groups | Separate the population into age groups |
| separate.into.risk.groups | Separate the population into risk groups |
| stat_ci | Draw credibility intervals |
| StatCI | Stat object for drawing credible intervals |
| stratify_by_age | Stratify the population by age |
| stratify_by_risk | Stratify age groups into different risk groups |
| uptake | Data on the uptake rates of vaccination in the UK |
| vaccination_scenario | Calculate number of influenza cases given a vaccination... |
| vaccinationScenario | Calculate number of influenza cases given a vaccination... |
| vaccine_calendar | Vaccination uptake rate for the UK in 1999 |
| vaccine.calendar | Function to create a vaccine calendar object |
| vaccine_doses | Calculate number of vaccine doses needed based on vaccine... |
