Man pages for mrc-ide/squire
SEIR transmission model of COVID-19
| adjusted_eigen | Compute age-adjusted eigenvalue for mixing matrix |
| align | Align deaths |
| beta_est | Estimate beta for a squire model using model parameters |
| beta_est_explicit | Estimate beta parameter for explicit model |
| beta_est_simple | Estimate beta parameter |
| calibrate | Calibrate via particle filter grid search using time series... |
| check_squire | Check object is an squire_simulation |
| check_time_change | Check time change inputs are correct |
| compare_output | Compare model to death data |
| conduct_replicate | Handles simulating replicates within 'projections' |
| contact_matrices | Contact matrices |
| country_specific_healthcare_capacity | Country specific healthcare capacity |
| create_master_chain | create a master chain from a pmcmc_list object |
| default_durations | Return the default hospital durations for modelling |
| default_probs | Return the default probabilities for modelling |
| deterministic_model | Simple SEEIR model creation. We will use this structure to... |
| div_pop | Divide matrix by population |
| drjacoby_mcmc | Run an MCMC Sampler using drjacoby |
| elderly_pop | Elderly Population |
| explicit_model | Explicit SEEIR model creation. We will use this structure to... |
| extract_deaths | Extract deaths from model output |
| extract_hospital_occ | Extract hospital bed occupancy from model output |
| extract_ICU_occ | Extract ICU bed occupancy from model output |
| extract_infection_incidence | Extract infection incidence from model output |
| format_deterministic_output | Format deterministic model output as data.frame |
| format_output | Format model output as data.frame |
| format_output_simple_model | Format model output from simple as data.frame |
| get_elderly_population | Get elderly population data (5 year age-breakdown for 80-84,... |
| get_healthcare_capacity | Get healthcare capacity data |
| get_lmic_countries | Get supported LMIC countries |
| get_mixing_matrix | Get mixing matrix |
| get_population | Get population data |
| income_group | Income group |
| income_strata_healthcare_capacity | Income strata healthcare capacity |
| init_check | Check and set up initial values |
| init_check_explicit | Check and set up initial values for explicit model |
| intervention_dates_for_odin | Prepare intervention timing for odin |
| jc_prop_update | update_sigma |
| matrix_check | Check dimensions of inputs |
| matrix_set | Process set of contact matrices -> mixing matrices |
| parameters_explicit_SEEIR | Parmaters for explicit SEEIR model |
| parameters_simple_SEEIR | Parmeters for the simple SEEIR model |
| parse_country_severity | Parse country severity parameters |
| particle_filter | Run a particle filter |
| particle_filter_data | Prepare particle filter data |
| plot.squire_scan | squire scan plot |
| plot.squire_simulation | squire simulation plot |
| pmcmc | Run a Particle MCMC Sampler within the Squire Framework |
| population | Population |
| pos_num | Check argument is a single positive numeric |
| print.squire_simulation | squire simulation print |
| process_contact_matrix | Process a contact matrix |
| process_contact_matrix_scaled_age | Process a contact matrix with an extra |
| projection_plotting | Plot projections against each other |
| projections | Provide projections from calibrated simulations by changing... |
| run_deterministic_comparison | Run Deterministic model comparison |
| run_deterministic_SEIR_model | Run the deterministic explicit SEIR model |
| run_explicit_SEEIR_model | Run the explicit SEEIR model |
| run_particle_filter | Run particle filter |
| run_simple_SEEIR_model | Run the SEEIR model |
| sample_3d_grid_scan | Sample Grid Scan |
| sample_drjacoby | Sample from a drjacoby mcmc |
| sample_grid_scan | Sample Grid Scan |
| sample_pmcmc | Sample PMCMC |
| scan_R0_date | Grid search of R0 and start date |
| scan_R0_date_Meff | Grid search of R0 and start date |
| simple_model | Simple SEEIR model creation. We will use this structure to... |
| summary.squire_simulation | squire simulation summary |
| trigger_projections | Project lockdowns based on triggering |
