Man pages for bbolker/McMasterPandemic
Pandemic Model
| add_conv | Add Variable by Convolution |
| add_d_log | recursively log-ify expressions |
| add_factr | Intermediate Factors |
| add_lag_diff | Add Variable by Lag Differencing |
| add_opt_params | Optimization Parameters |
| add_outflow | Add Outflows |
| add_parallel_accumulators | Add Parallel Accumulators |
| add_pow | Add Power Law |
| add_rate | Add Rate |
| add_sim_report_expr | Add Expression to the Simulation History |
| add_state_mappings | Add State Mappings |
| add_state_param_sum | Sums of States and Parameters |
| add_updated_vaxrate | compute and add vaxrates to ratemat (returns whole ratemat... |
| aggregate_agecats | Aggregate age categories into larger age categories |
| aggregate.pansim | Temporal aggregation of pansim objects |
| as.character.struc | Convert struc Object to a character vector |
| as.flexmodel | Convert between Types of Flexmodels |
| as.matrix.struc | Convert struc Object to a matrix |
| avail_for | What Variables are Available? |
| calc_conv | calculate convolution |
| calibrate | Estimate model parameters from data |
| calibrate_comb | Combined calibration of model to multiple types of data |
| calibrate_flexmodel | Calibrate Flexmodel |
| check_age_cat_compatibility | Check compatibility of user-specified age categories with age... |
| check_contact_rate_setting | Helper function to check setting-specific contact rate list... |
| col_multiply | Compute elementwise multiplication of a vector by each column... |
| compare_grads | Compare Automatic and Numerical Differentiation |
| compare_sims | Compare TMB-based and classic MacPan Simulations |
| complement | Symbolic Complement and Inverse |
| condense | condense an object |
| condense_age | collapse age/testing/etc. categories (only; don't do other... |
| condense.pansim | Condense columns (infected, ICU, hospitalized) in a pansim... |
| condense_params_vax | condense vaxified parameters to base parameters |
| condense_state | collapse (non-accumulator) states into subcategories (ages,... |
| condense_vax | collapse vaccination categories (only; don't do other... |
| const_named_vector | Constant Named Vector |
| cross_mat | Cross Two Sets of Names in Matrix Form |
| deprecated_simulation_functions | Deprecated Simulation Functions |
| describe_params | Describe parameters |
| dev_is_tikz | Is 'tikzDevice' currently in use? |
| distribute_counts | distribute counts given a desired distribution (with smart... |
| do_step | Take a single simulation time step |
| expand_contract_struc | Expand and Contract struc and struc_expanded Objects |
| expand_names | Expand Names |
| expand_params_age | Expand parameter list to include age structure |
| expand_params_desc_age | Edit parameter description attribute to include age-specific... |
| expand_params_desc_variant | Edit parameter description attribute to include... |
| expand_params_desc_vax | Edit parameter description attribute to include vax-specific... |
| expand_params_mistry | Expand parameter list to include age structure using Mistry... |
| expand_params_S0 | Expand Parameter List to Include Initial Proportion of... |
| expand_params_variant | Expand parameter list to include variant strain |
| expand_params_vax | Expand parameter list to include vaccination |
| expand_state_age | expand state vector by age classes and population... |
| expand_stateval_testing | expand states and values to include |
| expand_state_vax | expand state vector by vaccination status |
| extend_end_date | Extend End Date |
| factory_fresh_macpan_options | Factory Fresh MacPan Options |
| fix_pars | adjust pars to match targets |
| fix_stored | convert 'old' forecast args to 'new' format |
| flexmodel | Initialize Flexible Compartmental Model |
| forecast_ensemble | find confidence envelopes by simulation |
| forecast_sim | simulate/forecast a single trajectory |
| get_and_set_model_parameters | Get and Set Model Parameters |
| getData | extract and return original fitting data |
| get_doses_per_day | Compute total number of vaccine doses actually administered... |
| get_evec | get dominant eigenvector |
| get_Gbar | compute mean generation interval from parameters |
| get_GI_moments | compute moments of generation interval (mean and CV^2) |
| get_kernel_moments | compute R0, r, etc. based on kernel computation |
| get_macpan_options | Get McMasterPandemic Options |
| get_opt_pars | generate reasonable default opt_pars |
| get_r | return growth rate (from Jacobian) |
| get_R0 | calculate R0 for a given set of parameters |
| gradfun | gradient function for ODE runs |
| index_sep | Get Substrings by Indices and Separators |
| initial_population | Initial Population |
| invlink_trans | apply inverse-link functions to parameter vector or list... |
| is_1by1 | Test if 1-by-1 |
| layered_zero_state | Layered Zero State Vector |
| macpan_regex_helpers | Regular Expression Conveniences |
| make_ageified_model | Converts a classic ageified model to a flexmodel |
| make_base_model | Represent a Standard Unstructured Model as a flexmodel |
| make_beta | construct vector of transmission multipliers |
| make_betavec | construct vector of transmission multipliers |
| make_delay_kernel | construct a Gamma-distributed delay kernel |
| make_hello_world_model | Hello World |
| make_jac | construct Jacobian matrix for ICU model (not quite complete:... |
| make_omicron_model | Make an Omicron invasion model |
| make_ratemat | Create transition matrix |
| make_sir_model | SIR Model |
| make_state | retrieve parameters from a CSV file |
| make_test_wtsvec | make weights vector for tests |
| make_vaccination_model | Make a Two-Dose Vaccination Model |
| make_vaxrate | generate per capita daily vaccination rates |
| mat_rate | Specify Matrix of Rates |
| McMasterPandemic-package | 'McMasterPandemic' |
| merge_named_vec_attr | Merge Named Vector Attribute |
| merge_named_vectors | Merge One Vector into Another by Name |
| mk_agecats | Construct vector of age category labels |
| mk_contact_rate_setting | Helper function to generate a vector of setting-specific... |
| mk_mistry_Nvec | Make population distribution using Mistry et al. data |
| mk_Nvec | generate a population distribution (as a vector of counts) |
| mk_pmat | generate a contact matrix (where each row is a probability... |
| mk_vaxcats | Construct vector of vaccine category labels |
| mle_fun | negative log-likelihood function |
| nlist | self-naming list (copied from lme4:::namedList) |
| non_expanded_states | global variables for testify expansion |
| ontario_data | Sample data and fit from Ontario (up to 2020-04-18) |
| ontario_fits | Fitted models to Ontario data |
| optim_flexmodel | Wrapped Optimizers for Flexmodels |
| opt_obj | Optimizer Object |
| parse_formula | Parse a Flexmodel Formula |
| pivot | pivot an object |
| plot.pansim | plot method for simulations |
| plot.predict_pansim | plot forecasts from fits |
| plot_res_by_age | Plot age-structured simulation result faceted by age... |
| plot_res_by_state | Plot age-structured simulation result faceted by state |
| predict.fit_pansim | make forecasts from sim |
| prep_res_for_plotting | Prepare age-structured simulation results data frame for... |
| print.params_pansim | print parameters, possibly with detailed description |
| rate_summary | Rate Summary |
| read_params | read simulation parameters |
| repair_names_age | Repair ageified names |
| rep_rate | Repeat a Rate for Several Rate Matrix Elements |
| restore | convert a parameter vector back to a structured list Like... |
| rExp | run a pure-exponential sim; uses run_sim_range with a... |
| r_mode | R Mode |
| r_tmb_comparable | Compare R and TMB Engines |
| run_sim | Run pandemic simulation |
| run_sim_ageify | Ageify a basic simulation |
| run_sim_break | run simulation with one or more breakpoints |
| run_sim_loglin | run with log-linear model applied to beta |
| run_sim_mobility | run with transmission propto relative mobility |
| run_sim_range | Run simulation across a range of times |
| same_dims | Test if struc Objects have the Same Dimensions |
| set_spec_version | Set and Reset Spec Version |
| show_ratemat | visualize rate (per-capita flow) matrix |
| simulate_ensemble | Ensemble Simulation |
| simulation_history | Simulation History |
| spec_check | Spec and Feature Checks |
| spec_version | Spec Version |
| string_concatenation_operators | String Concatenation Operators |
| struc | Construct a struc Object |
| struc_block | Repeat a Block |
| struc-class | Class to Represent Scalar, Vector, or Matrix Structure |
| struc_eval | Numerically Evaluate Struc Object |
| struc_expanded | Construct a struc_expanded Object |
| struc_expanded-class | Class to Represent an Expanded Matrix Structure Object |
| struc_stretch | Stretch a Block |
| summary.params_pansim | summary method for 'pansim' parameter objects |
| testify | expand rate matrix for testing status |
| texify | Convert expression string to TeX format |
| tibble_row_to_named_vec | convert a tibble row (with all entries of the same data type)... |
| time_wrap | Time Two Expressions |
| tmb_fun | Make Objective Function with TMB |
| tmb_mode | TMB Mode |
| tmb_params | Extract Parameter Vector to Pass to a TMB Function |
| tmb_params_trans | Parameter Vectors Transformed for TMB |
| topological_sort | Topological Sort |
| trans_state_vars | Translate state variables |
| unpack | unpack a list into the current (calling) environment this is... |
| update_condense_map | Specify and Name Variables for Condensation |
| update_contact_rate_setting | Helper function to update setting-specific contact rate list |
| update_disease_free_state | Update Disease-Free State |
| update_error_dist | Update Error Distribution |
| update_foi | calculate only updated force of infection at present, this is... |
| update_initial_state | Update Initial State |
| update_linearized_params | Update Linearized Model Parameters |
| update_loss_params | Update Observation Error |
| update_observed | Update Observed Data |
| update_params | Update Default Parameters |
| update_params_mistry | Update Mistry-based parameters |
| update.params_pansim | update parameters within a list of parameters |
| update_piece_wise | Update the Piece-Wise Parameter Time-Variation Schedule |
| update_ranef_params | Update Random Effect Parameters |
| update_simulation_bounds | Update Simulation Bounds |
| update_tmb_indices | Update TMB Indices |
| v2d | Vector to Data Frame |
| vec_factr | Vectors of Intermediate Factors |
| vec_rate | Specify Vector of Rates |
| vis_model | display flow chart on current graphics device |
| write_params | write parameters to CSV file |
