Function reference • McMasterPandemic

All functions
`McMasterPandemic-package`	McMasterPandemic
`add_conv()`	Add Variable by Convolution
`add_factr()`	Intermediate Factors
`add_lag_diff()` `add_lag_diff_uneven()`	Add Variable by Lag Differencing
`add_opt_params()` `update_opt_params()` `initialize_opt_params()` `initialize_opt_tv_params()` `update_opt_tv_params()` `add_opt_tv_params()`	Optimization Parameters
`add_linearized_outflow()` `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 because the update part is non-trivial)
`aggregate(<pansim>)`	Temporal aggregation of pansim objects
`aggregate_agecats()`	Aggregate age categories into larger age categories
`as.character(<struc>)`	Convert struc Object to a character vector
`as.flexmodel()` `as.flexmodel_to_calibrate()` `as.flexmodel_obs_error()` `as.flexmodel_one_step()`	Convert between Types of Flexmodels
`as.matrix(<struc>)`	Convert struc Object to a matrix
`avail_for_rate()` `avail_for_sum()` `avail_for_factr()` `avail_for_pow()` `avail_for_expr()` `avail_for_conv()` `avail_for_lag()`	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 categories in Mistry data
`check_contact_rate_setting()`	Helper function to check setting-specific contact rate list initialization
`col_multiply()`	Compute elementwise multiplication of a vector by each column in a matrix This is implemented for performance reasons, as it is much faster than sweep.
`compare_grads()` `compare_hessians()`	Compare Automatic and Numerical Differentiation
`compare_sims()` `compare_sims_cbind()` `compare_sims_plot()` `compare_sims_diffmat()` `compare_sims_unlist()`	Compare TMB-based and classic MacPan Simulations
`complement()` `inverse()`	Symbolic Complement and Inverse
`condense()`	condense an object
`condense(<pansim>)`	Condense columns (infected, ICU, hospitalized) in a pansim output
`condense_age()`	collapse age/testing/etc. categories (only; don't do other condensation)
`condense_params_vax()`	condense vaxified parameters to base parameters
`condense_state()`	collapse (non-accumulator) states into subcategories (ages, vax status)
`condense_vax()`	collapse vaccination categories (only; don't do other condensation)
`const_named_vector()`	Constant Named Vector
`cross_mat()`	Cross Two Sets of Names in Matrix Form
`changing_ratemat_elements()` `simulate_changing_ratemat_elements()` `concatenated_state_vector()` `simulate_state_vector()` `initial_state_vector()` `final_state_vector()` `penultimate_state_vector()` `final_state_ratio()` `initial_ratemat()` `simulation_condensed()` `condense_flexmodel()` `simulate(<flexmodel>)` `simulation_fitted()`	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 rounding)
`do_step()`	Take a single simulation time step
`expand_struc()`	Expand and Contract struc and struc_expanded Objects
`expand_names()`	Expand Names
`expand_params_S0()`	Expand Parameter List to Include Initial Proportion of Susceptibles
`expand_params_age()`	Expand parameter list to include age structure
`expand_params_desc_age()`	Edit parameter description attribute to include age-specific definitions (helper function for `expand_params_age()`)
`expand_params_desc_variant()`	Edit parameter description attribute to include variant-specific definitions (helper function for `expand_params_variant()`)
`expand_params_desc_vax()`	Edit parameter description attribute to include vax-specific definitions (helper function for `expand_params_vax()`)
`expand_params_mistry()`	Expand parameter list to include age structure using Mistry et al. data
`expand_params_variant()`	Expand parameter list to include variant strain
`expand_params_vax()`	Expand parameter list to include vaccination
`expand_state_age()` `ageify()`	expand state vector by age classes and population distribution
`expand_state_vax()`	expand state vector by vaccination status
`expand_stateval_testing()`	expand states and values to include
`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()` `init_model()`	Initialize Flexible Compartmental Model
`forecast_ensemble()`	find confidence envelopes by simulation
`forecast_sim()`	simulate/forecast a single trajectory
`getData()`	extract and return original fitting data
`get_GI_moments()`	compute moments of generation interval (mean and CV^2)
`get_Gbar()`	compute mean generation interval from parameters
`get_R0()`	calculate R0 for a given set of parameters
`pars_base_sim()` `pars_base_init()` `pars_base_opt()` `pars_time_sim()` `pars_time_spec()` `pars_time_opt()` `pars_time_series()` `pars_infer_init()` `pars_infer_opt()` `pars_infer_conf()` `pars_base_sim<-`()	Get and Set Model Parameters
`get_doses_per_day()`	Compute total number of vaccine doses actually administered per day in a simulation
`get_evec()`	get dominant eigenvector
`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)
`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 based on names
`is_1by1()`	Test if 1-by-1
`layered_zero_state()`	Layered Zero State Vector
`alt_group()` `wrap_exact()` `all_in()` `any_var()` `all_except()`	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: doesn't include flows to R)
`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_test_posvec()`	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
`merge_named_vec_attr()`	Merge Named Vector Attribute
`merge_named_vectors()`	Merge One Vector into Another by Name
`mk_Nvec()`	generate a population distribution (as a vector of counts)
`mk_agecats()`	Construct vector of age category labels
`mk_contact_rate_setting()`	Helper function to generate a vector of setting-specific contact rates
`mk_mistry_Nvec()`	Make population distribution using Mistry et al. data
`mk_pmat()`	generate a contact matrix (where each row is a probability distribution)
`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` `test_extensions` `test_accumulators` `asymp_cat` `severe_cat` `cryptic_cat`	global variables for testify expansion
`ont_all` `comb_sub` `ont_all_sub`	Sample data and fit from Ontario (up to 2020-04-18)
`ont_cal1` `ont_cal_2brks` `ont_cal_mob1` `bd`	Fitted models to Ontario data
`opt_obj()` `convergence_info()`	Optimizer Object
`optim_flexmodel()` `nlminb_flexmodel()` `bbmle_flexmodel()` `fitted(<flexmodel_calibrated>)`	Wrapped Optimizers for Flexmodels
`parse_formula()` `rateform_as_char()`	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 categories
`plot_res_by_state()`	Plot age-structured simulation result faceted by state
`predict(<fit_pansim>)` `plot(<fit_pansim>)`	make forecasts from sim
`prep_res_for_plotting()`	Prepare age-structured simulation results data frame for plotting
`print(<params_pansim>)`	print parameters, possibly with detailed description
`rExp()`	run a pure-exponential sim; uses run_sim_range with a population of 1 (proportions) and a very small starting value, run for 100 steps (by default) used to calculate either r (technically r0) or eigenvector (for distributing initial exposed across states)
`r_mode()`	R Mode
`r_tmb_comparable()`	Compare R and TMB Engines
`rate_summary()`	Rate Summary
`read_params()`	read simulation parameters
`rep_rate()`	Repeat a Rate for Several Rate Matrix Elements
`repair_names_age()`	Repair ageified names
`restore()`	convert a parameter vector back to a structured list Like `relist`, but adds the capability to fill in parameters from a "fixed-parameter" vector
`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()` `reset_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()` `feature_check()`	Spec and Feature Checks
`spec_version()` `spec_ver_eq()` `spec_ver_gt()` `spec_ver_lt()` `spec_ver_btwn()`	Spec Version
`%_%` `%~%` `%+%`	String Concatenation Operators
``(<struc>,<struc>) `+`(<struc>,<struc>) `%%`(<struc>,<struc>) `kronecker(<struc>,<struc>)` `t(<struc>)` `sum(<struc>)` `prod(<struc>)` `rowSums(<struc>)` `colSums(<struc>)` `dim(<struc>)`	Class to Represent Scalar, Vector, or Matrix Structure
`struc()` `scal()` `vec()` `mat()` `as.struc()`	Construct a struc Object
`struc_block()`	Repeat a Block
`struc_eval()`	Numerically Evaluate Struc Object
`struc_expanded-class`	Class to Represent an Expanded Matrix Structure Object
`struc_expanded()`	Construct a struc_expanded 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) to a named vector (used in `condense_state()`)
`time_wrap()`	Time Two Expressions
`tmb_fun()` `tmb_fun_args()`	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 a replacement for `with()` (which is hard to debug) and `attach()` (which is frowned upon by CRAN/triggers package-check warnings) (for more traditional Python tuple unpacking see the `zeallot` package)
`update(<params_pansim>)`	update parameters within a list of parameters
`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
`add_error_dist()` `update_error_dist()` `reset_error_dist()`	Update Error Distribution
`update_foi()`	calculate only updated force of infection at present, this is the only state-dependent per capita rate maybe more efficient than modifying & returning the whole matrix
`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_piece_wise()` `add_piece_wise()` `initialize_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()` `add_tmb_indices()` `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

Reference

All functions