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 |
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