Function reference

extrapolate_polymod()
 Fit allofpolymod model and extrapolate to a given population an age breaks

apply_vaccination()
 Apply vaccination effects to next generation contact matrices

generate_ngm()
 Calculate next generation contact matrices

autoplot(<conmat_prediction_matrix>)
autoplot(<conmat_setting_prediction_matrix>)
 Plot setting matrices using ggplot2
ABS Data accessors and helpers
Functions and data objects to access data from the Australian Bureau of Statistics

abs_age_lga()
abs_age_state()
 Return Australian Bureau of Statistics (ABS) age population data for a given Local Government Area (LGA) or state

abs_education_state
 ABS education by state for 20062020

abs_education_state_2020
 2020 ABS education population data, interpolated into 1 year bins, by state.

abs_employ_age_lga
 ABS employment by age and LGA for 2016

abs_household_lga
 ABS household data for 2016

abs_household_size_population()
 Get population associated with each household size in an LGA or a state

abs_lga_lookup
 ABS lookup table of states, lga code and lga name

abs_per_capita_household_size_lga()
 Get household size distribution based on LGA name

abs_per_capita_household_size_state()
 Get household size distribution based on state name

abs_pop_age_lga_2016
 ABS population by age for 2016 for LGAs

abs_pop_age_lga_2020
 ABS population by age for 2020 for LGAs

abs_state_age
 ABS state population data for 2020

data_abs_lga_education
 LGA wise ABS education population data on different ages for year 2016

data_abs_lga_work
 LGA wise ABS work population data on different ages for year 2016

data_abs_state_education
 State wise ABS education population data on different ages for year 2016

data_abs_state_work
 State wise ABS work population data on different ages for year 2016

get_data_abs_age_education()
 Return data on educated population for a given age and state or lga of Australia.

get_data_abs_age_work()
 Return data on employed population for a given age and state or lga of Australia

get_household_size_distribution()
 Get household size distribution based on state or LGA name

get_per_capita_household_size()
 Get per capita household size based on state or LGA name

abbreviate_states()
 Abbreviate Australian State Names

unabbreviate_states()
 Unabbreviate Australian state names
Data and model objects
Functions and objects for accessing data, models, and assisting with model fitting.

get_polymod_contact_data()
 Format POLYMOD data and filter contacts to certain settings

get_polymod_per_capita_household_size()
 Get polymod per capita houshold size.

get_polymod_population()
 Return the polymodaverage population age distribution in 5y

get_polymod_setting_data()
 Get polymod setting data

age_population()
 Get cleaned population data with lower and upper limits of age.

vaccination_effect_example_data
 Example dataset with information on age based vaccination coverage, acquisition and transmission

polymod_setting_models
 Polymod Settings models

davies_age_extended
 Susceptibility and clinical fraction parameters from Davies et al.

eyre_transmission_probabilities
 Transmission probabilities of COVID19 from Eyre et al.

polymod
 Polymod data

setting_weights
 Setting weights computed for transmission probabilities.

age_group_lookup
 Lookup table of age groups in 5 year bins

get_setting_transmission_matrices()
 Get Setting Transmission Matrices
Extra functions for model fitting and prediction
Functions for model fitting and predictions  for more advanced use

fit_single_contact_model()
 Fit a single GAM contact model to a dataset

fit_setting_contacts()
 Fit a contact model to a survey poulation

aggregate_predicted_contacts()
 Aggregate predicted contacts to specified age breaks

estimate_setting_contacts()
 Get predicted setting specific as well as combined contact matrices

predict_contacts()
 Predict contact rate between two age populations, given some model.

predict_contacts_1y()
 Predict contact rate to a given population at full 1y resolution

predict_setting_contacts()
 Predict setting contacts

predictions_to_matrix()
 Convert dataframe of predicted contacts into matrix

matrix_to_predictions()
 Convert a contact matrix as output into a longform tibble

get_age_population_function()
 Return an interpolating function for populations in 1y age increments

per_capita_household_size()
 Get per capita household size with household size distribution

add_intergenerational()
 Add column, "intergenerational"

add_modelling_features()
 Add features required for modelling to the dataset

add_offset()
 Adds offset variables

add_population_age_to()
 Add the population distribution for contact ages.

add_school_work_participation()
 Add columns describing the fractions of the population in each age group that attend school/work (average FTE)

add_symmetrical_features()
 Add symmetrical, age based features
Creating and accessing information on conmat_population
objects
Store and use age and population information in a dataframe for use in other functions in conmat.

conmat_population()
 Define a conmat population

as_conmat_population()
 Convert to conmat population

age()
age_label()
population_label()
population()
 Accessing conmat attributes