Adds new functions:
age_breaks() accessor function for conmat_setting_prediction_matrixsetting_prediction_matrix()as_setting_prediction_matrix() for coercing lists into a setting_prediction_matrixtransmission_probability_matrix() for creating new transmission probability
matricespartial_effects() and partial_effects_sum() to provide partial
predictions allow you to explore and understand the impact of each of the
covariates used in the conmat GAM model. (#88).there is now a print method for age group information in setting matrices - #139
improved age break checking #138
extended add_school_work_participation(), add_modelling_features(), fit_single_contact_model(), fit_setting_contacts(), estimate_setting_contacts() to use different school and work demographics arguments. (#82 and #15, resolved by #153).
exports new_ngm_setting_matrix() and new_setting_data()
Exports new age_breaks() method for class setting_contact_model (used in fit_setting_contacts()).
use |> over %>% (#206)
Resolve dplyr::case_when() issue (#207)
get_per_capita_household_size to get_abs_per_capita_household_sizeget_data_abs_age_work to abs_age_workget_data_abs_age_education to abs_age_educationget_household_size_distribution -> get_abs_household_size_distributionabs_household_size_population -> get_abs_household_size_populationabs_per_capita_household_size_lga -> get_abs_per_capita_household_size_lgaabs_per_capita_household_size_state -> get_abs_per_capita_household_size_stateabbreviate_states -> abs_abbreviate_statesunabbreviate_states -> abs_unabbreviate_statesconmat_age_matrix class, replaces conmat_prediction_matrix, knows about its age breaksage_breaks(), which accesses age break informationconmat_age_matrixraw_eigenvalue() for getting the raw eigenvalue from a next generation matrix, "ngm_setting_matrix".scaling for getting the value of R_target/raw eigenvalue.autoplot methods for ngm, vaccination, and transmission probabilitygenerate_ngm no longer accepts LGA or state inputs, which now occurs in generate_ngm_oz. The generate_ngm function has had S3 methods created for it,
so it can take input from conmat_population (such as the output from
[abs_age_lga()]), or a conmat_setting_prediction_matrix, which is the
output from [extrapolate_polymod()] or [predict_setting_contacts()].NEWS.md file to track changes to the package.fit_setting_contacts to
fit models, and predict_setting_contacts to predict. Fixes #7furrr. Resolves #31fit_setting_contacts from survey_population to just populationapply_vaccination to take in vaccination rates of ages and apply to contact matrices #40get_polymod_population has been revised as a result of the socialmixr package being updated to version 0.2.0, where the world population data has been updated to 2017 by switching from the wpp2015 to wpp2017 package. We have explored the new data and found it to be very similar and should not introduce any errant errors. See the exploration here.conmat_setting_prediction_matrix, conmat_prediction_matrix, ngm_setting_matrix, setting_contact_model, setting_vaccination_matrix, and setting_data, see #116. Main change is that list objects don't return the entire list and output but a summary of the list contents and details on what that object contains.conmat_population to avoid fragile use of the lower.age.limit variable name. This resolves #77.