Changelog

Source: NEWS.md

conmat 0.0.2.9000

Changes

• Adds new functions:

  • age_breaks() accessor function for conmat_setting_prediction_matrix
  • setting_prediction_matrix()
  • as_setting_prediction_matrix() for coercing lists into a setting_prediction_matrix
  • transmission_probability_matrix() for creating new transmission probability matrices
  • partial_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()).

Breaking changes

• change get_per_capita_household_size to get_abs_per_capita_household_size
• change get_data_abs_age_work to abs_age_work
• change get_data_abs_age_education to abs_age_education
• change get_household_size_distribution -> get_abs_household_size_distribution
• change abs_household_size_population -> get_abs_household_size_population
• change abs_per_capita_household_size_lga -> get_abs_per_capita_household_size_lga
• change abs_per_capita_household_size_state -> get_abs_per_capita_household_size_state
• abbreviate_states -> abs_abbreviate_states
• unabbreviate_states -> abs_unabbreviate_states

conmat 0.0.1.9000

Changes

• new conmat_age_matrix class, replaces conmat_prediction_matrix, knows about its age breaks
• accessor method, age_breaks(), which accesses age break information
• updated autoplot method for conmat_age_matrix
• accessor method, raw_eigenvalue() for getting the raw eigenvalue from a next generation matrix, “ngm_setting_matrix”.
• accessor method, scaling for getting the value of R_target/raw eigenvalue.
• add autoplot methods for ngm, vaccination, and transmission probability

Breaking Changes

• generate_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()].

conmat 0.0.0.9004

• Added a NEWS.md file to track changes to the package.
• Decouple prediction and estimation of models with fit_setting_contacts to fit models, and predict_setting_contacts to predict. Fixes #7
• Implement parallelisation with furrr. Resolves #31
• Change argument of fit_setting_contacts from survey_population to just population
• Reduce vignette size, closes #28
• Add transmission probability data from Eyre et al., closes #39
• Add household adjustment - #41
• Added setting weights, related to #44 (but no longer Eyre weights)
• Added apply_vaccination to take in vaccination rates of ages and apply to contact matrices #40
• Data from get_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.
• Added new print methods for: 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.
• Added a new S3 method for conmat_population to avoid fragile use of the lower.age.limit variable name. This resolves #77.