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
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()).

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

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

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()].

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.