Man pages for njtierney/conmat
Builds Contact Matrices using GAMs and Population Data
| abs_abbreviate_states | Abbreviate Australian State Names |
| abs_age_data | Return Australian Bureau of Statistics (ABS) age population... |
| abs-age-education | Return data on educated population for a given age and state... |
| abs-age-work | Return data on employed population for a given age and state... |
| abs_avg_school | ABS education data for 2016 |
| abs_avg_work | ABS work data for 2016 |
| abs_education_state | ABS education by state for 2006-2020 |
| abs_education_state_2020 | 2020 ABS education population data, interpolated into 1 year... |
| abs_employ_age_lga | ABS employment by age and LGA for 2016 |
| abs_household_lga | ABS household data for 2016 |
| abs_lga_lookup | ABS lookup table of states, lga code and lga 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 |
| abs_unabbreviate_states | Un-abbreviate Australian state names |
| accessors | Accessing conmat attributes |
| 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... |
| add_symmetrical_features | Add symmetrical, age based features |
| age_breaks | Extract age break attribute information |
| age_group_lookup | Lookup table of age groups in 5 year bins |
| age_population | Get cleaned population data with lower and upper limits of... |
| aggregate_predicted_contacts | Aggregate predicted contacts to specified age breaks |
| apply_vaccination | Apply vaccination effects to next generation contact matrices |
| as_conmat_population | Convert to conmat population |
| as_setting_prediction_matrix | Coerce object to a setting prediction matrix |
| autoplot-conmat | Plot setting matrices using ggplot2 |
| autoplot-conmat-partial | Plot partial predictive plots using ggplot2 |
| check_dimensions | Check dimensions |
| check_if_list | Check if data is a list |
| check_school_demographics | Check School Demographics |
| check_work_demographics | Check Work Demographics |
| clean_age_population_year | Prepare age population data |
| conmat_original_school_demographics | Original school demographics for conmat |
| conmat_original_work_demographics | Original work demographics for conmat |
| conmat-package | conmat: Builds Contact Matrices using GAMs and Population... |
| conmat_population | Define a conmat population |
| data_abs_lga_education | LGA wise ABS education population data on different ages for... |
| data_abs_lga_work | LGA wise ABS work population data on different ages for year... |
| data_abs_state_education | State wise ABS education population data on different ages... |
| data_abs_state_work | State wise ABS work population data on different ages for... |
| davies_age_extended | Susceptibility and clinical fraction parameters from Davies... |
| estimate_setting_contacts | Get predicted setting specific as well as combined contact... |
| extrapolate_polymod | Fit all-of-polymod model and extrapolate to a given... |
| eyre_transmission_probabilities | Transmission probabilities of COVID19 from Eyre et al. |
| fit_setting_contacts | Fit a contact model to a survey population |
| fit_single_contact_model | Fit a single GAM contact model to a dataset |
| formula-terms | Extract out formula terms |
| generate_ngm | Calculate next generation contact matrices |
| generate_ngm_oz | Calculate next generation contact matrices from ABS data |
| get_abs_household_size_distribution | Get household size distribution based on state or LGA name |
| get_abs_household_size_population | Get population associated with each household size in an LGA... |
| get_abs_per_capita_household_size | Get per capita household size based on state or LGA name |
| get_abs_per_capita_household_size_lga | Get household size distribution based on LGA name |
| get_abs_per_capita_household_size_state | Get household size distribution based on state name |
| get_age_population_function | Return an interpolating function for populations in 1y age... |
| get_polymod_contact_data | Format POLYMOD data and filter contacts to certain settings |
| get_polymod_per_capita_household_size | Get polymod per capita household size. |
| get_polymod_population | Return the polymod-average population age distribution in 5y |
| get_polymod_setting_data | Get polymod setting data |
| get_setting_transmission_matrices | Get Setting Transmission Matrices |
| matrix_to_predictions | Convert a contact matrix as output into a long-form tibble |
| new_age_matrix | Build new age matrix |
| new_conmat_population | Create a new 'conmat_population' class object |
| new_ngm_setting_matrix | Establish new BGM setting data |
| new_setting_data | Establish new setting data |
| partial-prediction | Create partial predictions and partial prediction plots. |
| partial-prediction-sum | Create partial predictive plots for a set of fitted models. |
| per_capita_household_size | Get per capita household size with household size... |
| pipe | Pipe operator |
| polymod | Social contact data from 8 European countries (imported from... |
| polymod_setting_models | Polymod Settings models |
| predict_contacts | Predict contact rate between two age populations, given some... |
| predict_contacts_1y | Predict contact rate to a given population at full 1y... |
| predictions_to_matrix | Convert dataframe of predicted contacts into matrix |
| predict_setting_contacts | Predict setting contacts |
| prem_germany_contact_matrices | Contact matrices as calculated by Prem. et al. |
| prepare_population_for_modelling | Prepare population data for generating an age population... |
| raw_eigenvalue | Get raw eigvenvalue from NGM matrix |
| reexports | Objects exported from other packages |
| scaling | Get the scaling from NGM matrix |
| separate_age_group | Separate age groups |
| setting_prediction_matrix | Create a setting prediction matrix |
| setting_weights | Setting weights computed for transmission probabilities. |
| transmission_probability_matrix | Create a setting transmission matrix |
| vaccination_effect_example_data | Example dataset with information on age based vaccination... |
