Files in njtierney/conmat
Builds Contact Matrices using GAMs and Population Data

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.github/workflows/draft-pdf.yml

.github/workflows/pkgdown.yaml

.github/workflows/test-coverage.yaml

.gitignore

CODE_OF_CONDUCT.md

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

NEWS.md R/abbreviate_states.R R/abs-helpers.R R/abs_age_education.R R/abs_age_work.R R/abs_household_size_population.R R/abs_per_capita_household_size_lga.R R/abs_per_capita_household_size_state.R R/add_modelling_features.R R/add_offset.R R/add_population_age_to.R R/add_school_work_participation.R R/add_symmetrical_features.R R/adjust_household_contact_matrix.R R/age-population.R R/aggregate_predicted_contacts.R R/apply_vaccination.R R/autoplot.R R/check_work_school_demographics.R R/checkers.R R/conmat-package.R R/conmat-population.R R/constructors.R R/data-abs-avg-work-school.R R/data-abs-pop-age-lga-2016.R R/data-abs-pop-age-lga-2020.R R/data-davies-age-extended.R R/data_abs_education_state.R R/data_abs_education_state_2020.R R/data_abs_employ_age_lga.R R/data_abs_household_lga.R R/data_abs_lga_education.R R/data_abs_lga_lookup.R R/data_abs_lga_work.R R/data_abs_state_age.R R/data_abs_state_education.R R/data_abs_state_work.R R/data_age_group_lookup.R R/data_example_vaccination_effect.R R/data_eyre_transmission_probabilities.R R/data_original_school_work.R R/data_polymod_model.R R/data_prem_contact_matrices.R R/data_setting_weights.R R/estimate_setting_contacts.R R/extrapolate_polymod.R R/fit_setting_contacts.R R/fit_single_contact_model.R R/generate-ngm.R R/get-age-population-function-internals.R R/get_abs_per_capita_household_size.R R/get_age_population_function.R R/get_household_size_distribution.R R/get_polymod_contact_data.R R/get_polymod_per_capita_household_size.R R/get_polymod_population.R R/get_polymod_setting_data.R R/get_setting_transmission_matrices.R R/matrix_to_predictions.R R/model-tidiers.R R/partial-prediction-helpers.R R/per_capita_household_size.R R/plot_matrix.R R/plot_setting_matrices.R R/polymod-data.R R/predict_contacts.R R/predict_contacts_1y.R R/predict_setting_contacts.R R/predictions_to_matrix.R R/setting-prediction-matrix.R R/setting-transmission-matrix.R

R/sysdata.rda

R/utils-pipe.R R/utils.R README.Rmd README.md

_pkgdown.yml

codecov.yml

conmat.Rproj

cran-comments.md

data-raw/2011_lga_state.csv

data-raw/2016_abs_census_labour_status.csv

data-raw/2016_abs_census_lga_work.csv

data-raw/2016_abs_lga_education.xls

data-raw/2016_census_education.csv

data-raw/31010do001_202012.xls

data-raw/32350DS0003_2020.xls

data-raw/32350ds0015_lga_2016.xls

data-raw/ABS_C16_G43_LGA_06092021163109650.csv.zip

data-raw/ABS_C16_T23_LGA_06092021160753604.csv

data-raw/ABS_CENSUS2011_B30_LGA_06092021155248143.csv

data-raw/Table 42b Number of Full-time and Part-time Students, 2006-2020.xlsx

data-raw/abs-avg-work-school.R data-raw/clean-education-2020.R data-raw/clean-education.R data-raw/clean-employment.R data-raw/clean-household.R data-raw/clean-lga-lookup.R data-raw/clean-population-by-age-2016.R data-raw/clean-population-by-age-2020.R data-raw/clean-state-age-pop.R data-raw/conmat-original-school-work-demographics.R data-raw/create-age-lookup.R data-raw/create-polymod-model.R data-raw/data_abs_census_education_2016.R data-raw/data_abs_census_education_lga_2016.R data-raw/data_abs_census_work_2016.R data-raw/data_abs_census_work_lga_2016.R data-raw/digitise_eyre_matrix.R data-raw/euclidean_join.R

data-raw/example_coverage.csv

data-raw/example_vaccination_effect.R

data-raw/example_vaccine_coverage_effects.csv

data-raw/example_ves.csv

data-raw/eyre_legend_raw.png

data-raw/eyre_transmission_events_activities.png

data-raw/eyre_transmission_household.png

data-raw/eyre_transmission_household_visitor.png

data-raw/eyre_transmission_probabilities.csv.gz

data-raw/eyre_transmission_work_education.png

data-raw/get_age_group_lookup.R

data-raw/population_data.csv

data-raw/prem/contact_all.rdata

data-raw/prem/contact_home.rdata

data-raw/prem/contact_others.rdata

data-raw/prem/contact_school.rdata

data-raw/prem/contact_work.rdata

data-raw/prem/rural/contact_all_rural.rdata

data-raw/prem/rural/contact_home_rural.rdata

data-raw/prem/rural/contact_others_rural.rdata

data-raw/prem/rural/contact_school_rural.rdata

data-raw/prem/rural/contact_work_rural.rdata

data-raw/prem/urban/contact_all_urban.rdata

data-raw/prem/urban/contact_home_urban.rdata

data-raw/prem/urban/contact_others_urban.rdata

data-raw/prem/urban/contact_school_urban.rdata

data-raw/prem/urban/contact_work_urban.rdata

data-raw/prem_germany_contact_matrices.R data-raw/read_eyre_transmission_probabilities.R data-raw/read_setting_weights.R data-raw/susceptibility_clinical_fraction.R data-raw/use-polymod.R

data/abs_avg_school.rda

data/abs_avg_work.rda

data/abs_education_state.rda

data/abs_education_state_2020.rda

data/abs_employ_age_lga.rda

data/abs_household_lga.rda

data/abs_lga_lookup.rda

data/abs_pop_age_lga_2016.rda

data/abs_pop_age_lga_2020.rda

data/abs_state_age.rda

data/age_group_lookup.rda

data/conmat_original_school_demographics.rda

data/conmat_original_work_demographics.rda

data/data_abs_lga_education.rda

data/data_abs_lga_work.rda

data/data_abs_state_education.rda

data/data_abs_state_work.rda

data/davies_age_extended.rda

data/eyre_transmission_probabilities.rda

data/polymod.rda

data/polymod_setting_models.rda

data/prem_germany_contact_matrices.rda

data/setting_weights.rda

data/vaccination_effect_example_data.rda

flint/config.yml

flint/rules/builtin/T_and_F_symbol.yml

flint/rules/builtin/absolute_path.yml

flint/rules/builtin/any_duplicated.yml

flint/rules/builtin/any_is_na.yml

flint/rules/builtin/class_equals.yml

flint/rules/builtin/condition_message.yml

flint/rules/builtin/double_assignment.yml

flint/rules/builtin/duplicate_argument.yml

flint/rules/builtin/empty_assignment.yml

flint/rules/builtin/equal_assignment.yml

flint/rules/builtin/equals_na.yml

flint/rules/builtin/expect_comparison.yml

flint/rules/builtin/expect_identical.yml

flint/rules/builtin/expect_length.yml

flint/rules/builtin/expect_named.yml

flint/rules/builtin/expect_not.yml

flint/rules/builtin/expect_null.yml

flint/rules/builtin/expect_true_false.yml

flint/rules/builtin/expect_type.yml

flint/rules/builtin/for_loop_index.yml

flint/rules/builtin/function_return.yml

flint/rules/builtin/implicit_assignment.yml

flint/rules/builtin/is_numeric.yml

flint/rules/builtin/length_levels.yml

flint/rules/builtin/length_test.yml

flint/rules/builtin/lengths.yml

flint/rules/builtin/library_call.yml

flint/rules/builtin/list_comparison.yml

flint/rules/builtin/literal_coercion.yml

flint/rules/builtin/matrix_apply.yml

flint/rules/builtin/missing_argument.yml

flint/rules/builtin/nested_ifelse.yml

flint/rules/builtin/numeric_leading_zero.yml

flint/rules/builtin/outer_negation.yml

flint/rules/builtin/package_hooks.yml

flint/rules/builtin/paste.yml

flint/rules/builtin/redundant_equals.yml

flint/rules/builtin/redundant_ifelse.yml

flint/rules/builtin/rep_len.yml

flint/rules/builtin/right_assignment.yml

flint/rules/builtin/sample_int.yml

flint/rules/builtin/semicolon.yml

flint/rules/builtin/seq.yml

flint/rules/builtin/sort.yml

flint/rules/builtin/stopifnot_all.yml

flint/rules/builtin/todo_comment.yml

flint/rules/builtin/undesirable_function.yml

flint/rules/builtin/undesirable_operator.yml

flint/rules/builtin/unnecessary_nesting.yml

flint/rules/builtin/unreachable_code.yml

flint/rules/builtin/which_grepl.yml

inst/WORDLIST

man/abs-age-education.Rd man/abs-age-work.Rd man/abs_abbreviate_states.Rd man/abs_age_data.Rd man/abs_avg_school.Rd man/abs_avg_work.Rd man/abs_education_state.Rd man/abs_education_state_2020.Rd man/abs_employ_age_lga.Rd man/abs_household_lga.Rd man/abs_lga_lookup.Rd man/abs_pop_age_lga_2016.Rd man/abs_pop_age_lga_2020.Rd man/abs_state_age.Rd man/abs_unabbreviate_states.Rd man/accessors.Rd man/add_intergenerational.Rd man/add_modelling_features.Rd man/add_offset.Rd man/add_population_age_to.Rd man/add_school_work_participation.Rd man/add_symmetrical_features.Rd man/age_breaks.Rd man/age_group_lookup.Rd man/age_population.Rd man/aggregate_predicted_contacts.Rd man/apply_vaccination.Rd man/as_conmat_population.Rd man/as_setting_prediction_matrix.Rd man/autoplot-conmat-partial.Rd man/autoplot-conmat.Rd man/check_dimensions.Rd man/check_if_list.Rd man/check_school_demographics.Rd man/check_work_demographics.Rd man/clean_age_population_year.Rd man/conmat-package.Rd man/conmat_original_school_demographics.Rd man/conmat_original_work_demographics.Rd man/conmat_population.Rd man/data_abs_lga_education.Rd man/data_abs_lga_work.Rd man/data_abs_state_education.Rd man/data_abs_state_work.Rd man/davies_age_extended.Rd man/estimate_setting_contacts.Rd man/extrapolate_polymod.Rd man/eyre_transmission_probabilities.Rd

man/figures/README-eyre-transmission-probabilities-1.png

man/figures/README-fairfield-synth-5-plot-1.png

man/figures/README-matrix-plot-1.png

man/figures/README-plot-matrix-differents-1.png

man/figures/README-plot-matrix-differents-2.png

man/figures/README-plot-matrix-differents-3.png

man/figures/README-plot-matrix-differents-4.png

man/figures/README-plot-matrix-differents-5.png

man/figures/README-sydney-synth-5-plot-1.png

man/figures/README-unnamed-chunk-4-1.png

man/fit_setting_contacts.Rd man/fit_single_contact_model.Rd man/formula-terms.Rd man/generate_ngm.Rd man/generate_ngm_oz.Rd man/get_abs_household_size_distribution.Rd man/get_abs_household_size_population.Rd man/get_abs_per_capita_household_size.Rd man/get_abs_per_capita_household_size_lga.Rd man/get_abs_per_capita_household_size_state.Rd man/get_age_population_function.Rd man/get_polymod_contact_data.Rd man/get_polymod_per_capita_household_size.Rd man/get_polymod_population.Rd man/get_polymod_setting_data.Rd man/get_setting_transmission_matrices.Rd man/matrix_to_predictions.Rd man/new_age_matrix.Rd man/new_conmat_population.Rd man/new_ngm_setting_matrix.Rd man/new_setting_data.Rd man/partial-prediction-sum.Rd man/partial-prediction.Rd man/per_capita_household_size.Rd man/pipe.Rd man/polymod.Rd man/polymod_setting_models.Rd man/predict_contacts.Rd man/predict_contacts_1y.Rd man/predict_setting_contacts.Rd man/predictions_to_matrix.Rd man/prem_germany_contact_matrices.Rd man/prepare_population_for_modelling.Rd man/raw_eigenvalue.Rd man/reexports.Rd man/scaling.Rd man/separate_age_group.Rd man/setting_prediction_matrix.Rd man/setting_weights.Rd man/transmission_probability_matrix.Rd man/vaccination_effect_example_data.Rd

paper/.gitignore

paper/paper.bib

paper/paper.html.log

paper/paper.html.md paper/paper.html.pdf.md paper/paper.md

paper/paper.qmd

paper/paper_files/figure-html/fig-autoplot-contacts-1.png

paper/paper_files/figure-html/fig-show-partial-plots-1.png

paper/paper_files/libs/bootstrap/bootstrap-c0367b04c37547644fece4185067e4a7.min.css

paper/paper_files/libs/bootstrap/bootstrap-e19dc0c07aeef78048e587c3f1edba7a.min.css

paper/paper_files/libs/bootstrap/bootstrap-icons.css

paper/paper_files/libs/bootstrap/bootstrap-icons.woff

paper/paper_files/libs/bootstrap/bootstrap.min.css

paper/paper_files/libs/bootstrap/bootstrap.min.js

paper/paper_files/libs/clipboard/clipboard.min.js

paper/paper_files/libs/quarto-html/anchor.min.js

paper/paper_files/libs/quarto-html/popper.min.js

paper/paper_files/libs/quarto-html/quarto-syntax-highlighting-01c78b5cd655e4cd89133cf59d535862.css

paper/paper_files/libs/quarto-html/quarto-syntax-highlighting-2f5df379a58b258e96c21c0638c20c03.css

paper/paper_files/libs/quarto-html/quarto-syntax-highlighting.css

paper/paper_files/libs/quarto-html/quarto.js

paper/paper_files/libs/quarto-html/tippy.css

paper/paper_files/libs/quarto-html/tippy.umd.min.js

tests/spelling.R tests/testthat.R tests/testthat/_snaps/abbreviation.md tests/testthat/_snaps/abs-age-education.md tests/testthat/_snaps/abs-age-lga.md tests/testthat/_snaps/abs-age-work.md tests/testthat/_snaps/age-population.md tests/testthat/_snaps/apply_vaccination.md

tests/testthat/_snaps/autoplot/autoplot-all-settinge.svg

tests/testthat/_snaps/autoplot/autoplot-ngm.svg

tests/testthat/_snaps/autoplot/autoplot-single-setting.svg

tests/testthat/_snaps/autoplot/autoplot-vaccination.svg

tests/testthat/_snaps/autoplot/autoplot.svg

tests/testthat/_snaps/partial-prediction/gg-partials-home.svg

tests/testthat/_snaps/partial-prediction/gg-partials-setting.svg

tests/testthat/_snaps/partial-prediction/gg-partials-sum-home.svg

tests/testthat/_snaps/partial-prediction/gg-partials-sum-setting.svg

touchstone/.gitignore

touchstone/config.json

touchstone/footer.R touchstone/header.R touchstone/script.R touchstone/touchstone-setup.R

vignettes/.gitignore

vignettes/conmat-population.Rmd vignettes/data-sources.Rmd vignettes/example-pipeline.Rmd vignettes/getting-started.Rmd vignettes/other-data-sources.Rmd vignettes/parallel-computing.Rmd vignettes/sir-model.Rmd vignettes/visualising-conmat.Rmd

njtierney/conmat documentation built on April 17, 2025, 10:27 p.m.

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njtierney/conmat
Builds Contact Matrices using GAMs and Population Data

Files in njtierney/conmat
Builds Contact Matrices using GAMs and Population Data

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njtierney/conmat Builds Contact Matrices using GAMs and Population Data

Files in njtierney/conmat Builds Contact Matrices using GAMs and Population Data

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njtierney/conmat
Builds Contact Matrices using GAMs and Population Data

Files in njtierney/conmat
Builds Contact Matrices using GAMs and Population Data