Files in mrc-ide/naomi
Naomi Model for Subnational HIV Estimates
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/docker.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
Makefile
NAMESPACE
NEWS.md
R/Lproj.R
R/aaa.R
R/areas.R
R/calibrate.R
R/car.R
R/data-anc.R
R/data-areas.R
R/data-documentation.R
R/data-population.R
R/data-survey.R
R/data.R
R/downloads.R
R/hintr-plot-data.R
R/input-time-series.R
R/inputs-shiny90.R
R/inputs-spectrum.R
R/metadata.R
R/model-options.R
R/model.R
R/naomi-package.R
R/outputs.R
R/pepfar-datapack.R
R/read-data.R
R/report-plots.R
R/run-model.R
R/tmb-model-r-implementation.R
R/tmb-model.R
R/tmb-sdreport-jointprecision.R
R/unaids-navigator.R
R/utils-pipe.R
R/utils.R
R/warnings.R
R/zzz.R
README.md
data-raw/areas.R
data-raw/demo-subnational-pjnz/README.md
data-raw/demo-subnational-pjnz/demo_mwi2019_central.PJNZ
data-raw/demo-subnational-pjnz/demo_mwi2019_central_small.PJNZ
data-raw/demo-subnational-pjnz/demo_mwi2019_central_small_v6.2.PJNZ
data-raw/demo-subnational-pjnz/demo_mwi2019_northern.PJNZ
data-raw/demo-subnational-pjnz/demo_mwi2019_northern_small.PJNZ
data-raw/demo-subnational-pjnz/demo_mwi2019_northern_small_v6.2.PJNZ
data-raw/demo-subnational-pjnz/demo_mwi2019_region-pjnz.zip
data-raw/demo-subnational-pjnz/demo_mwi2019_region-pjnz_v6.2.zip
data-raw/demo-subnational-pjnz/demo_mwi2019_southern.PJNZ
data-raw/demo-subnational-pjnz/demo_mwi2019_southern_small.PJNZ
data-raw/demo-subnational-pjnz/demo_mwi2019_southern_small_v6.2.PJNZ
data-raw/demo-subnational-pjnz/region-distribution.R
data-raw/mdhs15-district-prevalence.csv
data-raw/mdhs2015-16_hiv-prevalence-tables.R
data-raw/pjnz.R
data-raw/population.R
data-raw/population/Pop projections 2008-2030 Master file_transformed.xlsx
data-raw/population/Series A. Population Tables.xlsx
data-raw/population/mwi-demo-asfr.csv
data-raw/programme.R
data-raw/programme/mwi-simulated-vls.csv
data-raw/programme/mwi_dha_ancrt.csv
data-raw/programme/mwi_dha_arttot.csv
data-raw/survey-alternate.R
data-raw/survey.R
data/demo_anc_testing.rda
data/demo_area_boundaries.rda
data/demo_area_hierarchy.rda
data/demo_area_levels.rda
data/demo_areas.rda
data/demo_art_number.rda
data/demo_population_agesex.rda
data/demo_survey_biomarker.rda
data/demo_survey_clusters.rda
data/demo_survey_hiv_indicators.rda
data/demo_survey_individuals.rda
data/demo_survey_meta.rda
data/demo_survey_regions.rda
docker/Dockerfile
docker/bin/check_self
docker/bin/install_packages
docker/bin/install_remote
docker/bin/test_self
docker/build
docker/check
docker/clear_docker
docker/common
docker/push
docker/test
images/naomi_hex.png
images/naomi_hex.svg
images/naomi_hex_300.png
images/naomi_hex_72.png
images/sida_sid_300.png
inst/datapack/README.md
inst/datapack/datapack_age_group_mapping.csv
inst/datapack/datapack_indicator_mapping.csv
inst/datapack/datapack_psnu_area_id_map.csv
inst/datapack/datapack_psnu_area_level.csv
inst/datapack/datapack_sex_mapping.csv
inst/extdata/README.md
inst/extdata/areas/area_boundaries.geojson
inst/extdata/areas/area_hierarchy.csv
inst/extdata/areas/area_levels.csv
inst/extdata/demo-subnational-pjnz/demo_anc_testing_zone.csv
inst/extdata/demo-subnational-pjnz/demo_areas_region-pjnz.geojson
inst/extdata/demo-subnational-pjnz/demo_art_number_zone.csv
inst/extdata/demo-subnational-pjnz/demo_mwi2019_region-pjnz.zip
inst/extdata/demo-subnational-pjnz/demo_mwi2019_region-pjnz_v6.2.zip
inst/extdata/demo-subnational-pjnz/demo_population_zone.csv
inst/extdata/demo_anc_testing.csv
inst/extdata/demo_areas.geojson
inst/extdata/demo_art_number.csv
inst/extdata/demo_mwi2019.PJNZ
inst/extdata/demo_mwi2019_v6.2.PJNZ
inst/extdata/demo_mwi2019_v6.21-shiny90.PJNZ
inst/extdata/demo_population_agesex.csv
inst/extdata/demo_survey_hiv_indicators.csv
inst/extdata/survey/demo_survey_biomarker.csv
inst/extdata/survey/demo_survey_clusters.csv
inst/extdata/survey/demo_survey_hiv_indicators_alt.csv
inst/extdata/survey/demo_survey_individuals.csv
inst/extdata/survey/demo_survey_meta.csv
inst/extdata/survey/demo_survey_regions.csv
inst/metadata/README.md
inst/metadata/colour_scales.csv
inst/metadata/meta_age_group.csv
inst/metadata/meta_indicator.csv
inst/metadata/metadata.csv
inst/metadata/navigator_validation.yml
inst/metadata/time_series_plot_metadata.csv
inst/report/README.Rmd
inst/report/UNAIDS.png
inst/report/comparison_report.Rmd
inst/report/header.html
inst/report/naomi_hex.png
inst/report/sida_sid_300.png
inst/report/styles.css
inst/report/summary_report.Rmd
inst/traduire/en-translation.json
inst/traduire/fr-translation.json
inst/traduire/pt-translation.json
man/Imports.Rd
man/add_output_labels.Rd
man/age_bar_plotly.Rd
man/aggregate_anc.Rd
man/aggregate_art.Rd
man/align_inputs_outputs.Rd
man/anc_spectrum_warning.Rd
man/anc_testing_prev_mf.Rd
man/art_spectrum_warning.Rd
man/artnum_mf.Rd
man/assert_pjnz_shiny90.Rd
man/bar_plotly.Rd
man/build_hierarchy_label.Rd
man/cache_invariant.Rd
man/calculate_prevalence_art_coverage.Rd
man/calibrate_outputs.Rd
man/cmc_date.Rd
man/create_adj_matrix.Rd
man/create_area_aggregation.Rd
man/create_areas.Rd
man/create_edge_list.Rd
man/cut_naomi_age_group.Rd
man/data_type_labels.Rd
man/demo_anc_testing.Rd
man/demo_area_boundaries.Rd
man/demo_area_hierarchy.Rd
man/demo_area_levels.Rd
man/demo_population_agesex.Rd
man/demo_survey_biomarker.Rd
man/demo_survey_clusters.Rd
man/demo_survey_hiv_indicators.Rd
man/demo_survey_individuals.Rd
man/demo_survey_meta.Rd
man/demo_survey_regions.Rd
man/disaggregate_0to4_outputs.Rd
man/district_barplot.Rd
man/dropdown_buttons.Rd
man/extract_pjnz_naomi.Rd
man/extract_pjnz_program_data.Rd
man/extract_shiny90_age_sex.Rd
man/fit_tmb.Rd
man/format_spectrum_total_warning.Rd
man/generate_comparison_report.Rd
man/generate_output_summary_report.Rd
man/get_age_group_out.Rd
man/get_age_groups.Rd
man/get_area_collection.Rd
man/get_colour_scale.Rd
man/get_five_year_age_groups.Rd
man/get_meta_indicator.Rd
man/get_metadata.Rd
man/get_plot_type_column_metadata.Rd
man/get_plotting_metadata.Rd
man/get_spec_aggr_interpolation.Rd
man/hintr_calibrate.Rd
man/hintr_calibrate_plot.Rd
man/hintr_comparison_plot.Rd
man/hintr_prepare_agyw_download.Rd
man/hintr_prepare_coarse_age_group_download.Rd
man/hintr_prepare_comparison_report_download.Rd
man/hintr_prepare_spectrum_download.Rd
man/hintr_prepare_summary_report_download.Rd
man/hintr_run_model.Rd
man/hintr_validate_anc.Rd
man/hintr_validate_art.Rd
man/interpolate_population_agesex.Rd
man/log_linear_interp.Rd
man/map_outputs.Rd
man/naomi_model_frame.Rd
man/naomi_objective_function_r.Rd
man/naomi_output_frame.Rd
man/output_naomi_warning.Rd
man/output_package.Rd
man/pipe.Rd
man/pop_pyramid_outputs.Rd
man/prepare_input_time_series_anc.Rd
man/prepare_input_time_series_art.Rd
man/prepare_tmb_inputs.Rd
man/quarter_year_labels.Rd
man/read_csv_partial_cols.Rd
man/read_hintr_output.Rd
man/read_metadata.Rd
man/read_population.Rd
man/read_spectrum_projection_name.Rd
man/read_spectrum_region_code.Rd
man/read_spectrum_region_name.Rd
man/report_tmb.Rd
man/sample_tmb.Rd
man/save_output.Rd
man/save_output_package.Rd
man/scale_gmrf_precision.Rd
man/scatter_plotly.Rd
man/sdreport_joint_precision.Rd
man/select_naomi_data.Rd
man/spread_areas.Rd
man/subset_naomi_output.Rd
man/subset_output_package.Rd
man/survey_mf.Rd
man/tag_data_inputs.Rd
man/th_map.Rd
man/validate_model_options.Rd
man/write_datapack_csv.Rd
man/write_navigator_checklist.Rd
naomi.Rproj
scripts/build_test_data
scripts/update_web.sh
src/.gitignore
src/tmb.cpp
tests/testthat.R
tests/testthat/helper-testing.R
tests/testthat/helper-traduire.R
tests/testthat/refdata/invalid_files.zip
tests/testthat/refdata/naomi-2.5.5/output_data_2.5.5.rds
tests/testthat/setup-load-data.R
tests/testthat/setup-model-frame.R
tests/testthat/setup-run-model.R
tests/testthat/test-01-run-model.R
tests/testthat/test-02-model-options.R
tests/testthat/test-03-model-fit.R
tests/testthat/test-04-model-frame.R
tests/testthat/test-05-Lproj.R
tests/testthat/test-areas.R
tests/testthat/test-cache.R
tests/testthat/test-calibrate.R
tests/testthat/test-car.R
tests/testthat/test-data-anc.R
tests/testthat/test-data-areas.R
tests/testthat/test-data-population.R
tests/testthat/test-data-survey.R
tests/testthat/test-downloads.R
tests/testthat/test-example-data.R
tests/testthat/test-hintr-plot-data.R
tests/testthat/test-info.R
tests/testthat/test-input-time-series.R
tests/testthat/test-metadata.R
tests/testthat/test-objective-function.R
tests/testthat/test-outputs.R
tests/testthat/test-pepfar-datapack.R
tests/testthat/test-read-data.R
tests/testthat/test-report-plots.R
tests/testthat/test-run-model-options.R
tests/testthat/test-select-naomi-data.R
tests/testthat/test-spectrum.R
tests/testthat/test-traduire.R
tests/testthat/test-utils.R
tests/testthat/test-warning.R
tests/testthat/testdata/vmmc.xlsx
vignettes/README.md
vignettes/data-model.Rmd
vignettes/figure/age_specific_art_cov-1.png
vignettes/figure/age_specific_prev-1.png
vignettes/figure/art_cov_age_sex-1.png
vignettes/figure/art_cov_district-1.png
vignettes/figure/bubble_plot-1.png
vignettes/figure/data_model.png
vignettes/figure/prev_by_district_15-1.png
vignettes/figure/prev_by_zone_15-1.png
vignettes/model-workflow.Rmd
vignettes/script/create_data_model.R
vignettes_src/data-model.Rmd
vignettes_src/hintr-example.R
vignettes_src/hintr-example_zone-demo-data.R
vignettes_src/model-workflow.R
