{ "_id": "6accc408a14063b82c3a8e08", "Package": "cd2030.core", "Title": "Data Loading, Validation, and Reporting for Countdown 2030", "Version": "1.4.4", "Authors@R": "c(\nperson(\"David\", \"Kariuki\", , \"hello@damurka.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0003-6159-1107\")),\nperson(\"Martin\", \"Mutua\", role = c(\"aut\")),\nperson(\"Peter\", \"Kaberia\", , \"pkaberia@aphrc.org\", role = c(\"aut\")),\nperson(\"Godfrey\", \"Adero\", , \"gadero@aphrc.org\", role = c(\"aut\")),\nperson(\"Rornald\", \"Muhumuza\", , \"rmuhumuza@aphrc.org\", role = c(\"aut\")),\nperson(\"African Population and Health Research Center (APHRC)\",\nrole = c(\"cph\", \"fnd\"))\n)", "Description": "cd2030.core is an R package for managing and validating\ndata formatted according to Countdown 2030 standards. It\nprovides tools for data loading, cleaning, and validation,\ndetecting issues like missing values, inconsistencies,\noutliers, and ratio anomalies. The package ensures compliance\nwith Countdown 2030 guidelines and generates standardized data\nquality reports, enabling users to focus on analysis and\ninterpretation.", "License": "AGPL (>= 3)", "URL": "https://github.com/damurka/cd2030.core", "Remotes": [ "damurka/datasuite.ui" ], "Additional_repositories": "https://alkemalab.r-universe.dev", "Config/datasuite/onDemand": "bayescoveragemodel, bayescoveragedeploy", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "BugReports": "https://github.com/damurka/cd2030.core/issues", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libabsl-dev libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libgdal-dev gdal-bin\nlibgeos-dev make libharfbuzz-dev libicu-dev libjpeg-dev\nlibpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev\nlibssl-dev libproj-dev libsqlite3-dev libudunits2-dev\nlibx11-dev zlib1g-dev", "Repository": 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"calculate_derived_coverage", "title": "Generate coverage data with derived denominators", "topics": [ "calculate_derived_coverage" ] }, { "page": "calculate_district_completeness_summary", "title": "District-level completeness summary", "topics": [ "calculate_district_completeness_summary" ] }, { "page": "calculate_district_outlier_summary", "title": "District-level outlier summary by year", "topics": [ "calculate_district_outlier_summary" ] }, { "page": "calculate_district_ratios_summary", "title": "Calculate district adequacy summary", "topics": [ "calculate_district_ratios_summary" ] }, { "page": "calculate_district_reporting_rate", "title": "District-level reporting rates by year", "topics": [ "calculate_district_reporting_rate" ] }, { "page": "calculate_health_system_comparison", "title": "Compare health system metrics across levels", "topics": [ "calculate_health_system_comparison" ] }, { "page": "calculate_health_system_metrics", "title": "Calculate health system metrics", "topics": [ "calculate_health_system_metrics" ] }, { "page": "calculate_indicator_coverage", "title": "Calculate health coverage indicators", "topics": [ "calculate_indicator_coverage" ] }, { "page": "calculate_inequality", "title": "Analyze subnational health coverage data with inequality metrics", "topics": [ "calculate_inequality" ] }, { "page": "calculate_outliers_summary", "title": "Annual summary of outlier-free reporting rates", "topics": [ "calculate_outliers_summary" ] }, { "page": "calculate_overall_score", "title": "Calculate overall quality score for data quality metrics", "topics": [ "calculate_overall_score" ] }, { "page": "calculate_overall_score1", "title": "Calculate overall quality score from summaries", "topics": [ "calculate_overall_score1" ] }, { "page": "calculate_ratios_and_adequacy", "title": "Calculate indicator ratios and adequacy flags", "topics": [ "calculate_ratios_and_adequacy" ] }, { "page": "calculate_ratios_summary", "title": "Calculate yearly indicator ratios summary with expected ratios", "topics": [ "calculate_ratios_summary" ] }, { "page": "calculate_ratios_ui", "title": "Indicator ratios card", "concept": [ "Countdown app pages" ], "topics": [ "calculate_ratios_server", "calculate_ratios_ui" ] }, { "page": "calculate_threshold", "title": "Calculate coverage/dropout threshold attainment", "topics": [ "calculate_threshold" ] }, { "page": "cd_admin_level_choices", "title": "Choices of the admin level chip", "concept": [ "Countdown app filters" ], "topics": [ "cd_admin_level_choices" ] }, { "page": "cd_admin_level_ui", "title": "Admin level and region filter chips", "concept": [ "Countdown app filters" ], "topics": [ "cd_admin_level_server", "cd_admin_level_ui" ] }, { "page": "cd_admin_parts", "title": "Split the admin level filter's value into two reactives", "concept": [ "Countdown app filters" ], "topics": [ "cd_admin_parts" ] }, { "page": "cd_app", "title": "Build a Countdown app", "concept": [ "Countdown app frame" ], "topics": [ "cd_app" ] }, { "page": "cd_bayes_fit_task", "title": "Fit one Bayesian coverage model in a background worker", "concept": [ "Countdown app pages" ], "topics": [ "cd_bayes_fit_task" ] }, { "page": "cd_bayes_indicators", "title": "Indicators the Bayesian coverage model can be fitted for", "concept": [ "Countdown app pages" ], "topics": [ "cd_bayes_indicators" ] }, { "page": "cd_bayes_install_command", "title": "The R command that installs the Bayesian model's packages", "topics": [ "cd_bayes_install_command" ] }, { "page": "cd_bayes_packages_missing", "title": "The Bayesian model's packages that are not installed", "topics": [ "cd_bayes_packages_missing" ] }, { "page": "cd_cfg", "title": "Read one of the app's settings", "concept": [ "Countdown app frame" ], "topics": [ "cd_cfg" ] }, { "page": "cd_chart_catalog", "title": "The charts that have saved options", "topics": [ "cd_chart_catalog" ] }, { "page": "cd_chart_id", "title": "The id of a chart", "topics": [ "cd_chart_id" ] }, { "page": "cd_chartable_members", "title": "The CacheConnection members a custom chart may draw from", "topics": [ "cd_chartable_members" ] }, { "page": "cd_coverage_plot_ui", "title": "Chart with its tools and downloads", "concept": [ "Countdown app charts and tables" ], "topics": [ "cd_coverage_plot_server", "cd_coverage_plot_toolbar_ui", "cd_coverage_plot_ui" ] }, { "page": "cd_custom_chart_data", "title": "The table a custom chart draws", "topics": [ "cd_custom_chart_data" ] }, { "page": "cd_default_indicator_set", "title": "The indicators this app's tabbed chart cards show", "concept": [ "Countdown app layout" ], "topics": [ "cd_default_indicator_set" ] }, { "page": "cd_default_indicators", "title": "The standard indicators of a tabbed chart card", "concept": [ "Countdown app layout" ], "topics": [ "cd_default_indicators" ] }, { "page": "cd_denominator_chip_keys", "title": "Label and hint of a denominator chip", "concept": [ "Countdown app filters" ], "topics": [ "cd_denominator_chip_keys" ] }, { "page": "cd_denominator_choices", "title": "The standard denominator choices", "concept": [ "Countdown app filters" ], "topics": [ "cd_denominator_choices" ] }, { "page": "cd_denominator_header", "title": "Draw the denominator row in a page header", "concept": [ "Countdown app layout" ], "topics": [ "cd_denominator_header" ] }, { "page": "cd_denominator_labels", "title": "The denominator options' labels", "topics": [ "cd_denominator_labels" ] }, { "page": "cd_denominator_options", "title": "The denominators this app offers", "concept": [ "Countdown app filters" ], "topics": [ "cd_denominator_options" ] }, { "page": "cd_denominator_row", "title": "Row naming the denominators in use", "concept": [ "Countdown app layout" ], "topics": [ "cd_denominator_row" ] }, { "page": "cd_denominator_ui", "title": "Denominator filter chip", "concept": [ "Countdown app filters" ], "topics": [ "cd_denominator_server", "cd_denominator_ui" ] }, { "page": "cd_describe_columns", "title": "Read column names with the data dictionary", "topics": [ "cd_describe_columns" ] }, { "page": "cd_dictionary", "title": "The data dictionary: what the ids and column names in the package's data mean", "topics": [ "cd_dictionary" ] }, { "page": "cd_finish_plot", "title": "Finish a plot: apply the chart options", "topics": [ "cd_finish_plot" ] }, { "page": "cd_has_maternal", "title": "Whether this app has a maternal denominator", "concept": [ "Countdown app filters" ], "topics": [ "cd_has_maternal" ] }, { "page": "cd_indicator_labels", "title": "The indicators' labels", "topics": [ "cd_indicator_labels" ] }, { "page": "cd_indicator_ui", "title": "Indicator filter chip", "concept": [ "Countdown app filters" ], "topics": [ "cd_indicator_server", "cd_indicator_ui" ] }, { "page": "cd_member_data", "title": "The table a CacheConnection member gives", "topics": [ "cd_member_data" ] }, { "page": "cd_methodology_defaults", "title": "The constants of the Countdown methodology", "topics": [ "cd_methodology_defaults" ] }, { "page": "cd_minimal_theme", "title": "A minimal chart theme", "topics": [ "cd_minimal_theme" ] }, { "page": "cd_nav_start", "title": "The standard sidebar sections of a Countdown app", "concept": [ "Countdown app layout" ], "topics": [ "cd_nav_denominators", "cd_nav_national", "cd_nav_quality", "cd_nav_start", "cd_nav_subnational" ] }, { "page": "cd_only_denominators", "title": "Keep only the denominators this app offers", "concept": [ "Countdown app filters" ], "topics": [ "cd_only_denominators" ] }, { "page": "cd_palette_chip", "title": "Colour palette chip for a page's maps", "concept": [ "Countdown app filters" ], "topics": [ "cd_palette_chip" ] }, { "page": "cd_plot_arguments", "title": "Arguments every chart shares", "topics": [ "cd-plot-arguments", "cd_plot_arguments" ] }, { "page": "cd_population_ui", "title": "Population filter chip", "concept": [ "Countdown app filters" ], "topics": [ "cd_population_server", "cd_population_ui" ] }, { "page": "cd_rate_status_cell", "title": "Table cell showing a rate with its status", "concept": [ "Countdown app charts and tables" ], "topics": [ "cd_rate_status_cell" ] }, { "page": "cd_report_context", "title": "The report context of a dataset", "topics": [ "cd_report_context" ] }, { "page": "cd_request_bayes_packages", "title": "Ask DataSuite to install the Bayesian model's packages", "topics": [ "cd_request_bayes_packages" ] }, { "page": "cd_saved_copy_name", "title": "File name of a dataset's saved copy", "concept": [ "Countdown app wizard" ], "topics": [ "cd_saved_copy_name" ] }, { "page": "cd_scope", "title": "Define the scope of a scoped page", "concept": [ "Countdown app layout" ], "topics": [ "cd_scope" ] }, { "page": "cd_scope_filters", "title": "Filter bar of a scope", "concept": [ "Countdown app layout" ], "topics": [ "cd_scope_filters" ] }, { "page": "cd_scope_server", "title": "Admin level and region of a scope", "concept": [ "Countdown app layout" ], "topics": [ "cd_scope_server" ] }, { "page": "cd_scoped_page_ui", "title": "A whole page that runs an analysis at a scope", "concept": [ "Countdown app layout" ], "topics": [ "cd_scoped_page_server", "cd_scoped_page_ui" ] }, { "page": "cd_start_bayes_workers", "title": "Start the background workers that fit the Bayesian models", "concept": [ "Countdown app pages" ], "topics": [ "cd_start_bayes_workers" ] }, { "page": "cd_tab_indicator", "title": "The indicator of a tab of charts", "concept": [ "Countdown app layout" ], "topics": [ "cd_tab_indicator" ] }, { "page": "cd_tabbed_charts_ui", "title": "Chart card with one tab for each indicator", "concept": [ "Countdown app layout" ], "topics": [ "cd_tabbed_charts_server", "cd_tabbed_charts_ui" ] }, { "page": "cd_table_card_ui", "title": "Flextable in a card with picture and Excel downloads", "concept": [ "Countdown app charts and tables" ], "topics": [ "cd_table_card_server", "cd_table_card_ui" ] }, { "page": "cd_table_ui", "title": "Table card with a year or indicator control", "concept": [ "Countdown app charts and tables" ], "topics": [ "cd_table_server", "cd_table_ui" ] }, { "page": "cd_type_scale", "title": "The sizes of the text of a chart", "topics": [ "cd_type_scale" ] }, { "page": "cd_upload_data_ui", "title": "The Load Data screen", "concept": [ "Countdown app wizard" ], "topics": [ "cd_upload_data_server", "cd_upload_data_ui" ] }, { "page": "cd_wizard_check_group", "title": "Check that a loaded dataset belongs to the app's indicator group", "concept": [ "Countdown app wizard" ], "topics": [ "cd_wizard_check_group" ] }, { "page": "cd_wizard_config", "title": "The app's Load Data wizard configuration", "concept": [ "Countdown app wizard" ], "topics": [ "cd_wizard_config" ] }, { "page": "cd_wizard_field_group", "title": "Describe one group of fields of the National Rates step", "concept": [ "Countdown app wizard" ], "topics": [ "cd_wizard_field_group" ] }, { "page": "cd_wizard_indicator_group", "title": "The indicator group the running app is for", "concept": [ "Countdown app wizard" ], "topics": [ "cd_wizard_indicator_group" ] }, { "page": "cd_wizard_national_rate_fields", "title": "The five national rate fields every indicator group needs", "concept": [ "Countdown app wizard" ], "topics": [ "cd_wizard_national_rate_fields" ] }, { "page": "cd_wizard_survey_field", "title": "Describe one field of the National Rates step", "concept": [ "Countdown app wizard" ], "topics": [ "cd_wizard_rate_field", "cd_wizard_survey_field" ] }, { "page": "cd_years_input", "title": "The years a years chip means", "concept": [ "Countdown app filters" ], "topics": [ "cd_years_input" ] }, { "page": "cd_years_sync", "title": "Keep a years chip in step with the dataset", "concept": [ "Countdown app filters" ], "topics": [ "cd_years_sync" ] }, { "page": "check_admin_columns", "title": "Check that the Admin sheet has its required columns", "topics": [ "check_admin_columns" ] }, { "page": "check_admin_pairing_consistency", "title": "Check that each district has one admin level 1 name in the Admin sheet", "topics": [ "check_admin_pairing_consistency" ] }, { "page": "check_country_recognized", "title": "Check that the country in the Admin sheet is recognized", "topics": [ "check_country_recognized" ] }, { "page": "check_district_consistency", "title": "Check that districts are consistent across the dataset", "topics": [ "check_district_consistency" ] }, { "page": "check_district_cross_sheet", "title": "Check that districts match between the Admin sheet and the others", "topics": [ "check_district_cross_sheet" ] }, { "page": "check_district_year_completeness", "title": "Check that every district has every year in the Population sheet", "topics": [ "check_district_year_completeness" ] }, { "page": "check_indicator_emptiness", "title": "Flag indicators that have no data", "topics": [ "check_indicator_emptiness" ] }, { "page": "check_indicator_emptiness_presheet", "title": "Flag indicators that have no data, before merging", "topics": [ "check_indicator_emptiness_presheet" ] }, { "page": "check_month_language_consistency", "title": "Flag months that are written in more than one way", "topics": [ "check_month_language_consistency" ] }, { "page": "check_month_presence", "title": "Check that every district-year has all 12 months", "topics": [ "check_month_presence" ] }, { "page": "check_month_presence_presheet", "title": "Check that every district-year has all 12 months, before merging", "topics": [ "check_month_presence_presheet" ] }, { "page": "check_month_validity", "title": "Check that every month value is a recognized month", "topics": [ "check_month_validity" ] }, { "page": "check_month_validity_presheet", "title": "Check that every month value is a recognized month, before merging", "topics": [ "check_month_validity_presheet" ] }, { "page": "check_population_service_collision", "title": "Flag district-years where service births equal population births", "topics": [ "check_population_service_collision" ] }, { "page": "check_population_service_collision_presheet", "title": "Flag service births that equal population births, before merging", "topics": [ "check_population_service_collision_presheet" ] }, { "page": "check_population_vs_births", "title": "Check that population live births are not below reported births", "topics": [ "check_population_vs_births" ] }, { "page": "check_required_columns_presheet", "title": "Check that the sheets have the columns an indicator group needs", "topics": [ "check_required_columns_presheet" ] }, { "page": "check_shapefile_admin_names", "title": "Flag admin level 1 names with no matching shapefile region", "topics": [ "check_shapefile_admin_names" ] }, { "page": "check_single_country", "title": "Check that the Admin sheet names one country", "topics": [ "check_single_country" ] }, { "page": "check_survey_admin_names", "title": "Flag admin level 1 names with no matching survey region", "topics": [ "check_survey_admin_names" ] }, { "page": "clean_error_message", "title": "Clean and validate error messages", "topics": [ "clean_error_message" ] }, { "page": "compute_indicator_numerator", "title": "Compute aggregated numerators for health indicators", "topics": [ "compute_indicator_numerator" ] }, { "page": "compute_service_utilization", "title": "Compute service utilization metrics", "topics": [ "compute_service_utilization" ] }, { "page": "compute_step_states", "title": "Work out the state of every Load Data wizard step", "concept": [ "Countdown app wizard" ], "topics": [ "compute_step_states" ] }, { "page": "consistency_check_ui", "title": "Consistency checks card", "concept": [ "Countdown app pages" ], "topics": [ "consistency_check_server", "consistency_check_ui" ] }, { "page": "consistency_pair_keys", "title": "Tab keys of the consistency check pairs", "concept": [ "Countdown app pages" ], "topics": [ "consistency_pair_keys" ] }, { "page": "consistency_pair_label", "title": "Tab label of a consistency check pair", "concept": [ "Countdown app pages" ], "topics": [ "consistency_pair_label" ] }, { "page": "countdown-pages", "title": "The Countdown pages, wizard, filters and app frame", "concept": [ "Countdown app frame" ], "topics": [ "countdown-pages" ] }, { "page": "coverage_trends_ui", "title": "Coverage trends by denominator card", "concept": [ "Countdown app pages" ], "topics": [ "coverage_trends_server", "coverage_trends_ui" ] }, { "page": "coverage_ui", "title": "Coverage charts for one geography", "concept": [ "Countdown app pages" ], "topics": [ "coverage_server", "coverage_ui" ] }, { "page": "create_mortality_ratios", "title": "Extract latest mortality ratios for UN comparison", "topics": [ "create_mortality_ratios" ] }, { "page": "create_mortality_summary", "title": "Create mortality summary object", "topics": [ "create_mortality_summary" ] }, { "page": "data_adjustment_ui", "title": "Data adjustment page", "concept": [ "Countdown app pages" ], "topics": [ "data_adjustment_server", "data_adjustment_ui" ] }, { "page": "data_completeness_ui", "title": "Data completeness page", "concept": [ "Countdown app pages" ], "topics": [ "data_completeness_server", "data_completeness_ui" ] }, { "page": "data_quality_ui", "title": "Data quality step of the Load Data wizard", "concept": [ "Countdown app wizard" ], "topics": [ "data_quality_server", "data_quality_ui" ] }, { "page": "den_indicators", "title": "Tabs of the denominator assessment chart", "concept": [ "Countdown app pages" ], "topics": [ "den_indicators" ] }, { "page": "denominator_assessment_ui", "title": "Denominator assessment page", "concept": [ "Countdown app pages" ], "topics": [ "denominator_assessment_server", "denominator_assessment_ui" ] }, { "page": "denominator_selection_ui", "title": "Denominator selection page", "concept": [ "Countdown app pages" ], "topics": [ "denominator_selection_server", "denominator_selection_ui" ] }, { "page": "detect_indicator_group", "title": "Auto-detect the best-matching indicator group from a vector of indicators", "topics": [ "detect_indicator_group" ] }, { "page": "equiplot", "title": "Create dot plots for equity analysis", "topics": [ "equiplot" ] }, { "page": "equiplot_area", "title": "A specialized dot plot for area of residence analysis", "topics": [ "equiplot_area" ] }, { "page": "equiplot_education", "title": "A specialized dot plot for maternal education analysis", "topics": [ "equiplot_education" ] }, { "page": "equiplot_wealth", "title": "A specialized dot plot for wealth quintile analysis", "topics": [ "equiplot_wealth" ] }, { "page": "equity_ui", "title": "Equity assessment page", "concept": [ "Countdown app pages" ], "topics": [ "equity_server", "equity_ui" ] }, { "page": "filter_high_performers", "title": "Filter high-performing areas by coverage", "topics": [ "filter_high_performers" ] }, { "page": "filter_out_years", "title": "Filter dataset by removing specified years", "topics": [ "filter_out_years" ] }, { "page": "generate_adjustment_values", "title": "Generate adjusted and unadjusted service counts by year", "topics": [ "generate_adjustment_values" ] }, { "page": "generate_admin1_keys", "title": "Generate a key for each admin level 1 unit", "topics": [ "generate_admin1_keys" ] }, { "page": "generate_admin1_mch_curative_index", "title": "Generate MCH vs curative index data", "topics": [ "generate_admin1_mch_curative_index" ] }, { "page": "generate_admin1_service_utilization", "title": "Generate service utilization admin level 1 data", "topics": [ "generate_admin1_service_utilization" ] }, { "page": "generate_bayes_model", "title": "Generate Bayesian coverage model object", "topics": [ "generate_bayes_model" ] }, { "page": "generate_coverage_data", "title": "Generate coverage data for continuum of care", "topics": [ "generate_coverage_data" ] }, { "page": "generate_fpet_summary", "title": "Load and generate FPET output", "topics": [ "generate_fpet_summary" ] }, { "page": "generate_health_system_table", "title": "Generate health system metrics data", "topics": [ "generate_health_system_table" ] }, { "page": "generate_phc_scatter_data", "title": "Generate PHC performance scatter data", "topics": [ "generate_phc_scatter_data" ] }, { "page": "generate_private_sector_data", "title": "Generate private sector ownership data", "topics": [ "generate_private_sector_data" ] }, { "page": "generate_service_dqa_summary", "title": "Generate service DQA summary", "topics": [ "generate_service_dqa_summary" ] }, { "page": "get_admin_columns", "title": "Determine grouping columns for administrative levels", "topics": [ "get_admin_columns" ] }, { "page": "get_all_indicators", "title": "Get All Indicators", "topics": [ "get_all_indicators" ] }, { "page": "get_analysis_indicators", "title": "Get Indicators excluding indicators without denominator", "topics": [ "get_analysis_indicators" ] }, { "page": "get_country_iso3", "title": "Get country ISO3 code", "topics": [ "get_country_iso3" ] }, { "page": "get_country_name", "title": "Get country name", "topics": [ "get_country_name" ] }, { "page": "get_country_shapefile", "title": "Load country shapefile for mapping", "topics": [ "get_country_shapefile" ] }, { "page": "get_coverage_indicators", "title": "Get Indicators for coverage calculation", "topics": [ "get_coverage_indicators" ] }, { "page": "get_excel_version", "title": "Format service utilization data for Excel export", "topics": [ "get_excel_version" ] }, { "page": "get_indicator_group_names", "title": "Get indicator group names", "topics": [ "get_indicator_group_names" ] }, { "page": "get_indicator_groups", "title": "Get the current indicator group definition", "topics": [ "get_indicator_groups" ] }, { "page": "get_mapping_data", "title": "Get mapping data for subnational coverage analysis", "topics": [ "get_mapping_data" ] }, { "page": "get_named_indicators", "title": "Get Named Indicator Vector", "topics": [ "get_named_indicators" ] }, { "page": "get_national_rates", "title": "Get the rates the denominators use from survey data", "topics": [ "get_national_rates" ] }, { "page": "get_plot_admin_column", "title": "Determine the administrative column to use for plotting", "topics": [ "get_plot_admin_column" ] }, { "page": "get_population_column", "title": "Get the population column for an indicator and denominator", "topics": [ "get_population_column" ] }, { "page": "get_selected_group", "title": "Get the globally selected indicator group", "topics": [ "get_selected_group" ] }, { "page": "inequality_ui", "title": "Sub-national inequality charts", "concept": [ "Countdown app pages" ], "topics": [ "inequality_server", "inequality_ui" ] }, { "page": "init_CacheConnection", "title": "Create a CacheConnection object", "topics": [ "init_CacheConnection" ] }, { "page": "internal_consistency_ui", "title": "Internal consistency page", "concept": [ "Countdown app pages" ], "topics": [ "internal_consistency_server", "internal_consistency_ui" ] }, { "page": "interpret", "title": "Generic interpretation method", "topics": [ "interpret" ] }, { "page": "interpret.cd_fpet_data", "title": "Interpret FPET results with emphasis on current estimates", "topics": [ "interpret.cd_fpet_data" ] }, { "page": "introduction_ui", "title": "Introduction page", "concept": [ "Countdown app pages" ], "topics": [ "introduction_server", "introduction_ui" ] }, { "page": "is_maternal_indicator", "title": "Detemine if an indicator is maternal indicator", "topics": [ "is_maternal_indicator" ] }, { "page": "list_indicator_groups", "title": "List available indicator group names", "topics": [ "list_indicator_groups" ] }, { "page": "list_missing_units", "title": "List the districts and months with a missing value", "topics": [ "list_missing_units" ] }, { "page": "list_outlier_units", "title": "Identify monthly outliers by district", "topics": [ "list_outlier_units" ] }, { "page": "list_tracer_vaccines", "title": "List tracer vaccines", "topics": [ "list_tracer_vaccines" ] }, { "page": "list_vaccine_indicators", "title": "List all vaccine and related coverage indicators", "topics": [ "list_vaccine_indicators" ] }, { "page": "load_cache_data", "title": "Initialize or load a cached Countdown 2030 connection", "topics": [ "load_cache_data" ] }, { "page": "load_csection_estimates", "title": "Load C-section share estimates", "topics": [ "load_csection_estimates" ] }, { "page": "load_data", "title": "Load Countdown 2030 data (Excel or Stata)", "topics": [ "load_data" ] }, { "page": "load_equity_data", "title": "Load and filter equity data", "topics": [ "load_equity_data" ] }, { "page": "load_excel_parts", "title": "Read and clean the sheets of a Countdown 2030 workbook", "topics": [ "load_excel_parts" ] }, { "page": "load_fpet_data", "title": "Load FPET data from CSV file or use provided data", "topics": [ "load_fpet_data" ] }, { "page": "load_private_sector_data", "title": "Load and prepare private sector data", "topics": [ "load_private_sector_data" ] }, { "page": "load_survey_data", "title": "Load and process survey data", "topics": [ "load_survey_data" ] }, { "page": "load_un_estimates", "title": "Load UN estimates", "topics": [ "load_un_estimates" ] }, { "page": "load_un_mortality_data", "title": "Load and filter UN mortality estimates", "topics": [ "load_un_mortality_data" ] }, { "page": "load_wuenic_data", "title": "Load WUENIC immunization data", "topics": [ "load_wuenic_data" ] }, { "page": "map_shapefile_ui", "title": "Map Shapefile Names step of the Load Data wizard", "concept": [ "Countdown app wizard" ], "topics": [ "map_shapefile_server", "map_shapefile_ui" ] }, { "page": "map_survey_ui", "title": "Map Survey Files step of the Load Data wizard", "concept": [ "Countdown app wizard" ], "topics": [ "map_survey_server", "map_survey_ui" ] }, { "page": "mapping_modal_ui", "title": "Dialog that matches the dataset's region names to another source", "concept": [ "Countdown app wizard" ], "topics": [ "mapping_modal_server", "mapping_modal_ui" ] }, { "page": "mapping_provenance_banner", "title": "Banner that says how a saved name mapping was matched", "concept": [ "Countdown app wizard" ], "topics": [ "mapping_provenance_banner" ] }, { "page": "merge_and_standardize", "title": "Merge and standardize sheets read by 'load_excel_parts()'", "topics": [ "merge_and_standardize" ] }, { "page": "national_coverage_ui", "title": "National coverage page", "concept": [ "Countdown app pages" ], "topics": [ "national_coverage_server", "national_coverage_ui" ] }, { "page": "national_inequality_ui", "title": "National inequality page", "concept": [ "Countdown app pages" ], "topics": [ "national_inequality_server", "national_inequality_ui" ] }, { "page": "national_rates_required_fields", "title": "The values the National Rates step requires", "concept": [ "Countdown app wizard" ], "topics": [ "national_rates_required_fields", "survey_estimates_required_fields" ] }, { "page": "national_rates_ui", "title": "National rates step of the Load Data wizard", "concept": [ "Countdown app wizard" ], "topics": [ "national_rates_server", "national_rates_ui" ] }, { "page": "national_target_ui", "title": "National coverage target page", "concept": [ "Countdown app pages" ], "topics": [ "national_target_server", "national_target_ui" ] }, { "page": "new_countdown", "title": "Create a 'cd_data' object from cleaned data and resolve the indicator group", "topics": [ "new_countdown" ] }, { "page": "notebook_data", "title": "Give DataSuite's notebooks a folder's Countdown datasets", "topics": [ "notebook_data" ] }, { "page": "nr_field", "title": "One number field of the wizard's forms", "concept": [ "Countdown app wizard" ], "topics": [ "nr_field" ] }, { "page": "nr_group", "title": "A titled group of fields in the wizard's forms", "concept": [ "Countdown app wizard" ], "topics": [ "nr_group" ] }, { "page": "outlier_detection_ui", "title": "Outlier detection page", "concept": [ "Countdown app pages" ], "topics": [ "outlier_detection_server", "outlier_detection_ui" ] }, { "page": "overall_score_ui", "title": "Overall score page", "concept": [ "Countdown app pages" ], "topics": [ "overall_score_server", "overall_score_ui" ] }, { "page": "internal_consistency", "title": "Internal consistency plot functions for indicator comparisons", "topics": [ "plot_comparison", "plot_comparison_anc1_penta1", "plot_comparison_opv1_opv3", "plot_comparison_penta1_penta3" ] }, { "page": "plot_comparison.cd_data", "title": "Plot comparison with linear fit and R-squared", "topics": [ "plot_comparison.cd_data" ] }, { "page": "plot_line_graph", "title": "Plot a line graph of several series", "topics": [ "plot_line_graph" ] }, { "page": "plot_mortality_plausibility", "title": "Plot subnational mortality plausibility", "topics": [ "plot_mortality_plausibility" ] }, { "page": "plot_national_health_metric", "title": "Plot national health system metrics", "topics": [ "plot_national_health_metric" ] }, { "page": "plot.cd_adjustment_values_filtered", "title": "Plot adjusted vs. unadjusted data for health indicators", "topics": [ "plot.cd_adjustment_values_filtered" ] }, { "page": "plot.cd_average_reporting_rate", "title": "Plot sub-national reporting rates by year and unit", "topics": [ "plot.cd_average_reporting_rate" ] }, { "page": "plot.cd_bayes_model", "title": "Plot S3 method for Bayesian coverage model", "topics": [ "plot.cd_bayes_model" ] }, { "page": "plot.cd_completeness_summary", "title": "Plot missing summary", "topics": [ "plot.cd_completeness_summary" ] }, { "page": "plot.cd_coverage", "title": "Plot coverage by region", "topics": [ "plot.cd_coverage" ] }, { "page": "plot.cd_coverage_filtered", "title": "Plot national coverage data", "topics": [ "plot.cd_coverage_filtered" ] }, { "page": "plot.cd_coverage_selected", "title": "Plot S3 method for coverage data", "topics": [ "plot.cd_coverage_selected" ] }, { "page": "plot.cd_derived_coverage", "title": "Plot derived vs traditional coverage over time", "topics": [ "plot.cd_derived_coverage" ] }, { "page": "plot.cd_district_reporting_rate", "title": "Plot district reporting rate summary", "topics": [ "plot.cd_district_reporting_rate" ] }, { "page": "plot.cd_fpet_data", "title": "Plot family planning estimation tool (FPET) data", "topics": [ "plot.cd_fpet_data" ] }, { "page": "plot.cd_health_system_comparison", "title": "Compare district vs admin level 1 health metrics", "topics": [ "plot.cd_health_system_comparison" ] }, { "page": "plot.cd_health_system_metric", "title": "Plot health metrics for admin level 1 units", "topics": [ "plot.cd_health_system_metric" ] }, { "page": "plot.cd_health_system_table", "title": "Plot S3 method for health system metrics", "topics": [ "plot.cd_health_system_table" ] }, { "page": "plot.cd_indicator_coverage", "title": "Plot national denominators and coverage indicators", "topics": [ "plot.cd_indicator_coverage" ] }, { "page": "plot.cd_inequality_filtered", "title": "Plot subnational health coverage analysis", "topics": [ "plot.cd_inequality_filtered" ] }, { "page": "plot.cd_mapping_filtered", "title": "Plot subnational coverage maps by indicator", "topics": [ "plot.cd_mapping_filtered" ] }, { "page": "plot.cd_mch_curative_index", "title": "Plot S3 method for MCH vs curative index", "topics": [ "plot.cd_mch_curative_index" ] }, { "page": "plot.cd_missing_district", "title": "Plot percent of districts with complete data", "topics": [ "plot.cd_missing_district" ] }, { "page": "plot.cd_mortality_ratio_summarised", "title": "Plot completeness of facility reporting ratios", "topics": [ "plot.cd_mortality_ratio_summarised" ] }, { "page": "plot.cd_mortality_summary", "title": "Plot mortality rate indicators", "topics": [ "plot.cd_mortality_summary" ] }, { "page": "plot.cd_mortality_summary_filtered", "title": "Plot filtered institutional mortality rates", "topics": [ "plot.cd_mortality_summary_filtered" ] }, { "page": "plot.cd_outlier", "title": "Visualize summary of outlier detection", "topics": [ "plot.cd_outlier" ] }, { "page": "plot.cd_outlier_list", "title": "Plot outlier time series for a region", "topics": [ "plot.cd_outlier_list" ] }, { "page": "plot.cd_overall_score", "title": "Plot S3 method for overall score", "topics": [ "plot.cd_overall_score" ] }, { "page": "plot.cd_phc_scatter", "title": "Plot S3 method for PHC performance scatter", "topics": [ "plot.cd_phc_scatter" ] }, { "page": "plot.cd_population_metrics", "title": "Plot national population or births metrics", "topics": [ "plot.cd_population_metrics" ] }, { "page": "plot.cd_private_sector", "title": "Plot S3 method for private sector ownership", "topics": [ "plot.cd_private_sector" ] }, { "page": "plot.cd_private_sector_plot_data", "title": "Plot private sector prevalence by sector and area/national level", "topics": [ "plot.cd_private_sector_plot_data" ] }, { "page": "plot.cd_ratios_summary", "title": "Plot ratios summary for indicator ratios summary object", "topics": [ "plot.cd_ratios_summary" ] }, { "page": "plot.cd_service_utilization_admin1", "title": "Plot S3 method for service utilization at admin level 1", "topics": [ "plot.cd_service_utilization_admin1" ] }, { "page": "plot.cd_service_utilization_filtered", "title": "Plot service utilization indicators", "topics": [ "plot.cd_service_utilization_filtered" ] }, { "page": "plot.cd_service_utilization_prepared", "title": "Plot filtered service utilization indicators", "topics": [ "plot.cd_service_utilization_prepared" ] }, { "page": "plot.cd_threshold", "title": "Plot target threshold attainment over time", "topics": [ "plot.cd_threshold" ] }, { "page": "plot.cd_utilization_dqa", "title": "Plot S3 method for service DQA summary", "topics": [ "plot.cd_utilization_dqa" ] }, { "page": "prepare_mapping_service_utlization", "title": "Filter and prepare service utilization data for mapping", "topics": [ "prepare_mapping_service_utlization" ] }, { "page": "prepare_population_metrics", "title": "Compute population metrics for DHIS-2 and UN data", "topics": [ "prepare_population_metrics" ] }, { "page": "prepare_private_sector_plot_data", "title": "Prepare private sector plot data", "topics": [ "prepare_private_sector_plot_data" ] }, { "page": "print.cd_data", "title": "Print method for 'cd_data' class", "topics": [ "print.cd_data" ] }, { "page": "push_upload_on_remount", "title": "Keep an upload zone showing the file the dataset already holds", "concept": [ "Countdown app wizard" ], "topics": [ "push_upload_on_remount" ] }, { "page": "quality_issues_table", "title": "Tabulate data quality results", "topics": [ "quality_issues_table" ] }, { "page": "read_shapefile_folder", "title": "Read a user-uploaded shapefile folder", "topics": [ "read_shapefile_folder" ] }, { "page": "reference_estimates_ui", "title": "Reference-data uploads of the wizard's Upload Data step", "concept": [ "Countdown app wizard" ], "topics": [ "reference_estimates_server", "reference_estimates_ui" ] }, { "page": "register_indicator_group", "title": "Register or override an indicator group (profile)", "topics": [ "register_indicator_group" ] }, { "page": "report_block_kinds", "title": "The charts and tables a report can contain", "topics": [ "report_block_kinds" ] }, { "page": "report_presets", "title": "The standard reports", "topics": [ "report_presets" ] }, { "page": "reporting_rate_ui", "title": "Reporting rate page", "concept": [ "Countdown app pages" ], "topics": [ "reporting_rate_server", "reporting_rate_ui" ] }, { "page": "reset_indicator_group", "title": "Reset (remove) a group override", "topics": [ "reset_indicator_group" ] }, { "page": "resolve_country_best_effort", "title": "Find the country of an Admin sheet without raising an error", "topics": [ "resolve_country_best_effort" ] }, { "page": "restore_default_control", "title": "A link that clears something the user set in the dataset", "concept": [ "Countdown app wizard" ], "topics": [ "restore_default_control" ] }, { "page": "robust_max", "title": "Robust maximum value calculation", "topics": [ "robust_max" ] }, { "page": "rr_indicators", "title": "Tabs of the reporting rate chart", "concept": [ "Countdown app pages" ], "topics": [ "rr_indicators" ] }, { "page": "run_all_quality_checks", "title": "Run all data quality checks and report every result", "topics": [ "run_all_quality_checks" ] }, { "page": "save_data", "title": "Save processed Countdown 2030 data to file", "topics": [ "save_data" ] }, { "page": "save_dhis2_excel", "title": "Save DHIS2 data to an Excel workbook", "topics": [ "save_dhis2_excel" ] }, { "page": "save_dhis2_master_data", "title": "Create a master dataset from DHIS2 data", "topics": [ "save_dhis2_master_data" ] }, { "page": "select_adjustment_value", "title": "Select one indicator's adjustment values", "topics": [ "select_adjustment_value" ] }, { "page": "select_coverage", "title": "Select one indicator's coverage", "topics": [ "select_coverage" ] }, { "page": "select_inequality", "title": "Select one indicator's inequality metrics", "topics": [ "select_inequality" ] }, { "page": "select_mapping_data", "title": "Select one indicator's mapping data", "topics": [ "select_mapping_data" ] }, { "page": "select_mortality_summary", "title": "Select one mortality rate, ready to map", "topics": [ "select_mortality_summary" ] }, { "page": "select_service_utilization", "title": "Select one service utilization indicator", "topics": [ "select_service_utilization" ] }, { "page": "set_selected_group", "title": "Set the selected indicator group globally", "topics": [ "set_selected_group" ] }, { "page": "shapefile_step_ui", "title": "Shapefile step of the Load Data wizard", "concept": [ "Countdown app wizard" ], "topics": [ "shapefile_step_server", "shapefile_step_ui" ] }, { "page": "slim_bayes_model", "title": "A Bayesian model without the sampler's draws and the compiled Stan model", "topics": [ "slim_bayes_model" ] }, { "page": "step_upload_complete", "title": "Tests of whether a Load Data wizard step is complete", "concept": [ "Countdown app wizard" ], "topics": [ "step_map_mapping_complete", "step_national_rates_complete", "step_quality_complete", "step_shapefile_complete", "step_shapefile_touched", "step_survey_files_complete", "step_survey_mapping_complete", "step_upload_complete" ] }, { "page": "subnational_coverage_ui", "title": "Sub-national coverage page", "concept": [ "Countdown app pages" ], "topics": [ "subnational_coverage_server", "subnational_coverage_ui" ] }, { "page": "subnational_denominator_ui", "title": "Sub-national coverage by denominator card", "concept": [ "Countdown app pages" ], "topics": [ "subnational_denominator_server", "subnational_denominator_ui" ] }, { "page": "subnational_inequality_ui", "title": "Sub-national inequality page", "concept": [ "Countdown app pages" ], "topics": [ "subnational_inequality_server", "subnational_inequality_ui" ] }, { "page": "subnational_mapping_ui", "title": "Sub-national coverage maps", "concept": [ "Countdown app pages" ], "topics": [ "subnational_mapping_server", "subnational_mapping_ui" ] }, { "page": "subnational_target_ui", "title": "Sub-national coverage target page", "concept": [ "Countdown app pages" ], "topics": [ "subnational_target_server", "subnational_target_ui" ] }, { "page": "summarise_completeness_ratio", "title": "Summarize completeness-adjusted mortality ratio", "topics": [ "summarise_completeness_ratio" ] }, { "page": "survey_comparison_ui", "title": "Coverage against the survey card", "concept": [ "Countdown app pages" ], "topics": [ "survey_comparison_server", "survey_comparison_ui" ] }, { "page": "survey_fields", "title": "The dataset fields of the five survey files", "concept": [ "Countdown app wizard" ], "topics": [ "survey_fields" ] }, { "page": "survey_upload_ui", "title": "Survey files step of the Load Data wizard", "concept": [ "Countdown app wizard" ], "topics": [ "survey_upload_server", "survey_upload_ui" ] }, { "page": "target_ui", "title": "Coverage target charts and table", "concept": [ "Countdown app pages" ], "topics": [ "target_server", "target_ui" ] }, { "page": "tbl_sum.cd_adjustment_values", "title": "Summary for 'cd_adjustment_values' Objects", "topics": [ "tbl_sum.cd_adjustment_values" ] }, { "page": "tbl_sum.cd_average_reporting_rate", "title": "Summary for average reporting rates by year", "topics": [ "tbl_sum.cd_average_reporting_rate" ] }, { "page": "tbl_sum.cd_completeness_summary", "title": "Summary for 'cd_completeness_summary'", "topics": [ "tbl_sum.cd_completeness_summary" ] }, { "page": "tbl_sum.cd_district_outliers_summary", "title": "Summary for 'cd_district_outliers_summary'", "topics": [ "tbl_sum.cd_district_outliers_summary" ] }, { "page": "tbl_sum.cd_district_ratios_summary", "title": "Summary for 'cd_district_ratios_summary' Object", "topics": [ "tbl_sum.cd_district_ratios_summary" ] }, { "page": "tbl_sum.cd_district_reporting_rate", "title": "Summary for district-level reporting rates by year", "topics": [ "tbl_sum.cd_district_reporting_rate" ] }, { "page": "tbl_sum.cd_indicator_coverage", "title": "Table summary for national coverage estimates", "topics": [ "tbl_sum.cd_indicator_coverage" ] }, { "page": "tbl_sum.cd_missing_district", "title": "Summary for 'cd_missing_district'", "topics": [ "tbl_sum.cd_missing_district" ] }, { "page": "tbl_sum.cd_outlier", "title": "Summary for 'cd_outlier'", "topics": [ "tbl_sum.cd_outlier" ] }, { "page": "tbl_sum.cd_population_metrics", "title": "Summary for 'cd_population_metrics'", "topics": [ "tbl_sum.cd_population_metrics" ] }, { "page": "tbl_sum.cd_ratios_summary", "title": "Summary for 'cd_ratios_summary' Object", "topics": [ "tbl_sum.cd_ratios_summary" ] }, { "page": "upload_box_ui", "title": "Main dataset upload of the Load Data wizard", "concept": [ "Countdown app wizard" ], "topics": [ "upload_box_server", "upload_box_ui" ] }, { 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"rstudioapi", "s2", "S7", "sass", "scales", "sf", "shiny", "shiny.i18n", "shiny.react", "sourcetools", "stringdist", "stringi", "stringr", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "timechange", "tinytex", "tzdb", "units", "utf8", "uuid", "vctrs", "viridisLite", "vroom", "withr", "wk", "xfun", "xml2", "xtable", "yaml", "zip" ], "_vignettes": [ { "source": "building-an-app.Rmd", "filename": "building-an-app.html", "title": "Building an app on cd2030.core", "engine": "knitr::rmarkdown", "headings": [ "How the packages fit", "The parts of an app", "1. 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