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show_target("vig_arch_tar_visnetwork")Interactive dependency graph of the full targets pipeline. Nodes represent targets; edges show dependencies. Hover for details, drag to rearrange.
This page shows how the micromort package is organized: the data pipeline, function hierarchy, user entry points, and development workflow. All diagrams are auto-generated from package metadata via the targets pipeline.
1. Data Pipeline
The targets pipeline processes risk data through five stages. Target counts update automatically when plan files change.
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emit_mermaid("vig_arch_pipeline_diagram",
"Pipeline diagram",
caption = "Figure 1: Data pipeline showing five processing stages from raw risk data through targets to vignette outputs.",
alt_text = "Mermaid flowchart showing the five-stage targets data pipeline: raw data ingestion, cleaning, aggregation, modelling, and vignette export.")2. Function Hierarchy
All exported functions grouped by category. Click any function to view its documentation.
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emit_mermaid("vig_arch_concept_diagram",
"Concept diagram",
caption = "Figure 2: Exported functions grouped by category — risk data, conversion utilities, regional analysis, visualisation, and quiz.",
alt_text = "Mermaid diagram showing all exported functions organised into five categories with links to their documentation pages.")3. User Journey
Which function should you start with? Follow the decision tree below.
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emit_mermaid("vig_arch_user_journey_diagram",
"User journey diagram",
caption = "Figure 3: Decision tree guiding users from their question (compare risks, explore regions, convert units) to the appropriate function.",
alt_text = "Mermaid decision tree flowchart with three entry points — compare risks, explore regions, convert units — leading to specific package functions.")4. Developer Workflow
The 9-step workflow for contributing to this package. Steps 4–5 follow the RED-GREEN TDD cycle.
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emit_mermaid("vig_arch_developer_diagram",
"Developer diagram",
caption = "Figure 4: Nine-step contributor workflow from issue creation through TDD (steps 4–5), documentation, CI checks, and PR merge.",
alt_text = "Mermaid flowchart showing a nine-step development workflow: issue, branch, plan, RED test, GREEN implementation, refactor, document, check, and PR.")5. Targets DAG
Auto-generated dependency graph of the full targets pipeline.
Pipeline Telemetry
Dependency Graph
%%{init: {‘theme’: ‘dark’, ‘themeVariables’: {‘primaryColor’: ‘#999999’, ‘primaryTextColor’: ‘#000000’, ‘primaryBorderColor’: ‘#CC0000’, ‘lineColor’: ‘#CC0000’, ‘secondaryColor’: ‘#999999’, ‘tertiaryColor’: ‘#999999’, ‘background’: ‘#000000’, ‘mainBkg’: ‘#999999’, ‘nodeBorder’: ‘#CC0000’, ‘clusterBkg’: ‘#333333’, ‘clusterBorder’: ‘#CC0000’, ‘titleColor’: ‘#000000’, ‘edgeLabelBackground’: ‘#999999’}}}%% graph LR acute_risks_merged –> pipeline_log acute_risks_merged –> dataset_summary acute_risks_merged –> export_acute chronic_risks_merged –> pipeline_log chronic_risks_merged –> export_chronic chronic_risks_merged –> dataset_summary export_acute –> export_validation export_acute –> pipeline_log export_chronic –> export_validation export_chronic –> pipeline_log export_sources –> export_validation export_sources –> pipeline_log leaderboard_raw –> leaderboard_stats_json leaderboard_stats_json –> site_verify parsed_acute_base –> acute_risks_merged parsed_chronic_base –> chronic_risks_merged parsed_sources –> risk_sources_merged pkgctx_audit –> pkgctx_sync pkgdown_build –> pkgdown_staged pkgdown_inputs –> pkgdown_build project_dirs_hash –> project_tree project_tree –> project_tree_formatted qa_coverage –> qa_quality_gate qa_no_raw_sql –> qa_quality_gate qa_self_review –> qa_quality_gate qa_test_results –> qa_quality_gate qa_vignette_compliance –> qa_quality_gate risk_sources_merged –> pipeline_log risk_sources_merged –> export_sources risk_sources_merged –> dataset_summary site_chronic_shinylive –> site_deploy_shinylive site_closeread –> site_verify site_deploy_shinylive –> site_verify site_document –> site_pkgdown site_pkgdown –> site_closeread site_pkgdown –> site_chronic_shinylive site_pkgdown –> site_quiz_shinylive site_pkgdown –> site_ranking_shinylive site_quiz_csv_export –> site_pkgdown site_quiz_shinylive –> site_deploy_shinylive site_ranking_shinylive –> site_deploy_shinylive site_rds_export –> site_pkgdown site_readme –> site_pkgdown site_source_hash –> site_document site_source_hash –> site_pkgdown src_acute_base –> parsed_acute_base src_chronic_base –> parsed_chronic_base src_covid_vaccine –> parsed_covid src_demographic –> parsed_demographic src_risk_sources –> parsed_sources vig_chronic_acute_country_shift –> vig_chronic_acute_country_display vig_chronic_acute_equivalences –> vig_chronic_acute_heroin_table vig_chronic_acute_waterfall –> vig_chronic_acute_waterfall_chronic vig_chronic_acute_waterfall –> vig_chronic_acute_waterfall_acute vig_chronic_csv_check –> qa_chronic_csv_gate vig_chronic_pairs –> vig_chronic_quiz_json_script vig_chronic_pairs –> vig_chronic_csv_check vig_equiv_everyday –> vig_equiv_everyday_chart vig_equiv_flight_duration –> vig_equiv_hedgeable_chart vig_equiv_flight_duration –> vig_equiv_flight_duration_chart vig_equiv_medical_focus –> vig_equiv_medical_exchange_chart vig_pipeline_summary –> vig_telemetry_top_by_time vig_pipeline_summary –> vig_telemetry_top_by_size vig_quiz_pairs –> vig_quiz_json_script vig_quiz_pairs –> vig_quiz_csv_check vig_quiz_pairs –> site_quiz_csv_export vig_radiation_timeline_data –> vig_equiv_radiation_timeline_chart vig_ranking_questions –> vig_ranking_csv_check vig_ranking_questions –> vig_ranking_quiz_json_script vig_regional_le_gap –> vig_regional_le_gap_text
Plans and Targets
Top 5 Targets by Storage Size
Top 5 Targets by Compute Time
Commit Velocity
Weekly commit frequency over the last 26 weeks. Each bar represents commits merged in a calendar week. Source: gert::git_log().
Issues and Pull Requests
Codebase Metrics
Reproducibility
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sessionInfo()
R version 4.5.2 (2025-10-31)
Platform: aarch64-apple-darwin24.6.0
Running under: macOS Tahoe 26.5.2
Matrix products: default
BLAS: /nix/store/gf17x1bj3m732n39jznn6kz69szbr5rb-blas-3/lib/libblas.dylib
LAPACK: /nix/store/5kg4z5bffhr8nry8bl8l5wlxvpy54dm2-openblas-0.3.30/lib/libopenblasp-r0.3.30.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Belfast
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] micromort_0.2.0 testthat_3.3.1
loaded via a namespace (and not attached):
[1] gtable_0.3.6 bslib_0.9.0 xfun_0.55 ggplot2_4.0.1
[5] htmlwidgets_1.6.4 visNetwork_2.1.4 processx_3.8.6 callr_3.7.6
[9] crosstalk_1.2.2 vctrs_0.6.5 tools_4.5.2 ps_1.9.1
[13] generics_0.1.4 base64url_1.4 tibble_3.3.0 pkgconfig_2.0.3
[17] data.table_1.18.0 checkmate_2.3.3 secretbase_1.0.5 RColorBrewer_1.1-3
[21] S7_0.2.1 desc_1.4.3 assertthat_0.2.1 lifecycle_1.0.4
[25] compiler_4.5.2 farver_2.1.2 credentials_2.0.3 brio_1.1.5
[29] codetools_0.2-20 sass_0.4.10 htmltools_0.5.9 sys_3.4.3
[33] usethis_3.2.1 yaml_2.3.12 jquerylib_0.1.4 pillar_1.11.1
[37] DT_0.34.0 openssl_2.3.4 cachem_1.1.0 tidyselect_1.2.1
[41] digest_0.6.39 dplyr_1.1.4 purrr_1.2.0 arrow_22.0.0
[45] rprojroot_2.1.1 fastmap_1.2.0 grid_4.5.2 cli_3.6.5
[49] magrittr_2.0.4 pkgbuild_1.4.8 withr_3.0.2 prettyunits_1.2.0
[53] scales_1.4.0 backports_1.5.0 bit64_4.6.0-1 rmarkdown_2.30
[57] igraph_2.2.1 bit_4.6.0 otel_0.2.0 askpass_1.2.1
[61] evaluate_1.0.5 knitr_1.51 rlang_1.1.6 gert_2.2.0
[65] Rcpp_1.1.0 glue_1.8.0 pkgload_1.4.1 jsonlite_2.0.0
[69] R6_2.6.1 targets_1.11.4 fs_1.6.6 units_1.0-0