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vis <- safe_tar_read("vig_arch_tar_visnetwork")
if (!is.null(vis)) visThis 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.
Show code
emit_mermaid("vig_arch_pipeline_diagram",
"Pipeline diagram not available. Run `targets::tar_make()` first.",
caption = "Figure 1: Data pipeline stages from raw Eurostat/CDC data through cleaning, decomposition, aggregation, and vignette output targets.",
alt_text = "Mermaid flowchart showing five pipeline stages: ingest, clean, decompose, aggregate, and vignette outputs, with target counts at each stage.")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 not available. Run `targets::tar_make()` first.",
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.
Show code
emit_mermaid("vig_arch_user_journey_diagram",
"User journey diagram not available. Run `targets::tar_make()` first.",
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.
Show code
emit_mermaid("vig_arch_developer_diagram",
"Developer diagram not available. Run `targets::tar_make()` first.",
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.
Reproducibility
Show code
sessionInfo()
#> R version 4.5.2 (2025-10-31)
#> Platform: aarch64-apple-darwin25.2.0
#> Running under: macOS Tahoe 26.3.1
#>
#> Matrix products: default
#> BLAS: /nix/store/ab8sq4g14lg45192ykfqcklgw6fvaswh-blas-3/lib/libblas.dylib
#> LAPACK: /nix/store/ssl6kfm7w37gz5pn57jn2x7xzw3bss24-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_0.1.0 testthat_3.3.2
#>
#> loaded via a namespace (and not attached):
#> [1] generics_0.1.4 digest_0.6.39 magrittr_2.0.4
#> [4] evaluate_1.0.5 grid_4.5.2 RColorBrewer_1.1-3
#> [7] pkgload_1.4.1 fastmap_1.2.0 rprojroot_2.1.1
#> [10] jsonlite_2.0.0 processx_3.8.6 pkgbuild_1.4.8
#> [13] backports_1.5.0 brio_1.1.5 secretbase_1.1.1
#> [16] ps_1.9.1 purrr_1.2.1 scales_1.4.0
#> [19] codetools_0.2-20 cli_3.6.5 rlang_1.1.7
#> [22] bit64_4.6.0-1 withr_3.0.2 yaml_2.3.12
#> [25] otel_0.2.0 tools_4.5.2 checkmate_2.3.3
#> [28] dplyr_1.1.4 ggplot2_4.0.1 base64url_1.4
#> [31] credentials_2.0.3 assertthat_0.2.1 vctrs_0.7.1
#> [34] R6_2.6.1 lifecycle_1.0.5 fs_1.6.6
#> [37] bit_4.6.0 usethis_3.2.1 targets_1.11.4
#> [40] arrow_22.0.0 callr_3.7.6 pkgconfig_2.0.3
#> [43] desc_1.4.3 pillar_1.11.1 gtable_0.3.6
#> [46] data.table_1.18.2.1 glue_1.8.0 gert_2.3.1
#> [49] xfun_0.56 tibble_3.3.1 tidyselect_1.2.1
#> [52] sys_3.4.3 knitr_1.51 farver_2.1.2
#> [55] igraph_2.2.1 htmltools_0.5.9 rmarkdown_2.30
#> [58] compiler_4.5.2 prettyunits_1.2.0 S7_0.2.1
#> [61] askpass_1.2.1 openssl_2.3.4