This vignette tracks the health and evolution of the micromort pipeline, codebase, and GitHub activity. All data is pre-computed via targets — zero inline computation.
1. Pipeline Metrics
Dependency Graph
Show code
dep_graph <- safe_tar_read("vig_pipeline_dependency_graph")
if (!is.null(dep_graph)) {
# Render mermaid via htmltools
htmltools::HTML(paste0(
'<script src="https://cdn.jsdelivr.net/npm/mermaid@11/dist/mermaid.min.js"></script>',
'<script>mermaid.initialize({startOnLoad: true, securityLevel: "loose", theme: "dark"});</script>',
'<div class="mermaid" style="background-color: #000000; padding: 1em;">\n', dep_graph, '\n</div>'
))
} else {
htmltools::p("Dependency graph not available. Run tar_make() first.")
}
Dependency graph not available. Run tar_make() first.
Target dependency graph showing data flow across the micromort pipeline. Nodes represent individual targets; edges show upstream dependencies. The graph spans data acquisition, normalization, export, logging, documentation, telemetry, and vignette output stages. Built from targets::tar_network() edges. See the introduction vignette for a conceptual overview of the pipeline architecture.
Plans and Targets
Show code
summary <- safe_tar_read("vig_pipeline_summary")
if (!is.null(summary)) {
summary$plans |>
DT::datatable(
caption = paste0(
"Target counts by plan file (",
summary$total_targets, " total targets)"
),
options = list(pageLength = 10, dom = "t"),
rownames = FALSE
)
}
Top 5 Targets by Storage Size
Top 5 Targets by Compute Time
2. GitHub Activity
Commit Velocity
Show code
velocity <- safe_tar_read("vig_commit_velocity")
if (!is.null(velocity)) {
ggplot2::ggplot(velocity, ggplot2::aes(x = week, y = commits)) +
ggplot2::geom_col(fill = "#1976D2") +
ggplot2::labs(
title = "Commit Velocity",
subtitle = "Last 26 weeks",
x = "Week",
y = "Commits"
) +
ggplot2::theme_minimal() +
ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1))
}
Issues and Pull Requests
Show code
activity <- safe_tar_read("vig_github_activity")
if (!is.null(activity)) {
activity |>
DT::datatable(
caption = "GitHub issues and pull requests summary",
options = list(pageLength = 5, dom = "t"),
rownames = FALSE
)
}
3. Project Structure
Show code
metrics <- safe_tar_read("vig_codebase_metrics")
if (!is.null(metrics)) {
metrics |>
DT::datatable(
caption = "Codebase metrics snapshot",
options = list(pageLength = 10, dom = "t"),
rownames = FALSE
)
}
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] DT_0.34.0 targets_1.11.4 micromort_0.1.0 testthat_3.3.2
#>
#> loaded via a namespace (and not attached):
#> [1] gtable_0.3.6 xfun_0.56 bslib_0.10.0
#> [4] ggplot2_4.0.1 htmlwidgets_1.6.4 processx_3.8.6
#> [7] callr_3.7.6 vctrs_0.7.1 tools_4.5.2
#> [10] crosstalk_1.2.2 ps_1.9.1 generics_0.1.4
#> [13] base64url_1.4 tibble_3.3.1 pkgconfig_2.0.3
#> [16] data.table_1.18.2.1 checkmate_2.3.3 secretbase_1.1.1
#> [19] RColorBrewer_1.1-3 S7_0.2.1 desc_1.4.3
#> [22] assertthat_0.2.1 lifecycle_1.0.5 compiler_4.5.2
#> [25] farver_2.1.2 credentials_2.0.3 brio_1.1.5
#> [28] codetools_0.2-20 sass_0.4.10 htmltools_0.5.9
#> [31] sys_3.4.3 usethis_3.2.1 yaml_2.3.12
#> [34] jquerylib_0.1.4 pillar_1.11.1 openssl_2.3.4
#> [37] cachem_1.1.0 tidyselect_1.2.1 digest_0.6.39
#> [40] dplyr_1.1.4 purrr_1.2.1 labeling_0.4.3
#> [43] arrow_22.0.0 rprojroot_2.1.1 fastmap_1.2.0
#> [46] grid_4.5.2 cli_3.6.5 magrittr_2.0.4
#> [49] pkgbuild_1.4.8 withr_3.0.2 prettyunits_1.2.0
#> [52] scales_1.4.0 backports_1.5.0 bit64_4.6.0-1
#> [55] rmarkdown_2.30 igraph_2.2.1 bit_4.6.0
#> [58] otel_0.2.0 askpass_1.2.1 evaluate_1.0.5
#> [61] knitr_1.51 rlang_1.1.7 gert_2.3.1
#> [64] glue_1.8.0 pkgload_1.4.1 jsonlite_2.0.0
#> [67] R6_2.6.1 fs_1.6.6
