From 236a3617b2baec7904064c9e278c71cde422d3e3 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 5 Sep 2026 02:05:09 +0000 Subject: [PATCH 1/8] Initial plan From 13f225fba20573be9ffe9b113b7a666cd9bcb386 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 5 Sep 2026 02:06:27 +0000 Subject: [PATCH 2/8] docs: replace absolute internal links with relative paths Co-authored-by: ilarsf <15234718+ilarsf@users.noreply.github.com> --- CONTRIBUTING.md | 2 +- README.md | 18 +++++++++--------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 3a87e16..875c8af 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -5,7 +5,7 @@ Update deterministic tests and documentation when model behavior or result fields change. Use the installation and dependency commands in the -[README](https://github.com/FritscheLab/phewasFlow#development), reinstall the +[README](README.md#development), reinstall the current source so parallel workers use it, then run: ```r diff --git a/README.md b/README.md index 9902984..c47ebbf 100644 --- a/README.md +++ b/README.md @@ -32,7 +32,7 @@ phewasflow --help ``` The R functions work without adding the command-line wrapper to `PATH`. -For an optional conda environment using [environment.yml](https://github.com/FritscheLab/phewasFlow/blob/main/environment.yml): +For an optional conda environment using [environment.yml](environment.yml): ```bash mamba env create --file environment.yml @@ -118,7 +118,7 @@ Phenotypes should already implement the intended observation window, case/control definition, and exclusions; `phewasFlow` fits models but does not derive phenotypes from raw clinical codes. -The [real-data workflow](https://fritschelab.github.io/phewasFlow/articles/real-data-workflow.html) gives the complete +The [real-data workflow](vignettes/real-data-workflow.Rmd) gives the complete participant-table and metadata requirements with working examples. ## Validate and run @@ -135,7 +135,7 @@ For a modest analysis, the generated runner performs every stage: Rscript run-local.R analysis-forward.yml ``` -For larger scans, use the [SLURM templates](https://github.com/FritscheLab/phewasFlow/tree/main/inst/examples/slurm) after +For larger scans, use the [SLURM templates](inst/examples/slurm/) after the same analysis succeeds locally on a representative phenotype set. ## Review the results @@ -164,11 +164,11 @@ count, or package version changes. ## Learn more -- [Run a PheWAS with your data](https://fritschelab.github.io/phewasFlow/articles/real-data-workflow.html) -- [PheWAS in both directions](https://fritschelab.github.io/phewasFlow/articles/two-directions.html) -- [Comparisons and plots](https://fritschelab.github.io/phewasFlow/articles/comparisons-and-plots.html) -- [Scale a successful PheWAS](https://fritschelab.github.io/phewasFlow/articles/large-runs.html) -- [Run a sharded PheWAS with SLURM](https://github.com/FritscheLab/phewasFlow/tree/main/inst/examples/slurm) +- [Run a PheWAS with your data](vignettes/real-data-workflow.Rmd) +- [PheWAS in both directions](vignettes/two-directions.Rmd) +- [Comparisons and plots](vignettes/comparisons-and-plots.Rmd) +- [Scale a successful PheWAS](vignettes/large-runs.Rmd) +- [Run a sharded PheWAS with SLURM](inst/examples/slurm/) ## Development @@ -192,7 +192,7 @@ documentation build and release procedure. ## Support Maintained by Lars Fritsche. Report reproducible problems through -[GitHub issues](https://github.com/FritscheLab/phewasFlow/issues), using synthetic +[GitHub issues](issues), using synthetic examples and sanitized logs. Keep participant data, credentials, and local analysis configuration outside this repository. Even aggregate results and provenance files require review before sharing. From eb2e77b4d26cc86163bf554e91f0d2e8f230d1b5 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 5 Sep 2026 02:07:05 +0000 Subject: [PATCH 3/8] docs: clarify relative links point to vignette sources Co-authored-by: ilarsf <15234718+ilarsf@users.noreply.github.com> --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index c47ebbf..f898814 100644 --- a/README.md +++ b/README.md @@ -118,7 +118,7 @@ Phenotypes should already implement the intended observation window, case/control definition, and exclusions; `phewasFlow` fits models but does not derive phenotypes from raw clinical codes. -The [real-data workflow](vignettes/real-data-workflow.Rmd) gives the complete +The [real-data workflow vignette source](vignettes/real-data-workflow.Rmd) gives the complete participant-table and metadata requirements with working examples. ## Validate and run @@ -164,10 +164,10 @@ count, or package version changes. ## Learn more -- [Run a PheWAS with your data](vignettes/real-data-workflow.Rmd) -- [PheWAS in both directions](vignettes/two-directions.Rmd) -- [Comparisons and plots](vignettes/comparisons-and-plots.Rmd) -- [Scale a successful PheWAS](vignettes/large-runs.Rmd) +- [Run a PheWAS with your data (vignette source)](vignettes/real-data-workflow.Rmd) +- [PheWAS in both directions (vignette source)](vignettes/two-directions.Rmd) +- [Comparisons and plots (vignette source)](vignettes/comparisons-and-plots.Rmd) +- [Scale a successful PheWAS (vignette source)](vignettes/large-runs.Rmd) - [Run a sharded PheWAS with SLURM](inst/examples/slurm/) ## Development From ed418aabee81746a3fb6a3c19c681423e1f12dcb Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 5 Sep 2026 02:07:34 +0000 Subject: [PATCH 4/8] docs: link README guides to relative rendered articles Co-authored-by: ilarsf <15234718+ilarsf@users.noreply.github.com> --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index f898814..2c34e19 100644 --- a/README.md +++ b/README.md @@ -118,7 +118,7 @@ Phenotypes should already implement the intended observation window, case/control definition, and exclusions; `phewasFlow` fits models but does not derive phenotypes from raw clinical codes. -The [real-data workflow vignette source](vignettes/real-data-workflow.Rmd) gives the complete +The [real-data workflow](articles/real-data-workflow.html) gives the complete participant-table and metadata requirements with working examples. ## Validate and run @@ -164,10 +164,10 @@ count, or package version changes. ## Learn more -- [Run a PheWAS with your data (vignette source)](vignettes/real-data-workflow.Rmd) -- [PheWAS in both directions (vignette source)](vignettes/two-directions.Rmd) -- [Comparisons and plots (vignette source)](vignettes/comparisons-and-plots.Rmd) -- [Scale a successful PheWAS (vignette source)](vignettes/large-runs.Rmd) +- [Run a PheWAS with your data](articles/real-data-workflow.html) +- [PheWAS in both directions](articles/two-directions.html) +- [Comparisons and plots](articles/comparisons-and-plots.html) +- [Scale a successful PheWAS](articles/large-runs.html) - [Run a sharded PheWAS with SLURM](inst/examples/slurm/) ## Development @@ -192,7 +192,7 @@ documentation build and release procedure. ## Support Maintained by Lars Fritsche. Report reproducible problems through -[GitHub issues](issues), using synthetic +[GitHub issues](https://github.com/FritscheLab/phewasFlow/issues), using synthetic examples and sanitized logs. Keep participant data, credentials, and local analysis configuration outside this repository. Even aggregate results and provenance files require review before sharing. From 812dea4568fd8d09165177fb2506c32b03f80fa5 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 5 Sep 2026 02:08:09 +0000 Subject: [PATCH 5/8] docs: use checked-in relative links in learn-more section Co-authored-by: ilarsf <15234718+ilarsf@users.noreply.github.com> --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 2c34e19..e7fbda5 100644 --- a/README.md +++ b/README.md @@ -164,10 +164,10 @@ count, or package version changes. ## Learn more -- [Run a PheWAS with your data](articles/real-data-workflow.html) -- [PheWAS in both directions](articles/two-directions.html) -- [Comparisons and plots](articles/comparisons-and-plots.html) -- [Scale a successful PheWAS](articles/large-runs.html) +- [Run a PheWAS with your data (vignette source)](vignettes/real-data-workflow.Rmd) +- [PheWAS in both directions (vignette source)](vignettes/two-directions.Rmd) +- [Comparisons and plots (vignette source)](vignettes/comparisons-and-plots.Rmd) +- [Scale a successful PheWAS (vignette source)](vignettes/large-runs.Rmd) - [Run a sharded PheWAS with SLURM](inst/examples/slurm/) ## Development From 482e8dd65a6ab82b5cc3f41611f701e2510997e5 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 5 Sep 2026 02:08:56 +0000 Subject: [PATCH 6/8] docs: finalize relative internal links to repository sources Co-authored-by: ilarsf <15234718+ilarsf@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e7fbda5..a955061 100644 --- a/README.md +++ b/README.md @@ -118,7 +118,7 @@ Phenotypes should already implement the intended observation window, case/control definition, and exclusions; `phewasFlow` fits models but does not derive phenotypes from raw clinical codes. -The [real-data workflow](articles/real-data-workflow.html) gives the complete +The [real-data workflow vignette source](vignettes/real-data-workflow.Rmd) gives the complete participant-table and metadata requirements with working examples. ## Validate and run From 2a0b28613ce721586798fbb31500e572205df259 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 5 Sep 2026 02:09:24 +0000 Subject: [PATCH 7/8] docs: clarify README links as vignette sources Co-authored-by: ilarsf <15234718+ilarsf@users.noreply.github.com> --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index a955061..58a1873 100644 --- a/README.md +++ b/README.md @@ -118,8 +118,8 @@ Phenotypes should already implement the intended observation window, case/control definition, and exclusions; `phewasFlow` fits models but does not derive phenotypes from raw clinical codes. -The [real-data workflow vignette source](vignettes/real-data-workflow.Rmd) gives the complete -participant-table and metadata requirements with working examples. +The [real-data workflow vignette source](vignettes/real-data-workflow.Rmd) documents +the participant-table and metadata requirements with source examples. ## Validate and run @@ -162,12 +162,12 @@ Completed matching shards are reusable after an interrupted run. Change the `analysis_id` and output directory whenever the data, model, thresholds, shard count, or package version changes. -## Learn more +## Vignette sources -- [Run a PheWAS with your data (vignette source)](vignettes/real-data-workflow.Rmd) -- [PheWAS in both directions (vignette source)](vignettes/two-directions.Rmd) -- [Comparisons and plots (vignette source)](vignettes/comparisons-and-plots.Rmd) -- [Scale a successful PheWAS (vignette source)](vignettes/large-runs.Rmd) +- [Run a PheWAS with your data](vignettes/real-data-workflow.Rmd) +- [PheWAS in both directions](vignettes/two-directions.Rmd) +- [Comparisons and plots](vignettes/comparisons-and-plots.Rmd) +- [Scale a successful PheWAS](vignettes/large-runs.Rmd) - [Run a sharded PheWAS with SLURM](inst/examples/slurm/) ## Development From 9da761e29d8de20e3eab06b4e34ae944502cffa2 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Sat, 5 Sep 2026 02:09:44 +0000 Subject: [PATCH 8/8] docs: add rendered workflow link alongside source Co-authored-by: ilarsf <15234718+ilarsf@users.noreply.github.com> --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 58a1873..abc0585 100644 --- a/README.md +++ b/README.md @@ -119,7 +119,8 @@ case/control definition, and exclusions; `phewasFlow` fits models but does not derive phenotypes from raw clinical codes. The [real-data workflow vignette source](vignettes/real-data-workflow.Rmd) documents -the participant-table and metadata requirements with source examples. +the participant-table and metadata requirements with source examples; for the +formatted walkthrough, see the [rendered article](https://fritschelab.github.io/phewasFlow/articles/real-data-workflow.html). ## Validate and run