Add HERS dataset linear regression example with interactions, interspersed with birthweight analysis (Vittinghoff Ch. 4) by Copilot · Pull Request #381 · d-morrison/rme

Copilot · 2026-04-07T19:33:00Z

Integrates a HERS dataset linear regression example into the "Linear Models Overview" chapter, interspersed with the existing birthweight analysis to mirror the narrative flow of Vittinghoff Ch. 4.

Changes Made

HERS content subfiles (all at repo root, for easy repositioning)

_sec_hers_data.qmd — HERS data introduction: data loading, scatter plot (faceted by HT with label_both), pairwise key-variables plot, and data notation (H, B, V variables)
_sec_hers_lm_parallel.qmd — Parallel lines model: LDL ~ HT + BMI; fitted-values plot faceted by HT
_sec_hers_lm_interact.qmd — Interaction model: LDL ~ HT + BMI + statins + BMI:statins; plot faceted by HT
_sec_hers_lm_gof.qmd — Goodness of fit: AIC/BIC table and deviance for both HERS models
_sec_hers_lm_diagnostics.qmd — Diagnostics: residuals vs fitted and QQ plots for both hers_lm1 and hers_lm2, all faceted by HT with label_both
_sec_hers_lm_model_selection.qmd — Model selection: LRT comparing the two HERS models

Structure in `_sec_linreg_understanding.qmd`

HERS data intro (_sec_hers_data.qmd) inserted directly after the birthweight dataset section
HERS parallel model included after the birthweight parallel lines coefficient interpretation
HERS interaction model included after the birthweight interaction coefficient comparison table

"Assessing model fit" section (`_sec_linreg_assess.qmd`)

HERS goodness-of-fit examples added after the birthweight GOF subsection
HERS diagnostic examples added after the birthweight Diagnostics subsection
HERS model selection examples added after the birthweight Model Selection subsection

Other

Interaction model uses BMI:statins (not BMI:HT); statin use $V$ added to data notation
All HERS plots faceted by HT using facet_wrap(~HT, labeller = label_both)
Factor reference levels explicitly set: relevel(ref = "placebo") for HT, relevel(ref = "no") for statins
GGally::ggpairs() key-variables panel added to the HERS data tabset, showing LDL, HT, BMI, statins, and age colored by treatment group
inst/WORDLIST deduplicated and sorted (105 unique words after merging with main)
Deleted unreferenced standalone _sec_exm_hers_lm.qmd

Testing

✅ Lint passes (lintr::lint() on all changed .qmd files)
✅ Spell check passes (spelling::spell_check_package())

…ter 4 Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/780d27e6-3176-4828-9ead-2f708a8dc707 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/780d27e6-3176-4828-9ead-2f708a8dc707 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

d-morrison · 2026-04-07T20:24:00Z

add a model with interactions, like we did for the birthweight data. intersperse the HERS analysis with the corresponding sections of the birthweight analysis

d-morrison · 2026-04-07T20:24:17Z

@copilot add a model with interactions, like we did for the birthweight data. intersperse the HERS analysis with the corresponding sections of the birthweight analysis

…tion model Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/5c9bd00e-5395-40df-8e43-9ea2e760fca2 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

…erator Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/5c9bd00e-5395-40df-8e43-9ea2e760fca2 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-04-07T20:45:52Z

@copilot add a model with interactions, like we did for the birthweight data. intersperse the HERS analysis with the corresponding sections of the birthweight analysis

Done in commit 27418f9. The HERS analysis is now interspersed with the birthweight sections:

2.2.4 Motivating example: hers data — data loading, scatter plot, and notation (H = HT treatment, B = BMI)
2.2.5 Parallel lines regression for hers data — LDL ~ HT + BMI, mirroring the birthweight parallel lines model
2.2.7 Interactions in hers data — LDL ~ HT + BMI + HT:BMI, added right after the birthweight interaction section (2.2.6)

Each HERS section follows the same structure as its birthweight counterpart: model equation, parameter table, and fitted-values plot.

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d-morrison · 2026-04-09T20:58:27Z

@copilot add interaction between bmi and statin use to the HERS model, and remove the interaction between bmi and HT

Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/f3c2ef8c-874d-4c6f-8c92-427a61e70055 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-04-09T21:06:45Z

@copilot add interaction between bmi and statin use to the HERS model, and remove the interaction between bmi and HT

Done in commit f7d07a6. The interaction model is now LDL ~ HT + BMI + statins + BMI:statins:

Removed HT:BMI interaction
Added statins as a main effect and BMI:statins as the interaction term
Added statin use ($U$/$V$) to the data notation section
Updated the scatter plot to colour/shape by statin use (no vs yes)

The model equation is now:
$$\mu(h,v,b) = \beta_0 + \beta_H h + \beta_V v + \beta_B b + \beta_{VB}(v \cdot b)$$

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If you need me to access, download, or install something from one of these locations, you can either:

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d-morrison · 2026-04-10T18:53:10Z

@copilot resolve merge conflicts

…ORDLIST duplicates Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/53ac613d-5e7f-468f-87c4-ed701a5c4220 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-04-14T18:51:01Z

@copilot apply changes based on the comments in this thread

Done in commit 8303639:

Deleted _sec_exm_hers_lm.qmd — the file was not referenced by any {{< include >}} directive or rendered page, and the standalone HERS section was already superseded by the interspersed _sec_hers_lm_parallel.qmd and _sec_hers_lm_interact.qmd subfiles.
Fixed inst/WORDLIST — reduced from 85 entries (21 duplicates) to 64 unique entries, sorted alphabetically.

github-actions · 2026-04-14T20:16:33Z

PR Preview Action v1.8.1
🚀 Preview available at: https://d-morrison.github.io/rme/pr-preview/pr-381/

_{Built to branch gh-pages at 2026-04-14 20:16 UTC.}

d-morrison · 2026-04-16T07:55:37Z

@copilot resolve the merge conflicts in this pull request

d-morrison

@copilot

always facet HERS graphs by HT (using label_both (https://ggplot2.tidyverse.org/reference/labellers.html)).
include examples with the HERS data for all the Evaluating model fit subsections
move the introduction of the HERS dataset from https://d-morrison.github.io/rme/pr-preview/pr-381/Linear-models-overview.html#motivating-example-hers-data to directly after the introduction of the birthweight data set
move all the new HERS data content into subfiles, so we can reposition them easily as needed

…odel-hers-dataset # Conflicts: # inst/WORDLIST Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-04-16T08:17:56Z

@copilot resolve the merge conflicts in this pull request

Done in commit 0bde169. The only conflict was in inst/WORDLIST — merged both sets (ours with HERS-specific terms like LDL, drinkany, drk, nw, smk; main's with new math/stats terms like bmatrix, idempotent, varepsilon, etc.), deduplicated, and sorted. Result: 105 unique words. Spell check passes.

- Extract HERS data intro into new _sec_hers_data.qmd - Update _sec_hers_lm_parallel.qmd: remove intro, add HT faceting to fitted values plot - Update _sec_hers_lm_interact.qmd: add HT faceting to interaction model plot - Insert HERS data include in _sec_linreg_understanding.qmd after birthweight data notation - Create _sec_hers_lm_gof.qmd with AIC/BIC/deviance/LRT examples - Create _sec_hers_lm_diagnostics.qmd with residuals and QQ plots faceted by HT - Create _sec_hers_lm_model_selection.qmd with LRT model comparison - Update _sec_linreg_assess.qmd to include new HERS assess subfiles All HERS scatter plots now use facet_wrap(~HT, labeller = label_both). Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

LRT is already covered in _sec_hers_lm_model_selection.qmd. The GOF file should focus on AIC, BIC, and deviance only. Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-04-16T08:38:05Z

@copilot

always facet HERS graphs by HT (using label_both (https://ggplot2.tidyverse.org/reference/labellers.html)).

include examples with the HERS data for all the Evaluating model fit subsecti...

Done in commits c46e981 and f9d6ec1:

HERS data intro moved: Extracted into _sec_hers_data.qmd and inserted directly after the birthweight dataset section (before "Parallel lines regression")
All HERS graphs faceted by HT: Added facet_wrap(~HT, labeller = label_both) to scatter plot in _sec_hers_data.qmd, fitted-values plot in _sec_hers_lm_parallel.qmd, and interaction model plot in _sec_hers_lm_interact.qmd
All HERS content in subfiles: _sec_hers_data.qmd, _sec_hers_lm_parallel.qmd, _sec_hers_lm_interact.qmd, _sec_hers_lm_gof.qmd, _sec_hers_lm_diagnostics.qmd, _sec_hers_lm_model_selection.qmd
HERS examples for all "Evaluating model fit" subsections:
- Goodness of fit: AIC/BIC table and deviance for hers_lm1 vs hers_lm2 (_sec_hers_lm_gof.qmd)
- Diagnostics: Residuals vs fitted and QQ plot, both faceted by HT (_sec_hers_lm_diagnostics.qmd)
- Model selection: LRT comparing the two HERS models (_sec_hers_lm_model_selection.qmd)

Copilot

Pull request overview

This PR integrates a HERS dataset linear regression example into the “Linear Models Overview” chapter, interleaving it with the existing birthweight analysis to follow the narrative flow of Vittinghoff Ch. 4.

Changes:

Adds new HERS-focused Quarto subfiles covering data intro, parallel-lines and interaction models, GOF, diagnostics, and model selection.
Inserts the new HERS subfiles into the “Understanding…” and “Assessing model fit” sections via {{< include ... >}}.
Updates inst/WORDLIST to reflect new terminology and deduplicate/sort entries.

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
inst/WORDLIST	Updates spelling whitelist for new HERS terms and general cleanup.
_subfiles/Linear-models-overview/_sec_linreg_understanding.qmd	Includes new HERS data + modeling sections into the narrative flow.
_subfiles/Linear-models-overview/_sec_linreg_assess.qmd	Includes new HERS GOF/diagnostics/model-selection examples after birthweight sections.
_sec_hers_data.qmd	New HERS dataset intro: load data, show table/plot, define notation.
_sec_hers_lm_parallel.qmd	New HERS parallel-lines model fit + coefficient table + fitted-values overlay plot.
_sec_hers_lm_interact.qmd	New HERS interaction model fit + interpretation + fitted overlay plot.
_sec_hers_lm_gof.qmd	New AIC/BIC and deviance comparisons for the HERS models.
_sec_hers_lm_diagnostics.qmd	New residual-vs-fitted and QQ diagnostics plots (currently for `hers_lm1`).
_sec_hers_lm_model_selection.qmd	New LRT comparison (`lrtest`) between `hers_lm1` and `hers_lm2`.

+
+::: notes
+
+{{< include _sec_hers_intro.qmd >}}


+::: notes
+"Placebo" is the **reference level** for the categorical variable $T$,
+and "no" is the **reference level** for statin use $U$.
+The choice of reference level is arbitrary;
+it only affects the interpretation of the intercept and corresponding indicator coefficients.


@@ -0,0 +1,34 @@
+### Diagnostics for `hers` models


d-morrison · 2026-04-16T19:30:16Z

@copilot apply changes based on the comments in this thread

also, add a graph of the key variables of the HERS data, including the treatment variable, the outcome variable, and the most important covariates

…ariables plot Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/a89643f9-3164-469b-9b64-621cc53426a0 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/a89643f9-3164-469b-9b64-621cc53426a0 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-04-16T19:37:56Z

@copilot apply changes based on the comments in this thread

also, add a graph of the key variables of the HERS data, inclu...

Done in commits f61a83b and 9d7eb27:

PR review fixes:

Fixed include path: {{< include _sec_hers_intro.qmd >}} → {{< include _subfiles/shared/_sec_hers_intro.qmd >}}
Added explicit relevel() calls: relevel(ref = "placebo") for HT and relevel(ref = "no") for statins (both were already in correct order from as_factor(), but now explicit)
Expanded diagnostics into two subsections — one for hers_lm1 (parallel-lines model) and one for hers_lm2 (interaction model), each with residuals vs fitted and QQ plots, both faceted by HT

Key variables graph:

Added a "Key variables" tab in the HERS data panel-tabset with a GGally::ggpairs() plot of LDL (outcome), HT (treatment), BMI, statins, and age — colored by HT treatment group

Initial plan

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add an example model with the HERS dataset for linear regression #380

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Add HERS dataset linear regression example following Vittinghoff Chap…

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Pre-compute coefficient values in named variables for maintainability

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Copilot AI changed the title ~~[WIP] Add an example model with the HERS dataset for linear regression~~ Add HERS dataset linear regression example (Vittinghoff Ch. 4) Apr 7, 2026

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Intersperse HERS analysis with birthweight sections; add HERS interac…

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Use explicit data= in geom_line instead of ggplot data replacement op…

27418f9

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Copilot AI changed the title ~~Add HERS dataset linear regression example (Vittinghoff Ch. 4)~~ Add HERS dataset linear regression example with interactions, interspersed with birthweight analysis (Vittinghoff Ch. 4) Apr 7, 2026

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Merge branch 'main' into copilot/add-example-model-hers-dataset

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Merge branch 'main' into copilot/add-example-model-hers-dataset

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Merge branch 'main' into copilot/add-example-model-hers-dataset

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Replace BMI×HT interaction with BMI×statins interaction in HERS model

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Merge branch 'main' into copilot/add-example-model-hers-dataset

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Address PR review: delete unreferenced standalone HERS file and fix W…

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Merge branch 'main' into copilot/add-example-model-hers-dataset

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Fix PR review issues: include path, factor levels, diagnostics, key-v…

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Fix ggpairs alpha placement and fig-cap quote formatting

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Merge branch 'main' into copilot/add-example-model-hers-dataset

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Changes Made

HERS content subfiles (all at repo root, for easy repositioning)

Structure in _sec_linreg_understanding.qmd

"Assessing model fit" section (_sec_linreg_assess.qmd)

Other

Testing

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Copilot AI commented Apr 7, 2026 •

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Structure in `_sec_linreg_understanding.qmd`

"Assessing model fit" section (`_sec_linreg_assess.qmd`)

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