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 (GGally::ggpairs()), 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
GGally (v2.4.0) added to DESCRIPTION Suggests and renv.lock
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.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

glmnet.stanford.edu
- Triggering command: /opt/R/4.5.3/lib/R/bin/exec/R /opt/R/4.5.3/lib/R/bin/exec/R --no-echo --no-restore --file=/opt/quarto/share/rmd/rmd.R (dns block)
- Triggering command: /opt/R/4.5.3/lib/R/bin/exec/R /opt/R/4.5.3/lib/R/bin/exec/R --no-echo --no-restore --file=/opt/quarto/share/rmd/rmd.R unam�� (dns block)
olsrr.rsquaredacademy.com
- Triggering command: /opt/R/4.5.3/lib/R/bin/exec/R /opt/R/4.5.3/lib/R/bin/exec/R --no-echo --no-restore --file=/opt/quarto/share/rmd/rmd.R (dns block)
- Triggering command: /opt/R/4.5.3/lib/R/bin/exec/R /opt/R/4.5.3/lib/R/bin/exec/R --no-echo --no-restore --file=/opt/quarto/share/rmd/rmd.R unam�� (dns block)
packagemanager.posit.co
- Triggering command: /usr/bin/curl /usr/bin/curl --config /tmp/Rtmpz21USI/renv-download-config-26a159b3cb76 (dns block)
- Triggering command: /usr/bin/curl /usr/bin/curl --config /tmp/Rtmpz21USI/renv-download-config-26a143be690e (dns block)
- Triggering command: /usr/bin/curl /usr/bin/curl --config /tmp/Rtmpz21USI/renv-download-config-26a1777d9204 (dns block)

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

Configure Actions setup steps to set up my environment, which run before the firewall is enabled
Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

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

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

rspm-sync.rstudio.com
- Triggering command: /usr/bin/curl /usr/bin/curl --config /tmp/RtmpdqGxja/renv-download-config-2677336aef2b (dns block)

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

Configure Actions setup steps to set up my environment, which run before the firewall is enabled
Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

d-morrison · 2026-04-10T18:53:10Z

@copilot resolve merge conflicts

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

Copilot

Pull request overview

Adds a new HERS linear regression walkthrough (parallel lines, interaction, GOF/diagnostics/model selection) into the Linear Models Overview chapter, interleaved with the existing birthweight narrative to mirror Vittinghoff Ch. 4.

Changes:

Inserts new HERS include subfiles into the “Understanding linear regression” and “Assessing model fit” subfiles.
Adds new Quarto subfiles at repo root for HERS data intro, two models, GOF, diagnostics, and LRT-based model selection.
Updates inst/WORDLIST with additional allowed technical terms.

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 spellcheck allowlist for new terminology used in the added HERS content.
`_subfiles/Linear-models-overview/_sec_linreg_understanding.qmd`	Includes the HERS intro + model examples into the “Understanding” flow.
`_subfiles/Linear-models-overview/_sec_linreg_assess.qmd`	Includes HERS GOF/diagnostics/model-selection examples into the “Assessing fit” flow.
`_sec_hers_data.qmd`	New HERS dataset introduction, plots, and notation.
`_sec_hers_lm_parallel.qmd`	New HERS parallel-lines model example and fitted-values visualization.
`_sec_hers_lm_interact.qmd`	New HERS interaction model example and visualization by statin use.
`_sec_hers_lm_gof.qmd`	New AIC/BIC and deviance comparisons for the two HERS models.
`_sec_hers_lm_diagnostics.qmd`	New residual-vs-fitted and QQ diagnostics for both HERS models.
`_sec_hers_lm_model_selection.qmd`	New LRT comparison between HERS models.

+hers_lm2 |>
+  parameters() |>
+  parameters::print_md(
+    include_reference = include_reference_lines,
+    select = "{estimate}"
+  )


 WCGS
 Welch
 Zhou
 biomarkers
+Biostat
 bmatrix
+BMI
 bmt


+### Motivating example: `hers` data {.smaller}
+
+:::{.callout-note}
+This section is based on @vittinghoff2e, Chapter 4.


d-morrison · 2026-04-21T01:17:16Z

@copilot add GGally package to renv and Description

Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/911ad1ab-e623-4550-9811-addaf2dbd9b9 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot · 2026-04-21T01:52:51Z

@copilot add GGally package to renv and Description

Done in commit 238201b. Added GGally to DESCRIPTION Suggests and ran renv::install("GGally"); renv::snapshot() to add GGally 2.4.0 (along with its new dependencies ggstats and patchwork) to renv.lock.

Initial plan

557fac2

Copilot AI assigned Copilot and d-morrison Apr 7, 2026

Copilot started work on behalf of d-morrison April 7, 2026 19:33 View session

Copilot AI linked an issue Apr 7, 2026 that may be closed by this pull request

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

Open

Copilot AI and others added 2 commits April 7, 2026 20:05

Add HERS dataset linear regression example following Vittinghoff Chap…

6303987

…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>

Pre-compute coefficient values in named variables for maintainability

a841ba7

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>

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

Copilot finished work on behalf of d-morrison April 7, 2026 20:08

Copilot AI requested a review from d-morrison April 7, 2026 20:08

Copilot started work on behalf of d-morrison April 7, 2026 20:24 View session

Copilot AI and others added 2 commits April 7, 2026 20:41

Intersperse HERS analysis with birthweight sections; add HERS interac…

e828c2f

…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>

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

27418f9

…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 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

Copilot finished work on behalf of d-morrison April 7, 2026 20:47

d-morrison added 3 commits April 7, 2026 23:21

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

ded1bb6

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

752d970

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

71fa75e

Copilot started work on behalf of d-morrison April 9, 2026 20:58 View session

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

f7d07a6

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 finished work on behalf of d-morrison April 9, 2026 21:07

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

90ae68a

Copilot started work on behalf of d-morrison April 10, 2026 18:53 View session

d-morrison removed their request for review April 10, 2026 18:54

Copilot finished work on behalf of d-morrison April 16, 2026 08:39

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

a0e362d

d-morrison requested a review from Copilot April 16, 2026 16:58

Copilot started reviewing on behalf of d-morrison April 16, 2026 16:59 View session

Copilot AI reviewed Apr 16, 2026

View reviewed changes

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

c8913d8

Copilot started work on behalf of d-morrison April 16, 2026 19:30 View session

Copilot AI and others added 2 commits April 16, 2026 19:36

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

f61a83b

…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>

Fix ggpairs alpha placement and fig-cap quote formatting

9d7eb27

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 finished work on behalf of d-morrison April 16, 2026 19:39

d-morrison marked this pull request as ready for review April 19, 2026 00:34

d-morrison added 2 commits April 18, 2026 17:34

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

e78dc81

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

1811f6a

Copilot AI review requested due to automatic review settings April 21, 2026 00:43

Copilot started reviewing on behalf of d-morrison April 21, 2026 00:43 View session

Copilot AI reviewed Apr 21, 2026

View reviewed changes

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

7f8014a

d-morrison removed their request for review April 21, 2026 01:17

Copilot started work on behalf of d-morrison April 21, 2026 01:48 View session

Add GGally to DESCRIPTION Suggests and renv.lock

238201b

Agent-Logs-Url: https://github.com/d-morrison/rme/sessions/911ad1ab-e623-4550-9811-addaf2dbd9b9 Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>

Copilot AI requested review from Copilot and removed request for Copilot April 21, 2026 01:52

Copilot finished work on behalf of d-morrison April 21, 2026 01:54

Copilot AI requested a review from d-morrison April 21, 2026 01:54

Conversation

Copilot AI commented Apr 7, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

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

Uh oh!

d-morrison commented Apr 7, 2026

Uh oh!

d-morrison commented Apr 7, 2026

Uh oh!

Copilot AI commented Apr 7, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

I tried to connect to the following addresses, but was blocked by firewall rules:

Uh oh!

d-morrison commented Apr 9, 2026

Uh oh!

Copilot AI commented Apr 9, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

I tried to connect to the following addresses, but was blocked by firewall rules:

Uh oh!

d-morrison commented Apr 10, 2026

Uh oh!

Copilot AI commented Apr 16, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

d-morrison commented Apr 16, 2026

Uh oh!

Copilot AI commented Apr 16, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

d-morrison commented Apr 21, 2026

Uh oh!

Copilot AI commented Apr 21, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Copilot AI commented Apr 7, 2026 •

edited

Loading

Structure in `_sec_linreg_understanding.qmd`

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

Copilot AI commented Apr 7, 2026 •

edited

Loading

Copilot AI commented Apr 9, 2026 •

edited

Loading