d-morrison · d-morrison · Dec 28, 2025 · Dec 28, 2025 · Dec 28, 2025 · Dec 28, 2025
diff --git a/.github/workflows/check-spelling.yaml b/.github/workflows/check-spelling.yaml
@@ -18,6 +18,8 @@ jobs:
     steps:
       - name: Checkout repo
         uses: actions/checkout@v3
+        with:
+          submodules: recursive
 
       - name: Run Spelling Check test
         uses: insightsengineering/[email protected]
diff --git a/.github/workflows/preview.yml b/.github/workflows/preview.yml
@@ -27,6 +27,8 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -13,6 +13,8 @@ jobs:
     steps:
       - name: Check out repository
         uses: actions/checkout@HEAD
+        with:
+          submodules: recursive
 
       - name: list files
         shell: bash

diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "latex-macros"]
+	path = latex-macros
+	url = https://github.com/d-morrison/macros.git
diff --git a/README.Rmd b/README.Rmd
@@ -3,6 +3,22 @@ title: "`rme`: Regression Models for Epidemiology"
 format: md
 ---
 
+## Getting Started
+
+This repository uses a git submodule for LaTeX macros. When cloning, use:
+
+```bash
+git clone --recurse-submodules https://github.com/d-morrison/rme.git
+```
+
+Or if already cloned:
+
+```bash
+git submodule update --init --recursive
+```
+
+For more details, see [SUBMODULE_SETUP.md](SUBMODULE_SETUP.md).
+
 ## Code of Conduct
 
 Please note that the `rme` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
diff --git a/SUBMODULE_SETUP.md b/SUBMODULE_SETUP.md
@@ -0,0 +1,43 @@
+# LaTeX Macros Submodule Setup
+
+## ✅ Setup Complete!
+
+The LaTeX macros submodule has been successfully configured and is now tracking the remote repository at https://github.com/d-morrison/macros.git.
+
+### Current Status
+
+- ✅ Submodule URL: https://github.com/d-morrison/macros.git
+- ✅ Submodule path: `latex-macros/`
+- ✅ Current commit: 902bab8
+- ✅ All 52 `.qmd` files updated to reference `latex-macros/macros.qmd`
+- ✅ GitHub Actions workflows configured to checkout submodules
+
+## For Future Clones
+
+After the submodule is properly set up on GitHub, others cloning this repository should run:
+
+```bash
+git clone --recurse-submodules https://github.com/d-morrison/rme.git
+```
+
+Or if already cloned:
+
+```bash
+git submodule update --init --recursive
+```
+
+## Updating the Macros
+
+To update the macros in the future:
+
+```bash
+cd latex-macros
+# Make changes to macros.qmd
+git add macros.qmd
+git commit -m "Update macros"
+git push
+cd ..
+git add latex-macros  # Update the submodule reference
+git commit -m "Update latex-macros submodule"
+git push
+```
diff --git a/_OUTTAKES-time-to-event models.qmd b/_OUTTAKES-time-to-event models.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ## Acknowledgements{.unnumbered}
 

diff --git a/_coxph-model-structure.qmd b/_coxph-model-structure.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 **Joint likelihood of data set**:
 $\Lik \eqdef \p(\vY= \vy, \vD = \vd | \mX = \mx)$

diff --git a/_def-hazard.qmd b/_def-hazard.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 :::{#def-hazard}
 
 ##### Hazard function, hazard rate, hazard rate function

diff --git a/_def-km-estimator.qmd b/_def-km-estimator.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#def-KM-estimator}
 

diff --git a/_def-ph-partial-lik.qmd b/_def-ph-partial-lik.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 $$
 \ba

diff --git a/_def_conditional_odds.qmd b/_def_conditional_odds.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ::: notes
 This course is about regression models, 

diff --git a/_exm_wcgs_coef_interp.qmd b/_exm_wcgs_coef_interp.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#exr-logistic-coef-interp}
 
@@ -17,7 +17,7 @@

 ```{r}
 # include: false
 age_offset = 0L
 ```

 $$

diff --git a/_exr-bernoulli-score.qmd b/_exr-bernoulli-score.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#exr-derive-bernoulli-score}
 Derive the score function for a single Bernoulli random variable $X$.

diff --git a/_exr-double-exponentials.qmd b/_exr-double-exponentials.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#exr-double-exponential}
 

diff --git a/_exr-exp-score.qmd b/_exr-exp-score.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ::: {#exr-exp-score-fn}
 

diff --git a/_exr-gauss-score.qmd b/_exr-gauss-score.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ::: {#exr-gauss-score-fn}
 

diff --git a/_exr-pois-score.qmd b/_exr-pois-score.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ::: {#exr-pois-score-fn}
 

diff --git a/_exr-review-exp-dist.qmd b/_exr-review-exp-dist.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#exr-review-exp-dist}
 Recall the key characteristics of the exponential distribution:

diff --git a/_sec-likelihood-with-censoring.qmd b/_sec-likelihood-with-censoring.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 If an event time $T$ is observed exactly as $T=t$, then the likelihood
 of that observation is just its probability density function:

diff --git a/_sec-score.qmd b/_sec-score.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 The first derivative^[a.k.a. the [gradient](https://en.wikipedia.org/wiki/Gradient)] of the log-likelihood, $\lik'(\th)$, is important enough to have its own name: the *score function*.
 

diff --git a/_sec-surv-conditional-hazards.qmd b/_sec-surv-conditional-hazards.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#def-cond-hazard}
 #### conditional hazard

diff --git a/_sec-surv-dists.qmd b/_sec-surv-dists.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ### The Probability Density Function (PDF)  {.smaller}
 

diff --git a/_sec-survival-dist-fns.qmd b/_sec-survival-dist-fns.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 Name | Symbols | Definition
 :-------------- | ------ | ----------

diff --git a/_sec-understand-coxph.qmd b/_sec-understand-coxph.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 <!-- {{< include _sec_cox-bio.qmd >}} -->
 

diff --git a/_sec_OR_inference.qmd b/_sec_OR_inference.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#exr-ci-OR}
 Given

diff --git a/_sec_OR_logistic.qmd b/_sec_OR_logistic.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#exr-logistic-OR-general}
 

diff --git a/_sec_OR_objections.qmd b/_sec_OR_objections.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 Some scholars have raised objections to the use of odds ratios as 
 an effect measurement [@sackett1996down; @norton2024requiem]. 

diff --git a/_sec_derive_logistic_hessian.qmd b/_sec_derive_logistic_hessian.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 $$
 {\hess(\vb)} = \sumin \olive{\hess_i(\vb)}

diff --git a/_sec_derive_logistic_loglik.qmd b/_sec_derive_logistic_loglik.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#exr-logistic-loglik}
 

diff --git a/_sec_derivs_MLE.qmd b/_sec_derivs_MLE.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{.callout-note}
 

diff --git a/_sec_exm_wcgs.qmd b/_sec_exm_wcgs.qmd
@@ -4,7 +4,7 @@ format:
     df-print: tibble
 ---
 
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 {{< include _sec_intro_wcgs.qmd >}}
 

diff --git a/_sec_fit-coxph.qmd b/_sec_fit-coxph.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ---
 

diff --git a/_sec_intro_bernoulli_models.qmd b/_sec_intro_bernoulli_models.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ## Risk estimation and prediction
 

diff --git a/_sec_invodds.qmd b/_sec_invodds.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#exr-odds-to-prob}
 

diff --git a/_sec_likelihood.qmd b/_sec_likelihood.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ### The likelihood function
 

diff --git a/_sec_linear_coef_interp_intxn.qmd b/_sec_linear_coef_interp_intxn.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ::: {#exr-male-coef-intxn-model}
 What is the interpretation of $\beta_{M}$ in [Model @eq-BW-lm-interact]?

diff --git a/_sec_logistic-fitting.qmd b/_sec_logistic-fitting.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ### Model
 

diff --git a/_sec_logistic_score_fn.qmd b/_sec_logistic_score_fn.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 As usual, by independence, we have:
 

diff --git a/_sec_logistic_slope_mean.qmd b/_sec_logistic_slope_mean.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#lem-d_logodds-d_x}
 

diff --git a/_sec_odds.qmd b/_sec_odds.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 {{< include _def-odds.qmd >}}
 

diff --git a/_sec_odds_fn.qmd b/_sec_odds_fn.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ::: {#exr-prob-to-odds}
 Find a general formula for converting probabilities into odds.

diff --git a/_sec_odds_ratios.qmd b/_sec_odds_ratios.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ::: notes
 

diff --git a/_sec_one_cov_logistic.qmd b/_sec_one_cov_logistic.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ---
 

diff --git a/_sec_overview_bernoulli_models.qmd b/_sec_overview_bernoulli_models.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#exr-def-logistic-regression}
 

diff --git a/_sec_pois-reg_intro.qmd b/_sec_pois-reg_intro.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ::: notes
 This chapter presents models for

diff --git a/_sol-double-exponential.qmd b/_sol-double-exponential.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 If $(a^b)^c = a^{(b^c)}$, then since $(a^b)^c = a^{bc}$,
 we have:

diff --git a/_surv_diagram.qmd b/_surv_diagram.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 $$
 \pdf(t)

diff --git a/_thm-d_pi_d_beta.qmd b/_thm-d_pi_d_beta.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 :::{#thm-d_pi_d_beta}
 

diff --git a/algebra.qmd b/algebra.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ## Elementary Algebra
 

diff --git a/coxph-model-building.qmd b/coxph-model-building.qmd
@@ -1,4 +1,4 @@
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ## Building Cox Proportional Hazards models
 

diff --git a/dobson-cyclone-example.qmd b/dobson-cyclone-example.qmd
@@ -2,7 +2,7 @@
 
 ### Data {#sec-dobson-cyclones-data}
 
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 The `cyclones` dataset in the `dobson` package (@tbl-cyclones-data) 
 records the number of tropical cyclones in Northeastern Australia 

diff --git a/estimation.qmd b/estimation.qmd
@@ -2,7 +2,7 @@
 
 ## Probabilistic models {.scrollable}
 
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 ---
 

diff --git a/glms.qmd b/glms.qmd
@@ -2,7 +2,7 @@
 
 ---
 
-{{< include macros.qmd >}}
+{{< include latex-macros/macros.qmd >}}
 
 This section is primarily adapted starting from the textbook "An Introduction to Generalized Linear Models" (4th edition, 2018)
 by Annette J. Dobson and Adrian G. Barnett:
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,7 +2,7 @@ @@
     ## Probabilistic models {.scrollable}
-    {{< include macros.qmd >}}
+    {{< include latex-macros/macros.qmd >}}
     ---
@@ Expand Down @@