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Fix skipped heading levels in r-config and count-regression #1428

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dem-extra1 merged 3 commits into from
Nov 1, 2026
Merged

Fix skipped heading levels in r-config and count-regression #1428

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52a2a48
Fix skipped heading levels in r-config and count-regression (#1427)
claude Oct 30, 2026
16e5f96
Raise headings nested under the shared Configuring R section (#1427)
claude Oct 30, 2026
a894906
Merge branch 'main' into claude/project-thread-ykzrw4
dem-extra1 Nov 1, 2026
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2 changes: 1 addition & 1 deletion chapters/binary-outcome-associations.qmd
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Expand Up @@ -19,7 +19,7 @@ format:
options(digits = 6)
```

## Acknowledgements {.unnumbered}
# Acknowledgements {.unnumbered}

This content is adapted from:

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4 changes: 2 additions & 2 deletions chapters/concept-map.qmd
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Expand Up @@ -56,7 +56,7 @@ type_palette <- c(
There are `r nrow(cg$nodes)` labeled definitions and results in the notes,
connected by `r nrow(cg$edges)` direct dependency links.

## Dependency diagram
# Dependency diagram

::: {.content-visible unless-format="pdf"}
::: {.content-visible unless-format="docx"}
Expand Down Expand Up @@ -184,7 +184,7 @@ The dependency diagram is only available in the

:::

## Descendants of each result {#sec-descendants-table}
# Descendants of each result {#sec-descendants-table}

@tbl-descendants lists every result that has at least one descendant,
sorted by the number of total descendants (direct or transitive).
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10 changes: 5 additions & 5 deletions chapters/count-regression.qmd
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Expand Up @@ -67,7 +67,7 @@ rather than the [maximum likelihood estimation](https://morrison-lab.github.io/s

# Inference for count regression models

### Maximum likelihood estimates for two groups
## Maximum likelihood estimates for two groups

<!-- No slidebreak here: the heading shares its slide with the thm-pois-two-group-mle div. -->

Expand All @@ -79,7 +79,7 @@ rather than the [maximum likelihood estimation](https://morrison-lab.github.io/s

{{< include _subfiles/count-regression/_exm-pois-two-group-mle.qmd >}}

### Fitted totals
## Fitted totals

<!-- No slidebreak here: the heading shares its slide with the thm-pois-fitted-totals div. -->

Expand All @@ -95,7 +95,7 @@ rather than the [maximum likelihood estimation](https://morrison-lab.github.io/s

{{< include _subfiles/count-regression/_exm-pois-fitted-totals-no-intercept.qmd >}}

### Confidence intervals for regression coefficients and rate ratios
## Confidence intervals for regression coefficients and rate ratios
{{< include _subfiles/count-regression/_sec_poisson_inference.qmd >}}

# Prediction
Expand All @@ -104,7 +104,7 @@ rather than the [maximum likelihood estimation](https://morrison-lab.github.io/s

# Diagnostics

### Residuals
## Residuals
{{< include _subfiles/count-regression/_sec_poisson_dx.qmd >}}

{{< slidebreak >}}
Expand All @@ -120,7 +120,7 @@ rather than the [maximum likelihood estimation](https://morrison-lab.github.io/s
{{< include _subfiles/count-regression/_exm-needle-sharing-dx.qmd >}}

# Zero-inflation
### Models for zero-inflated counts
## Models for zero-inflated counts

<!-- No slidebreak here: the heading shares its slide with the def-zip-reg div. -->

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2 changes: 1 addition & 1 deletion chapters/logistic-regression.qmd
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Expand Up @@ -21,7 +21,7 @@ options(digits = 6)
```


## Acknowledgements {.unnumbered}
# Acknowledgements {.unnumbered}

This content is adapted from:

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2 changes: 1 addition & 1 deletion chapters/r-config.qmd
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Expand Up @@ -2,7 +2,7 @@

---

### Configuring R {.unnumbered}
# Configuring R {.unnumbered}

Functions from these packages will be used throughout this document:

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