Dissertation draft: chapters 1–3 and the two chapter manuscripts

.Rbuildignore

@@ -12,9 +12,7 @@
 ^README\.Rmd$
 ^\.lintr\.R$
 ^_quarto\.yml$
-^AGENTS\.md$
-^CLAUDE\.md$
-^\.claude$
+^_typos\.toml$
 ^.*\.qmd$
 ^.*\.png$
 ^Vary.*\.r$
@@ -23,3 +21,6 @@
 ^shigella\.Rcheck$
 ^shigella.*\.tar\.gz$
 ^shigella.*\.tgz$
+^AGENTS\.md$
+^CLAUDE\.md$
+^\.claude$

.gitattributes

@@ -0,0 +1,41 @@
+# Line-ending normalisation.
+#
+# Without this file git stores whatever the working tree contains, so an editor
+# configured for Windows line endings can commit CRLF into a repository that is
+# otherwise LF throughout. That happened to chapter2.qmd, where the conversion
+# rewrote all 1,285 lines and buried seven real edits in a whole-file diff.
+#
+# `text=auto` makes git normalise to LF in the repository for anything it
+# detects as text. The `eol=lf` entries go further and keep LF in the working
+# tree as well, on every platform, so an editor never sees CRLF to preserve.
+
+* text=auto
+
+# Prose and analysis sources
+*.qmd  text eol=lf
+*.Rmd  text eol=lf
+*.md   text eol=lf
+
+# Code
+*.R    text eol=lf
+*.r    text eol=lf
+*.stan text eol=lf
+*.py   text eol=lf
+
+# Data and bibliography. The CSVs are written by the analysis scripts and read
+# back by read.csv, which accepts either ending; pinning LF keeps regenerated
+# tables diffable line by line. None contains an embedded newline in a quoted
+# field, so forcing the ending is safe.
+*.csv  text eol=lf
+*.bib  text eol=lf
+*.csl  text eol=lf
+
+# Configuration
+*.yml  text eol=lf
+*.yaml text eol=lf
+*.toml text eol=lf
+*.json text eol=lf
+
+# Binary: excluded from normalisation so text=auto can never mis-detect them.
+*.png  binary
+*.docx binary

.github/workflows/render-thesis-vignettes.yaml

@@ -0,0 +1,81 @@
+# Renders the dissertation and the two manuscripts to docx, on every push to the
+# branch and every pull request that touches them, and uploads the results as
+# artifacts.
+#
+# THE POINT. A reviewer — bot or human — can read the rendered documents without
+# installing anything, and a render failure shows up as a red check before
+# anyone spends time on the prose.
+#
+# WHY THIS IS CHEAP. The chunks in all three documents only read CSVs and build
+# flextables: no Stan, no JAGS, no model fitting. flextable and officer are the
+# whole dependency set, so the job finishes in a couple of minutes.
+
+name: Render thesis
+
+on:
+  push:
+    branches: [thesis-draft]
+    paths:
+      - 'vignettes/articles/thesis/**'
+      - '.github/workflows/render-thesis-vignettes.yaml'
+  pull_request:
+    paths:
+      - 'vignettes/articles/thesis/**'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  render:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: vignettes/articles/thesis
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: quarto-dev/quarto-actions/setup@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: vignettes/articles/thesis
+          packages: |
+            any::flextable
+            any::officer
+
+      # Renders the three documents named in thesis/_quarto.yml. Each lands
+      # beside its own .qmd.
+      - name: Render
+        run: quarto render
+
+      # Quarto wraps each captioned table in an outer single-row table, and
+      # flextable's own options reach only the inner one, so tables were
+      # breaking across pages. Setting cantSplit on every row moves a whole
+      # table to the next page instead of splitting it.
+      - name: Keep tables whole
+        run: |
+          python3 fix_table_breaks.py thesis_ch1_ch2_ch3.docx
+          python3 fix_table_breaks.py chapter2/chapter2.docx
+          python3 fix_table_breaks.py chapter3/chapter3.docx
+
+      - name: Upload dissertation
+        uses: actions/upload-artifact@v4
+        with:
+          name: dissertation
+          path: vignettes/articles/thesis/thesis_ch1_ch2_ch3.docx
+          retention-days: 30
+
+      - name: Upload manuscripts
+        uses: actions/upload-artifact@v4
+        with:
+          name: manuscripts
+          path: |
+            vignettes/articles/thesis/chapter2/chapter2.docx
+            vignettes/articles/thesis/chapter3/chapter3.docx
+          retention-days: 30

.gitignore

@@ -19,3 +19,4 @@ shigella.Rcheck/
 shigella*.tar.gz
 shigella*.tgz
 .DS_Store
+.claude/settings.local.json

NEWS.md

@@ -24,6 +24,7 @@
 * Recorded the roxygen2 version in `Config/roxygen2/version`, which roxygen2
   8.1.0 uses in place of `RoxygenNote` (#32)
 
+* Added dissertation and standalone chapter manuscript source files with automated DOCX rendering (#31)
 * Pinned `use-ai-config: true` explicitly on the Claude and Claude-review
   `Morrison-Lab/gha@v2` callers (#36).
   The reusable workflows already default that input to true,

_typos.toml

@@ -0,0 +1,25 @@
+# Configuration for crate-ci/typos, consumed by
+# .github/workflows/check-typos.yml.
+#
+# Every entry below is a term this repository uses deliberately, not an
+# accepted misspelling. Keep it that way: a real typo belongs fixed in the
+# source, not listed here.
+
+[files]
+extend-exclude = [
+  # Bibliographies are exported from reference managers and carry author
+  # surnames and non-English titles. "Leroux-Roels" alone accounts for three
+  # findings, and none of it is prose anyone wrote here.
+  "*.bib",
+  # {spelling}'s own accept-list. A file whose entire purpose is to hold
+  # unusual words cannot be spellchecked.
+  "inst/WORDLIST",
+]
+
+[default.extend-words]
+# Abbreviations used in Stan model code, analysis scripts, and figure labels.
+lik = "lik"   # likelihood: log_lik, .lik(), the LIK_FORM environment variable
+lod = "lod"   # limit of detection: fig-lod, the LOD covariate in ch3
+mis = "mis"   # the prefix, as in mis-centered / mis-extracted
+nd = "nd"     # per-chain draw count, inst/scripts/ch2/run_ch2_461.R
+pn = "pn"     # par_new summary, inst/scripts/ch2 and ch3

inst/WORDLIST

@@ -1,28 +1,218 @@
+AKU
+Aiemjoy
+Bernshtein
 CMD
+Centre
+Cheng
+Chisenga
 Codecov
+Cov
+CrI
+DOCX
+Diarrhoeal
+FIC
+Farzam
+Fogarty
+GMMA
 GitHub
+HlyE
+INV
 IgA
 IgG
+IpaB
 Iso
 Isotype
+Jiang
+Jiming
+Jong
+KA
+LKJ
+LMICs
+Lai
+Longrightarrow
+Luminex
+MCSE
 MFI
+MacConkey
+MassGeneral
+Mirpur
+NIAID
+Ndungo
 ORCID
+OSP
 PHI
+PLOS
+Paratyphi
 Postprocess
+Pre
+RLDT
+Richelle
+SEAP
+SERG
 SOSAR
+Schildhauer
+Schur
+Schwarz's
+Seon
+Seroepidemiology
+Seroincidence
+Serological
+Seroprevalence
 Seroresponse
+Serotype
+TTHc
+TW
+Tae
+Typhi
+UCD
+Unif
+Vaidya
+Yoon
+al
 allowlist
+altSonflex
+analyte
+antigenically
+bacteremic
+biomarker
+biomarkers
+boldsymbol
+boydii
 changelog
+codebase
+codebases
+comparator
+computable
+de
+dec
 df
+diag
+diarrheal
+dichotomization
+dichotomizes
+dt
+dy
+dysenteriae
+dysenteric
+eightfold
+elpd
+endemicity
+enterica
+estimand
+et
+fivefold
+flexneri
+frac
+funders
+ge
+generalizability
 ggplot
 gha
+glucosyl
+hemolysin
+heterologous
+humoral
+hyp
+hyperprior
+hyperpriors
+icddr
+iint
+ij
+ik
+immunoaffinity
+immunoassay
+immunologically
+immunoreactive
+immunosorbent
+infty
+interpretability
+io
+iok
+ipaH
 ipab
+isolable
 isotype
+isotype's
 isotypes
+jj
+le
+licensure
+ln
+logarithmically
+lp
+lpd
+mapsto
+mathbb
+mathbf
+mathcal
+mathrm
+mis
+misspecified
+mucoid
+mucosal
+multimodality
+ne
 newperson
+operatorname
+organismal
+pagebreak
+plasmid
+pmatrix
+polysaccharides
 pre
+precisions
+presentational
+qquad
+quadrivalent
+reparameterization
 repo
+reweight
+reweighting
+reweights
 roxygen
+rvert
+scalable
+sera
+sero
+serocalculator
+seroconversion
+serodiagnostic
 serodynamics
+seroepidemiologic
+seroepidemiology
+seroincidence
+serologic
+serological
+seroresponse
+seroresponses
+serosurveillance
+serosurvey
+serosurveys
 serotype
+serotype's
+serotypes
+serotyping
+serovars
+shigellosis
+sonnei
+spp
+subclinical
+sublinearly
+succ
+tetrasaccharide
+textbf
+textstyle
+tfrac
+th
+thirtyfold
 tibble
+titers
+underbrace
+underpowered
+uninterpretable
+unstratified
+untypeable
+varepsilon
+varrho
+widehat
+xrightarrow