Dissertation draft: chapters 1–3 and the two chapter manuscripts - #31

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Commits on Aug 21, 2026

Create new_file.R
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Add files via upload
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Create new_file.R
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Create new_fIle.R
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Create ch3
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Delete inst/scripts/ch3
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Create new_file.R
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Delete inst/scripts/new_file.R
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Add files via upload
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Delete inst/scripts/ch3/new_file.R
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Create newfile.R
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Delete inst/scripts/ch3/newfile.R
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Create newfile.R
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Add files via upload
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Delete thesis directory
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Delete vignettes/articles/thesis/newfile.R
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Create newfile.R
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Create newfile.R
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Commits on Aug 24, 2026

Add dissertation draft and the two chapter manuscripts
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Add workflow to render thesis and upload documents
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Update package metadata for thesis draft
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update WORDLIST
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Potential fix for pull request finding

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Potential fix for pull request finding

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Potential fix for pull request finding

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Apply remaining changes

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Kwan-Jenny
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e1df45e
Apply remaining changes

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Commits on Aug 28, 2026

Revise chapters 2 and 3
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update WORDLIST
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Merge main into thesis-draft

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Add a typos config so check-typos passes on the thesis sources

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Commits on Aug 29, 2026

Commits on Aug 30, 2026

# update chapter2,3 qmd
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Fix the rho_c prior claim and the "fit" overload in the two chapters
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# update chapter2,3 qmd files
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Add the three serocalculator words to WORDLIST and a .gitattributes
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# update 2 qmd files
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update qmd files
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Fix the scheme lookup, two sentences, a caption, and trailing newlines
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Name the forms in tbl-cov, guard its row pairing, and six prose fixes
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Say what tbl-collect counts, name the sites in full, and four prose fixes
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Commits on Aug 31, 2026

# update thesis qmd
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Commits on Sep 1, 2026

Commits on Sep 2, 2026

Commits on Sep 3, 2026

Chapter 3: thirteen edits from Kristen's review
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add writing standard guideline file
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chapter 3: HlyE placement, genus italics, redundant sentence, appendix heading
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chapter 3: subjective wording, ELISA expansion, duplicate values, unsourced figures
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# update guideline
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chapter 3: correct serocalculator attribution in methods and reproducibility
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Commits on Sep 4, 2026

chapter 3: antecedents, adjacent repetitions, and one duplicated sentence
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writing standard: record decided items and two extractor caveats
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chapter 3: record deferred review items
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chapters 2 and 3: correct the SEES expansion and separate it from SEAP
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chapter 2: restore statistical terminology and the two-source display
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chore: ignore the local Claude settings override
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# update
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update
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chapter 3: correct the reproducibility attribution and unify the naming of the established method and its implementation
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chapter 3: one name for the pair of codebases
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chapter 3: one name for the pair of codebases, everywhere
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chapter 3: name the estimator each sentence means
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update
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chapter 2: define the null/alternative pair, align the decay bound, expand abbreviations, and tidy equation labels
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chapter 2: remove the unreported Shigella comparison and state the data requirement directly
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chapter 2: drop a forward promise the sensitivity analysis does not keep
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chapter 2: one name for the alternative condition in both captions
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Commits on Sep 5, 2026

chapter 2: drop an objective the chapter no longer reports
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consolidate the deferred items for chapters 2 and 3 into one file
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chapter 2: one name for the model-free correlations
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record the ch2 L1012 repetition as deferred
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Appendix D: serocalculator is also used for the reference comparison
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Appendix D: chapter 3 fits no models
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bring chapters 2 and 3 up to date from the standalone manuscripts
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chapters 3 and thesis: the product form averages, it does not take medians
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Appendix D: say what chapter 3 does instead of fitting
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Introduction and Conclusion: cite what the chapters say about cohort size and sampling
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bridge: explain the pathogen change from what the model requires
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Introduction: summarise the bridge rather than assert what chapter 2 no longer says
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chore: record the current chapter and dissertation hashes
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abstract: state chapter 1's pooling result as chapter 1 states it
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add acknowledgments
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Commits on Sep 6, 2026

Commits on Sep 7, 2026

conclusion: drop an intensifier the numbers already carry
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record the last deferred items and remove the working standard
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set the table font for non-ASCII characters and restore the heading size hierarchy
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centre the front matter headings
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deferred.md: one sentence per line
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add acknowledgment names and two terms to the spellcheck dictionary
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thesis: add figure alt text for accessibility
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Commits on Sep 9, 2026

Commits on Sep 10, 2026

Commits on Sep 11, 2026

Commits on Sep 12, 2026

Merge branch 'main' into thesis-draft
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