From 97aaec32b2a58ba90f9d9465d7cff27e68538a1b Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Wed, 3 Jun 2026 12:57:29 -0700 Subject: [PATCH 1/4] Brace-protect capitalization in references.bib titles Wrap letters that must stay capitalized in sentence-case titles so sentence-case citation styles don't lowercase them: - acronyms: {EM}, {SAS}, {SPSS}, {WinBUGS} - software/proper nouns: {R} (mid-title), {BuCy2}, {Fisher}, {Bayesian} - named studies: {Nurses' Health Study}, {Heart and Estrogen/progestin Replacement Study}, {Western Collaborative Group Study}, {Gaspe Peninsula} (The hepatitis {C} fix in tsui2009hcv is on the count-regression PR branch, where that entry lives.) Co-Authored-By: Claude Opus 4.8 (1M context) Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com> --- references.bib | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/references.bib b/references.bib index c4c0be3eda..fb1b36a27c 100644 --- a/references.bib +++ b/references.bib @@ -100,7 +100,7 @@ @article{Walter2001 } @article{Grodstein2001, - title={Postmenopausal hormone use and secondary prevention of coronary events in the Nurses' Health Study: a prospective, observational study}, + title={Postmenopausal hormone use and secondary prevention of coronary events in the {Nurses' Health Study}: a prospective, observational study}, author={Grodstein, Francine and Manson, JoAnn E. and Stampfer, Meir J. and Colditz, Graham A. and Willett, Walter C. and Rosner, Bernard and Speizer, Frank E. and Hennekens, Charles H.}, journal={Annals of Internal Medicine}, year={2001}, @@ -121,7 +121,7 @@ @article{Orwoll1996 } @article{Vittinghoff2003, - title={Risk factors and secondary prevention in women with heart disease: the Heart and Estrogen/progestin Replacement Study}, + title={Risk factors and secondary prevention in women with heart disease: the {Heart and Estrogen/progestin Replacement Study}}, author={Vittinghoff, Eric and Shlipak, Michael G. and Varosy, Peter D. and McDermott, Mary and Robbins, John A. and Harris, Tamara B. and Newman, Anne B. and Bauer, Douglas C.}, journal={Annals of Internal Medicine}, year={2003}, @@ -202,7 +202,7 @@ @book{dobson4e } @book{mclachlan2007em, - title={The EM algorithm and extensions}, + title={The {EM} algorithm and extensions}, author={McLachlan, Geoffrey J and Krishnan, Thriyambakam}, year={2007}, edition={2}, @@ -276,7 +276,7 @@ @article{lawrance2020estimand } @article{efron1978assessing, - title={Assessing the accuracy of the maximum likelihood estimator: Observed versus expected Fisher information}, + title={Assessing the accuracy of the maximum likelihood estimator: Observed versus expected {Fisher} information}, author={Efron, Bradley and Hinkley, David V}, journal={Biometrika}, volume={65}, @@ -434,7 +434,7 @@ @Manual{venablescodingMatrices } @article{anderson1935irises, - title={The irises of the Gaspe Peninsula}, + title={The irises of the {Gaspe Peninsula}}, author={Anderson, Edgar}, journal={Bulletin of American Iris Society}, volume={59}, @@ -608,7 +608,7 @@ @book{kuhn2022tidy } @book{kleinman2009sas, - title={SAS and R: Data management, statistical analysis, and graphics}, + title={SAS and {R}: Data management, statistical analysis, and graphics}, author={Kleinman, Ken and Horton, Nicholas J}, year={2009}, publisher={Chapman and Hall/CRC}, @@ -652,7 +652,7 @@ @book{NahhasIntroR } @article{rosenman1975coronary, - title={Coronary heart disease in the Western Collaborative Group Study: Final follow-up experience of 8 1/2 years}, + title={Coronary heart disease in the {Western Collaborative Group Study}: Final follow-up experience of 8 1/2 years}, author={Rosenman, Ray H and Brand, Richard J and Jenkins, C David and Friedman, Meyer and Straus, Reuben and Wurm, Moses}, journal={JAMA}, volume={233}, @@ -749,7 +749,7 @@ @book{agresti2018introcat } @article{copelan1991treatment, - title={Treatment for acute myelocytic leukemia with allogeneic bone marrow transplantation following preparation with BuCy2}, + title={Treatment for acute myelocytic leukemia with allogeneic bone marrow transplantation following preparation with {BuCy2}}, author={Copelan, Edward A and Biggs, James C and Thompson, James M and Crilley, Pamela and Szer, Jeff and Klein, John P and Kapoor, Neena and Avalos, Belinda R and Cunningham, Isabel and Atkinson, Kerry}, year={1991}, doi={10.1182/blood.V78.3.838.838} @@ -882,7 +882,7 @@ @book{suarez2017applications } @book{muenchen2011r, - title={R for SAS and SPSS users}, + title={R for {SAS} and {SPSS} users}, author={Muenchen, Robert A}, year={2011}, publisher={Springer Science \& Business Media}, @@ -911,7 +911,7 @@ @inbook{newey1994large } @article{aragon2018population, - title={Population health thinking with Bayesian networks}, + title={Population health thinking with {Bayesian} networks}, author={Aragon, Tomas J}, year={2018}, url={https://escholarship.org/uc/item/8000r5m5} @@ -1381,14 +1381,14 @@ @book{realanalysislifesaver @book{kery-bayes-pop, author = {Kéry, Marc. and Schaub, Michael. and Beissinger, Steven R.}, address = {Boston}, -booktitle = {Bayesian population analysis using WinBUGS : a hierarchical perspective}, +booktitle = {Bayesian population analysis using {WinBUGS} : a hierarchical perspective}, edition = {1st ed.}, isbn = {9786613272829}, keywords = {Population biology -- Data processing ; R (Computer program language) ; WinBUGS}, language = {eng}, lccn = {2011029641}, publisher = {Academic Press}, -title = {Bayesian population analysis using WinBUGS : a hierarchical perspective }, +title = {Bayesian population analysis using {WinBUGS} : a hierarchical perspective }, year = {2012}, url={https://shop.elsevier.com/books/bayesian-population-analysis-using-winbugs/kery/978-0-12-387020-9} } @@ -1427,7 +1427,7 @@ @book{korner.bayes.ecology @book{statrethink2e, author = {McElreath, Richard}, address = {Boca Raton, FL}, -booktitle = {Statistical rethinking : a Bayesian course with examples in {R} and {Stan}}, +booktitle = {Statistical rethinking : a {Bayesian} course with examples in {R} and {Stan}}, edition = {Second edition}, isbn = {036713991X}, keywords = {Théorie de la décision bayésienne ; R (Langage de programmation) ; Théorème de Bayes ; Logiciels ; software ; Computer software ; Computer programs ; Bayesian statistical decision theory ; R (Computer program language) ; Bayes-Entscheidungstheorie ; R Programm ; Statistisches Modell ; Mathematics}, From 431db108fa277e5583cbfa637e283ff71bd589b3 Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Wed, 3 Jun 2026 13:06:39 -0700 Subject: [PATCH 2/4] Fix broken cross-references across the book From a whole-book crossref audit: - @sec-linreg-inference -> @sec-infer-LMs (the anchor was never defined; sec-infer-LMs is the LM-inference section). - Add the named anchors the links expect: {#sec-intro-MLEs} on the intro-MLEs H1 and {#sec-CI} on the "Confidence intervals" heading, so intro-MLEs.qmd#sec-intro-MLEs (x2) and inference.qmd#sec-CI resolve. - intro-bayes.qmd#sec-bayes -> bare intro-bayes.qmd (no such anchor; the link points at the chapter). - count-regression.qmd#sec-count-reg -> bare count-regression.qmd (no such anchor). - OR-RR.qmd (orphan, never rendered) -> logistic-regression.qmd#sec-OR-RR. The count-regression poisson.qmd#def-offset link is handled on the count-regression PR branch. Co-Authored-By: Claude Opus 4.8 (1M context) Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com> --- _subfiles/math-prereqs/_sec_linear_algebra.qmd | 2 +- .../_sec-surv-conditional-hazards.qmd | 2 +- chapters/basic-statistical-methods.qmd | 2 +- chapters/inference.qmd | 4 ++-- chapters/intro-MLEs.qmd | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/_subfiles/math-prereqs/_sec_linear_algebra.qmd b/_subfiles/math-prereqs/_sec_linear_algebra.qmd index b0aee58cc7..fdadc05a67 100644 --- a/_subfiles/math-prereqs/_sec_linear_algebra.qmd +++ b/_subfiles/math-prereqs/_sec_linear_algebra.qmd @@ -740,7 +740,7 @@ They occur frequently in statistics: - The residual sum of squares in linear regression (@sec-vector-calculus) is a quadratic form. - The variance of a linear combination of estimates - (@sec-linreg-inference) is a quadratic form: + (@sec-infer-LMs) is a quadratic form: $\Var{\tp{\vx}\hat{\vb}} = \tp{\vx}\,\Var{\hat{\vb}}\,\vx$. ::: diff --git a/_subfiles/proportional-hazards-models/_sec-surv-conditional-hazards.qmd b/_subfiles/proportional-hazards-models/_sec-surv-conditional-hazards.qmd index 903f8dba08..a6e07dbb0a 100644 --- a/_subfiles/proportional-hazards-models/_sec-surv-conditional-hazards.qmd +++ b/_subfiles/proportional-hazards-models/_sec-surv-conditional-hazards.qmd @@ -69,7 +69,7 @@ Now, let's define ***how*** the hazard function depends on covariates. We typically use a log link to model the relationship between the hazard function, $\haz(t|\vx)$, and the linear component, $\eta(t|\vx)$, -as we did for Poisson models in [models for count outcomes](count-regression.qmd#sec-count-reg); +as we did for Poisson models in [models for count outcomes](count-regression.qmd); that is: ::: diff --git a/chapters/basic-statistical-methods.qmd b/chapters/basic-statistical-methods.qmd index 5eea733146..6c8775ac2a 100644 --- a/chapters/basic-statistical-methods.qmd +++ b/chapters/basic-statistical-methods.qmd @@ -556,7 +556,7 @@ fisher.test(hers$exercise, hers$HT) ## Measures of association for 2×2 tables {#sec-2x2-measures} -See [Odds Ratios and Relative Risks](OR-RR.qmd) for definitions and formulas. +See [Odds Ratios and Relative Risks](logistic-regression.qmd#sec-OR-RR) for definitions and formulas. # Correlation {#sec-correlation} diff --git a/chapters/inference.qmd b/chapters/inference.qmd index 4e6c33b218..0676a20784 100644 --- a/chapters/inference.qmd +++ b/chapters/inference.qmd @@ -27,7 +27,7 @@ based on the data (and our prior beliefs). There are two predominant paradigms for statistical inference: -1. [Bayesian inference](intro-bayes.qmd#sec-bayes) +1. [Bayesian inference](intro-bayes.qmd) 2. [Frequentist inference](intro-MLEs.qmd#sec-intro-MLEs) # Interpretation of Negative Findings @@ -68,7 +68,7 @@ To do: convert this sketch into a nicely formatted figure. See also @vittinghoff2e §3.7 (p64). -# Confidence intervals +# Confidence intervals {#sec-CI} :::{#def-margin-error} ## margin of error diff --git a/chapters/intro-MLEs.qmd b/chapters/intro-MLEs.qmd index b3772617ec..0f9cef3b90 100644 --- a/chapters/intro-MLEs.qmd +++ b/chapters/intro-MLEs.qmd @@ -20,7 +20,7 @@ Some material was also taken from @mclachlan2007em and @CaseBerg01. {{< include shared-config.qmd >}} -# Overview of maximum likelihood estimation +# Overview of maximum likelihood estimation {#sec-intro-MLEs} {{< include _subfiles/intro-MLEs/_sec_likelihood.qmd >}} From 320b507b6288d58338300d945a027a8e7506e5d0 Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Wed, 3 Jun 2026 15:27:14 -0700 Subject: [PATCH 3/4] fix(bib): brace-protect SAS at start of kleinman2009sas title Only the first character of a title is auto-protected in BibTeX sentence-case conversion, so AS would be lowercased to 'as'. Wrap SAS in braces to preserve the acronym. Co-Authored-By: Claude Opus 4.8 --- references.bib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/references.bib b/references.bib index fb1b36a27c..845703a653 100644 --- a/references.bib +++ b/references.bib @@ -608,7 +608,7 @@ @book{kuhn2022tidy } @book{kleinman2009sas, - title={SAS and {R}: Data management, statistical analysis, and graphics}, + title={{SAS} and {R}: Data management, statistical analysis, and graphics}, author={Kleinman, Ken and Horton, Nicholas J}, year={2009}, publisher={Chapman and Hall/CRC}, From 8fdc87c6a09745058f304004147fa2dcc1cebcc3 Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Thu, 4 Jun 2026 14:27:18 -0700 Subject: [PATCH 4/4] Fix crossrefs swallowed by Pandoc example-list syntax MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit A `(@ref)` at the start of a (wrapped) line inside a bullet-list item is parsed by Pandoc as an example-list marker `(@label)`, not a cross-reference: the label is consumed and the following text becomes an `
    ` item, so the crossref silently vanishes in the rendered output. Move the `(@ref)` to the end of the preceding line so it parses inline: - _sec_linear_algebra.qmd: @sec-vector-calculus, @sec-infer-LMs (the "quadratic forms" list — both were rendering blank). - _calc_integrals_ftc.qmd: @eq-ftc-deriv-of-integral, @eq-ftc-part2 (the FTC Part 1 / Part 2 list). (Six other `(@…)`-at-line-start spots exist but sit in plain paragraphs, not list items, so Pandoc renders them correctly; left unchanged.) Co-Authored-By: Claude Opus 4.8 (1M context) --- _subfiles/math-prereqs/_calc_integrals_ftc.qmd | 6 ++---- _subfiles/math-prereqs/_sec_linear_algebra.qmd | 8 ++++---- 2 files changed, 6 insertions(+), 8 deletions(-) diff --git a/_subfiles/math-prereqs/_calc_integrals_ftc.qmd b/_subfiles/math-prereqs/_calc_integrals_ftc.qmd index d8ae941bde..2550ad1215 100644 --- a/_subfiles/math-prereqs/_calc_integrals_ftc.qmd +++ b/_subfiles/math-prereqs/_calc_integrals_ftc.qmd @@ -45,11 +45,9 @@ $$\int_a^x \dif{F}{t}\,dt = F(x) - F(a)$$ The two parts of the FTC together express that **differentiation and integration are inverse operations**: -- Part 1: differentiating the integral of $f$ recovers $f$ - (@eq-ftc-deriv-of-integral). +- Part 1: differentiating the integral of $f$ recovers $f$ (@eq-ftc-deriv-of-integral). - Part 2: the integral of $f$ over $[a, b]$ equals the difference of - any antiderivative's values at the endpoints - (@eq-ftc-part2), + any antiderivative's values at the endpoints (@eq-ftc-part2), which rearranges to "integrating the derivative of $F$ recovers the net change in $F$" (@eq-ftc-integral-of-deriv). diff --git a/_subfiles/math-prereqs/_sec_linear_algebra.qmd b/_subfiles/math-prereqs/_sec_linear_algebra.qmd index fdadc05a67..61cb8b1fa1 100644 --- a/_subfiles/math-prereqs/_sec_linear_algebra.qmd +++ b/_subfiles/math-prereqs/_sec_linear_algebra.qmd @@ -737,10 +737,10 @@ and $\matr{S}$ is a $p \times p$ matrix. Quadratic forms are the matrix generalizations of the scalar expression $c x^2$. They occur frequently in statistics: -- The residual sum of squares in linear regression - (@sec-vector-calculus) is a quadratic form. -- The variance of a linear combination of estimates - (@sec-infer-LMs) is a quadratic form: +- The residual sum of squares in linear regression (@sec-vector-calculus) + is a quadratic form. +- The variance of a linear combination of estimates (@sec-infer-LMs) + is a quadratic form: $\Var{\tp{\vx}\hat{\vb}} = \tp{\vx}\,\Var{\hat{\vb}}\,\vx$. :::