Merge branch 'main' into style/apply-some-style-fixes

includes/papers.bib

@@ -212,6 +212,24 @@ @article{hejazi_nonparametric_2023
 	file = {Full Text:C\:\\Users\\au302898\\Zotero\\storage\\AXW83NSR\\Hejazi et al. - 2023 - Nonparametric causal mediation analysis for stocha.pdf:application/pdf;Snapshot:C\:\\Users\\au302898\\Zotero\\storage\\LPH48GQ5\\6518842.html:text/html},
 }
 
+@article{tennant_use_2021,
+	title = {Use of directed acyclic graphs ({DAGs}) to identify confounders in applied health research: review and recommendations},
+	volume = {50},
+	issn = {0300-5771},
+	shorttitle = {Use of directed acyclic graphs ({DAGs}) to identify confounders in applied health research},
+	url = {https://doi.org/10.1093/ije/dyaa213},
+	doi = {10.1093/ije/dyaa213},
+	abstract = {Directed acyclic graphs (DAGs) are an increasingly popular approach for identifying confounding variables that require conditioning when estimating causal effects. This review examined the use of DAGs in applied health research to inform recommendations for improving their transparency and utility in future research.Original health research articles published during 1999–2017 mentioning ‘directed acyclic graphs’ (or similar) or citing DAGitty were identified from Scopus, Web of Science, Medline and Embase. Data were extracted on the reporting of: estimands, DAGs and adjustment sets, alongside the characteristics of each article’s largest DAG.A total of 234 articles were identified that reported using DAGs. A fifth (n = 48, 21\%) reported their target estimand(s) and half (n = 115, 48\%) reported the adjustment set(s) implied by their DAG(s). Two-thirds of the articles (n = 144, 62\%) made at least one DAG available. DAGs varied in size but averaged 12 nodes [interquartile range (IQR): 9–16, range: 3–28] and 29 arcs (IQR: 19–42, range: 3–99). The median saturation (i.e. percentage of total possible arcs) was 46\% (IQR: 31–67, range: 12–100). 37\% (n = 53) of the DAGs included unobserved variables, 17\% (n = 25) included ‘super-nodes’ (i.e. nodes containing more than one variable) and 34\% (n = 49) were visually arranged so that the constituent arcs flowed in the same direction (e.g. top-to-bottom).There is substantial variation in the use and reporting of DAGs in applied health research. Although this partly reflects their flexibility, it also highlights some potential areas for improvement. This review hence offers several recommendations to improve the reporting and use of DAGs in future research.},
+	number = {2},
+	urldate = {2023-11-13},
+	journal = {International Journal of Epidemiology},
+	author = {Tennant, Peter W G and Murray, Eleanor J and Arnold, Kellyn F and Berrie, Laurie and Fox, Matthew P and Gadd, Sarah C and Harrison, Wendy J and Keeble, Claire and Ranker, Lynsie R and Textor, Johannes and Tomova, Georgia D and Gilthorpe, Mark S and Ellison, George T H},
+	month = apr,
+	year = {2021},
+	pages = {620--632},
+	file = {Full Text PDF:C\:\\Users\\au302898\\Zotero\\storage\\8VHSWBIW\\Tennant et al. - 2021 - Use of directed acyclic graphs (DAGs) to identify .pdf:application/pdf;Snapshot:C\:\\Users\\au302898\\Zotero\\storage\\66YCGNQA\\6012812.html:text/html},
+}
+
 @article{imai_experimental_2013,
 	title = {Experimental designs for identifying causal mechanisms},
 	volume = {176},
@@ -227,3 +245,114 @@ @article{imai_experimental_2013
 	pages = {5--32},
 	file = {JSTOR Full Text PDF:C\:\\Users\\au302898\\Zotero\\storage\\VVDRTH4L\\Imai et al. - 2013 - Experimental designs for identifying causal mechan.pdf:application/pdf},
 }
+
+@article{hernan_definition_2004,
+	title = {A definition of causal effect for epidemiological research},
+	volume = {58},
+	issn = {0143-005X},
+	url = {https://jech.bmj.com/lookup/doi/10.1136/jech.2002.006361},
+	doi = {10.1136/jech.2002.006361},
+	language = {en},
+	number = {4},
+	urldate = {2024-05-06},
+	journal = {Journal of Epidemiology \& Community Health},
+	author = {Hernan, M A},
+	month = apr,
+	year = {2004},
+	pages = {265--271},
+	file = {Hernan - 2004 - A definition of causal effect for epidemiological .pdf:C\:\\Users\\au302898\\Zotero\\storage\\8AUZ5YHH\\Hernan - 2004 - A definition of causal effect for epidemiological .pdf:application/pdf},
+}
+
+@article{knoch_diminishing_2006,
+	title = {Diminishing {Reciprocal} {Fairness} by {Disrupting} the {Right} {Prefrontal} {Cortex}},
+	volume = {314},
+	url = {https://www.science.org/doi/10.1126/science.1129156},
+	doi = {10.1126/science.1129156},
+	abstract = {Humans restrain self-interest with moral and social values. They are the only species known to exhibit reciprocal fairness, which implies the punishment of other individuals' unfair behaviors, even if it hurts the punisher's economic self-interest. Reciprocal fairness has been demonstrated in the Ultimatum Game, where players often reject their bargaining partner's unfair offers. Despite progress in recent years, however, little is known about how the human brain limits the impact of selfish motives and implements fair behavior. Here we show that disruption of the right, but not the left, dorsolateral prefrontal cortex (DLPFC) by low-frequency repetitive transcranial magnetic stimulation substantially reduces subjects' willingness to reject their partners' intentionally unfair offers, which suggests that subjects are less able to resist the economic temptation to accept these offers. Importantly, however, subjects still judge such offers as very unfair, which indicates that the right DLPFC plays a key role in the implementation of fairness-related behaviors.},
+	number = {5800},
+	urldate = {2024-05-07},
+	journal = {Science},
+	author = {Knoch, Daria and Pascual-Leone, Alvaro and Meyer, Kaspar and Treyer, Valerie and Fehr, Ernst},
+	month = nov,
+	year = {2006},
+	note = {Publisher: American Association for the Advancement of Science},
+	pages = {829--832},
+	file = {Full Text:C\:\\Users\\au302898\\Zotero\\storage\\JYUF88C2\\Knoch et al. - 2006 - Diminishing Reciprocal Fairness by Disrupting the .pdf:application/pdf},
+}
+
+@article{vanderweele_unification_2014,
+	title = {A unification of mediation and interaction: a four-way decomposition},
+	volume = {25},
+	issn = {1044-3983},
+	shorttitle = {A unification of mediation and interaction},
+	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4220271/},
+	doi = {10.1097/EDE.0000000000000121},
+	abstract = {It is shown that the overall effect of an exposure on an outcome, in the presence of a mediator with which the exposure may interact, can be decomposed into four components: (i) the effect of the exposure in the absence of the mediator, (ii) the interactive effect when the mediator is left to what it would be in the absence of exposure, (iii) a mediated interaction, and (iv) a pure mediated effect. These four components, respectively, correspond to the portion of the effect that is due to neither mediation nor interaction, to just interaction (but not mediation), to both mediation and interaction, and to just mediation (but not interaction). This four-way decomposition unites methods that attribute effects to interactions and methods that assess mediation. Certain combinations of these four components correspond to measures for mediation, while other combinations correspond to measures of interaction previously proposed in the literature. Prior decompositions in the literature are in essence special cases of this four-way decomposition. The four-way decomposition can be carried out using standard statistical models, and software is provided to estimate each of the four components. The four-way decomposition provides maximum insight into how much of an effect is mediated, how much is due to interaction, how much is due to both mediation and interaction together, and how much is due to neither.},
+	number = {5},
+	urldate = {2024-05-14},
+	journal = {Epidemiology (Cambridge, Mass.)},
+	author = {VanderWeele, Tyler J.},
+	month = sep,
+	year = {2014},
+	pmid = {25000145},
+	pmcid = {PMC4220271},
+	pages = {749--761},
+	file = {PubMed Central Full Text PDF:C\:\\Users\\au302898\\Zotero\\storage\\KP58X3BY\\VanderWeele - 2014 - A unification of mediation and interaction a four.pdf:application/pdf},
+}
+
+@article{valeri_mediation_2013,
+	title = {Mediation analysis allowing for exposure-mediator interactions and causal interpretation: theoretical assumptions and implementation with {SAS} and {SPSS} macros},
+	volume = {18},
+	issn = {1082-989X},
+	shorttitle = {Mediation analysis allowing for exposure-mediator interactions and causal interpretation},
+	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3659198/},
+	doi = {10.1037/a0031034},
+	abstract = {Mediation analysis is a useful and widely employed approach to studies in the field of psychology and in the social and biomedical sciences. The contributions of this paper are several-fold. First we seek to bring the developments in mediation analysis for non linear models within the counterfactual framework to the psychology audience in an accessible format and compare the sorts of inferences about mediation that are possible in the presence of exposure-mediator interaction when using a counterfactual versus the standard statistical approach. Second, the work by , ) is extended here to allow for dichotomous mediators and count outcomes. Third, we provide SAS and SPSS macros to implement all of these mediation analysis techniques automatically and we compare the types of inferences about mediation that are allowed by a variety of software macros.},
+	number = {2},
+	urldate = {2024-05-14},
+	journal = {Psychological methods},
+	author = {Valeri, Linda and VanderWeele, Tyler J.},
+	month = jun,
+	year = {2013},
+	pmid = {23379553},
+	pmcid = {PMC3659198},
+	pages = {137--150},
+	file = {PubMed Central Full Text PDF:C\:\\Users\\au302898\\Zotero\\storage\\KU33GJNP\\Valeri and VanderWeele - 2013 - Mediation analysis allowing for exposure-mediator .pdf:application/pdf},
+}
+
+@article{lee_guideline_2021,
+	title = {A {Guideline} for {Reporting} {Mediation} {Analyses} of {Randomized} {Trials} and {Observational} {Studies}: {The} {AGReMA} {Statement}},
+	volume = {326},
+	issn = {0098-7484},
+	shorttitle = {A {Guideline} for {Reporting} {Mediation} {Analyses} of {Randomized} {Trials} and {Observational} {Studies}},
+	url = {https://doi.org/10.1001/jama.2021.14075},
+	doi = {10.1001/jama.2021.14075},
+	abstract = {Mediation analyses of randomized trials and observational studies can generate evidence about the mechanisms by which interventions and exposures may influence health outcomes. Publications of mediation analyses are increasing, but the quality of their reporting is suboptimal.To develop international, consensus-based guidance for the reporting of mediation analyses of randomized trials and observational studies (A Guideline for Reporting Mediation Analyses; AGReMA).The AGReMA statement was developed using the Enhancing Quality and Transparency of Health Research (EQUATOR) methodological framework for developing reporting guidelines. The guideline development process included (1) an overview of systematic reviews to assess the need for a reporting guideline; (2) review of systematic reviews of relevant evidence on reporting mediation analyses; (3) conducting a Delphi survey with panel members that included methodologists, statisticians, clinical trialists, epidemiologists, psychologists, applied clinical researchers, clinicians, implementation scientists, evidence synthesis experts, representatives from the EQUATOR Network, and journal editors (n = 19; June-November 2019); (4) having a consensus meeting (n = 15; April 28-29, 2020); and (5) conducting a 4-week external review and pilot test that included methodologists and potential users of AGReMA (n = 21; November 2020).A previously reported overview of 54 systematic reviews of mediation studies demonstrated the need for a reporting guideline. Thirty-three potential reporting items were identified from 3 systematic reviews of mediation studies. Over 3 rounds, the Delphi panelists ranked the importance of these items, provided 60 qualitative comments for item refinement and prioritization, and suggested new items for consideration. All items were reviewed during a 2-day consensus meeting and participants agreed on a 25-item AGReMA statement for studies in which mediation analyses are the primary focus and a 9-item short-form AGReMA statement for studies in which mediation analyses are a secondary focus. These checklists were externally reviewed and pilot tested by 21 expert methodologists and potential users, which led to minor adjustments and consolidation of the checklists.The AGReMA statement provides recommendations for reporting primary and secondary mediation analyses of randomized trials and observational studies. Improved reporting of studies that use mediation analyses could facilitate peer review and help produce publications that are complete, accurate, transparent, and reproducible.},
+	number = {11},
+	urldate = {2024-05-15},
+	journal = {JAMA},
+	author = {Lee, Hopin and Cashin, Aidan G. and Lamb, Sarah E. and Hopewell, Sally and Vansteelandt, Stijn and VanderWeele, Tyler J. and MacKinnon, David P. and Mansell, Gemma and Collins, Gary S. and Golub, Robert M. and McAuley, James H. and {AGReMA group}},
+	month = sep,
+	year = {2021},
+	pages = {1045--1056},
+	file = {Full Text:C\:\\Users\\au302898\\Zotero\\storage\\NQXZ9UJC\\Lee et al. - 2021 - A Guideline for Reporting Mediation Analyses of Ra.pdf:application/pdf;Snapshot:C\:\\Users\\au302898\\Zotero\\storage\\64DKNNTG\\2784353.html:text/html},
+}
+
+@article{shi_cmaverse_2021,
+	title = {{CMAverse}: {A} {Suite} of {Functions} for {Reproducible} {Causal} {Mediation} {Analyses}},
+	volume = {32},
+	issn = {1044-3983},
+	shorttitle = {{CMAverse}},
+	url = {https://journals.lww.com/epidem/fulltext/2021/09000/cmaverse__a_suite_of_functions_for_reproducible.23.aspx},
+	doi = {10.1097/EDE.0000000000001378},
+	abstract = {An abstract is unavailable.},
+	language = {en-US},
+	number = {5},
+	urldate = {2024-05-27},
+	journal = {Epidemiology},
+	author = {Shi, Baoyi and Choirat, Christine and Coull, Brent A. and VanderWeele, Tyler J. and Valeri, Linda},
+	month = sep,
+	year = {2021},
+	pages = {e20},
+	file = {Snapshot:C\:\\Users\\au302898\\Zotero\\storage\\F2IBK8FH\\cmaverse__a_suite_of_functions_for_reproducible.23.html:text/html},
+}