Literature DB >> 33499782

A biologist's guide to model selection and causal inference.

Zachary M Laubach1,2, Eleanor J Murray3, Kim L Hoke4, Rebecca J Safran1, Wei Perng5.   

Abstract

A goal of many research programmes in biology is to extract meaningful insights from large, complex datasets. Researchers in ecology, evolution and behavior (EEB) often grapple with long-term, observational datasets from which they construct models to test causal hypotheses about biological processes. Similarly, epidemiologists analyse large, complex observational datasets to understand the distribution and determinants of human health. A key difference in the analytical workflows for these two distinct areas of biology is the delineation of data analysis tasks and explicit use of causal directed acyclic graphs (DAGs), widely adopted by epidemiologists. Here, we review the most recent causal inference literature and describe an analytical workflow that has direct applications for EEB. We start this commentary by defining four distinct analytical tasks (description, prediction, association, causal inference). The remainder of the text is dedicated to causal inference, specifically focusing on the use of DAGs to inform the modelling strategy. Given the increasing interest in causal inference and misperceptions regarding this task, we seek to facilitate an exchange of ideas between disciplinary silos and provide an analytical framework that is particularly relevant for making causal inference from observational data.

Entities:  

Keywords:  association; causal inference; description; directed acyclic graphs; epidemiology; prediction

Mesh:

Year:  2021        PMID: 33499782      PMCID: PMC7893255          DOI: 10.1098/rspb.2020.2815

Source DB:  PubMed          Journal:  Proc Biol Sci        ISSN: 0962-8452            Impact factor:   5.349


  23 in total

1.  When is baseline adjustment useful in analyses of change? An example with education and cognitive change.

Authors:  M Maria Glymour; Jennifer Weuve; Lisa F Berkman; Ichiro Kawachi; James M Robins
Journal:  Am J Epidemiol       Date:  2005-06-29       Impact factor: 4.897

2.  Directed acyclic graphs, sufficient causes, and the properties of conditioning on a common effect.

Authors:  Tyler J VanderWeele; James M Robins
Journal:  Am J Epidemiol       Date:  2007-08-16       Impact factor: 4.897

3.  Causal diagrams for epidemiologic research.

Authors:  S Greenland; J Pearl; J M Robins
Journal:  Epidemiology       Date:  1999-01       Impact factor: 4.822

4.  The Simpson's paradox unraveled.

Authors:  Miguel A Hernán; David Clayton; Niels Keiding
Journal:  Int J Epidemiol       Date:  2011-03-30       Impact factor: 7.196

5.  An introduction to g methods.

Authors:  Ashley I Naimi; Stephen R Cole; Edward H Kennedy
Journal:  Int J Epidemiol       Date:  2017-04-01       Impact factor: 7.196

6.  Ensemble learning of inverse probability weights for marginal structural modeling in large observational datasets.

Authors:  Susan Gruber; Roger W Logan; Inmaculada Jarrín; Susana Monge; Miguel A Hernán
Journal:  Stat Med       Date:  2014-10-15       Impact factor: 2.373

7.  Assessing mediation using marginal structural models in the presence of confounding and moderation.

Authors:  Donna L Coffman; Wei Zhong
Journal:  Psychol Methods       Date:  2012-08-20

8.  "Toward a clearer definition of confounding" revisited with directed acyclic graphs.

Authors:  Penelope P Howards; Enrique F Schisterman; Charles Poole; Jay S Kaufman; Clarice R Weinberg
Journal:  Am J Epidemiol       Date:  2012-08-17       Impact factor: 4.897

9.  The Challenges of Parameterizing Direct Effects in Individual-Level Simulation Models.

Authors:  Eleanor J Murray; James M Robins; George R Seage; Kenneth A Freedberg; Miguel A Hernán
Journal:  Med Decis Making       Date:  2020-01       Impact factor: 2.583

10.  Overadjustment bias and unnecessary adjustment in epidemiologic studies.

Authors:  Enrique F Schisterman; Stephen R Cole; Robert W Platt
Journal:  Epidemiology       Date:  2009-07       Impact factor: 4.822

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  10 in total

1.  Maternal Diet Quality Is Associated with Placental Proteins in the Placental Insulin/Growth Factor, Environmental Stress, Inflammation, and mTOR Signaling Pathways: The Healthy Start ECHO Cohort.

Authors:  Ellen C Francis; Dana Dabelea; Kristen E Boyle; Thomas Jansson; Wei Perng
Journal:  J Nutr       Date:  2022-03-03       Impact factor: 4.798

2.  Both prey and predator features predict the individual predation risk and survival of schooling prey.

Authors:  Jolle Wolter Jolles; Matthew M G Sosna; Geoffrey P F Mazué; Colin R Twomey; Joseph Bak-Coleman; Daniel I Rubenstein; Iain D Couzin
Journal:  Elife       Date:  2022-07-19       Impact factor: 8.713

3.  Associations between Toxoplasma gondii infection and steroid hormone levels in spotted hyenas.

Authors:  Zachary M Laubach; Eben Gering; Erik Yang; Tracy M Montgomery; Thomas Getty; Kay E Holekamp
Journal:  Int J Parasitol Parasites Wildl       Date:  2021-11-29       Impact factor: 2.674

4.  Dissecting Genomic Determinants of Positive Selection with an Evolution-Guided Regression Model.

Authors:  Yi-Fei Huang
Journal:  Mol Biol Evol       Date:  2022-01-07       Impact factor: 16.240

5.  Coevolution of relative brain size and life expectancy in parrots.

Authors:  Simeon Q Smeele; Dalia A Conde; Annette Baudisch; Simon Bruslund; Andrew Iwaniuk; Johanna Staerk; Timothy F Wright; Anna M Young; Mary Brooke McElreath; Lucy Aplin
Journal:  Proc Biol Sci       Date:  2022-03-23       Impact factor: 5.349

6.  Matrilateral bias of grandparental investment in grandchildren persists despite the grandchildren's adverse early life experiences.

Authors:  Samuli Helle; Antti O Tanskanen; David A Coall; Mirkka Danielsbacka
Journal:  Proc Biol Sci       Date:  2022-02-16       Impact factor: 5.349

Review 7.  Applications of conceptual models from lifecourse epidemiology in ecology and evolutionary biology.

Authors:  Zachary M Laubach; Kay E Holekamp; Izzuddin M Aris; Natalie Slopen; Wei Perng
Journal:  Biol Lett       Date:  2022-07-20       Impact factor: 3.812

8.  Characterization of Maternal Psychosocial Stress During Pregnancy: The Healthy Start Study.

Authors:  Satvinder K Dhaliwal; Dana Dabelea; Angela E Lee-Winn; Deborah H Glueck; Greta Wilkening; Wei Perng
Journal:  Womens Health Rep (New Rochelle)       Date:  2022-08-04

9.  Using relative brain size as predictor variable: Serious pitfalls and solutions.

Authors:  Simeon Q Smeele
Journal:  Ecol Evol       Date:  2022-09-20       Impact factor: 3.167

10.  Repeated Measures of Modified Rankin Scale Scores to Assess Functional Recovery From Stroke: AFFINITY Study Findings.

Authors:  Alexander Chye; Maree L Hackett; Graeme J Hankey; Erik Lundström; Osvaldo P Almeida; John Gommans; Martin Dennis; Stephen Jan; Gillian E Mead; Andrew H Ford; Christopher Etherton Beer; Leon Flicker; Candice Delcourt; Laurent Billot; Craig S Anderson; Katharina Stibrant Sunnerhagen; Qilong Yi; Severine Bompoint; Thang Huy Nguyen; Thomas Lung
Journal:  J Am Heart Assoc       Date:  2022-08-05       Impact factor: 6.106

  10 in total

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