Network analysis: a brief overview and tutorial

References

• Abegaz, F., & Wit, E. (2013). Sparse time series chain graphical models for reconstructing genetic networks. Biostatistics (Oxford, England), 14(3), 586–599. doi: 10.1093/biostatistics/kxt005
   PubMed Web of Science ®Google Scholar
• Ajzen, I. (1985). From intentions to actions: A theory of planned behavior. In J. Kuhl, & J. Beckman (Eds.), Action-control: From cognition to behavior (pp. 11–39). Heidelberg: Springer.
   Google Scholar
• Ajzen, I. (2011). The theory of planned behaviour: Reactions and reflections. Psychology & Health, 26, 1113–1127. doi: 10.1080/08870446.2011.613995
   PubMed Web of Science ®Google Scholar
• Babyak, M. A. (2004). What you see may not be what you get: A brief, nontechnical introduction to overfitting in regression-type models. Psychosomatic Medicine, 66(3), 411–421. doi: 10.1097/00006842-200405000-00021
   PubMed Web of Science ®Google Scholar
• Barabási, A. L. (2012). The network takeover. Nature Physics, 8, 14–16. doi: 10.1038/nphys2188
   Web of Science ®Google Scholar
• Beard, C., Millner, A. J., Forgeard, M. J. C., Fried, E. I., Hsu, K. J., Treadway, M. T., … Björgvinsson, T. (2016). Network analysis of depression and anxiety symptom relationships in a psychiatric sample. Psychological Medicine, 46(16), 3359–3369. doi: 10.1017/S0033291716002300
   PubMed Web of Science ®Google Scholar
• Bentler, P. M., & Satorra, A. (2010). Testing model nesting and equivalence. Psychological Methods, 15(2), 111–123. doi: 10.1037/a0019625
   PubMed Web of Science ®Google Scholar
• Blanken, T. F., Deserno, M. K., Dalege, J., Borsboom, D., Blanken, P., Kerkhof, G. A., & Cramer, A. O. J. (2018). The role of stabilizing and communicating symptoms given overlapping communities in psychopathology networks. Scientific Reports, 8, 59. doi: 10.1038/s41598-018-24224-2
   PubMed Web of Science ®Google Scholar
• Bollen, K. A., & Stine, R. A. (1992). Bootstrapping goodness-of-fit measures in structural equation models. Sociological Methods &Research, 21(2), 205–229. doi: 10.1177/0049124192021002004
   Web of Science ®Google Scholar
• Borgatti, S. P. (2005). Centrality and network flow. Social Networks, 27, 55–71. doi: 10.1016/j.socnet.2004.11.008
   Web of Science ®Google Scholar
• Borgatti, S. P., Everett, M. G., & Freeman, L. C. (2002). Ucinet for windows: Software for social network analysis. Harvard, MA: Analytic Technologies.
   Google Scholar
• Borgatti, S. P., Mehra, A., Brass, D. J., & Labianca, G. (2009). Network analysis in the social sciences. Science, 323, 892–895. doi: 10.1126/science.1165821
   PubMed Web of Science ®Google Scholar
• Borsboom, D. (2017). A network theory of mental disorders. World Psychiatry, 16, 5–13. doi: 10.1002/wps.20375
   PubMed Web of Science ®Google Scholar
• Borsboom, D., & Cramer, A. O. J. (2013). Network analysis: An integrative approach to the structure of psychopathology. Annual Review of Clinical Psychology, 9, 91–121. doi: 10.1146/annurev-clinpsy-050212-185608
   PubMed Web of Science ®Google Scholar
• Borsboom, D., Fried, E. I., Epskamp, S., Waldorp, L. J., van Borkulo, C. D., van der Maas, H. L. J., & Cramer, A. O. J. (2017). False alarm? A comprehensive reanalysis of “evidence that psychopathology symptom networks have limited replicability” by Forbes, Wright, Markon, and Krueger (2017). Journal of Abnormal Psychology, 126(7), 989–999. doi: 10.1037/abn0000306
   PubMed Web of Science ®Google Scholar
• Bringmann, L. F., Pe, M. L., Vissers, N., Ceulemans, E., Borsboom, D., Vanpaemel, W., … Kuppens, P. (2016). Assessing temporal emotion dynamics using networks. Assessment, 23(4), 425–435. doi: 10.1177/1073191116645909
   PubMed Web of Science ®Google Scholar
• Bringmann, L. F., Vissers, N., Wichers, M., Geschwind, N., Kuppens, P., Peeters, F., … de Erausquin, G. A. (2013). A network approach to psychopathology: New insights into clinical longitudinal data. PLoS ONE, 8(4), e60188. doi: 10.1371/journal.pone.0060188
   PubMed Web of Science ®Google Scholar
• Bullmore, E., & Sporns, O. (2009). Complex brain networks: Graph theoretical analysis of structural and functional systems. Nature Reviews Neuroscience, 10(3), 186–198. doi: 10.1038/nrn2575
   PubMed Web of Science ®Google Scholar
• Chen, J., & Chen, Z. (2008). Extended Bayesian information criteria for model selection with large model spaces. Biometrika, 95(3), 759–771. doi: 10.1093/biomet/asn034
   Web of Science ®Google Scholar
• Chernick, M. R. (2011). Bootstrap methods: A guide for practitioners and researchers. New York: Wiley.
   Google Scholar
• Clifton, A., & Webster, G. D. (2017). An introduction to social network analysis for personality and social psychologists. Social Psychological and Personality Science, 8(4), 442–453. doi: 10.1177/1948550617709114
   Web of Science ®Google Scholar
• Conner, M. (2015). Extending not retiring the theory of planned behaviour: A commentary on Sniehotta, Presseau and Araújo-Soares. Health Psychology Review, 9(2), 141–145. doi: 10.1080/17437199.2014.899060
   PubMed Web of Science ®Google Scholar
• Costantini, G., Epskamp, S., Borsboom, D., Perugini, M., Mõttus, R., Waldorp, L. J., & Cramer, A. O. J. (2015). State of the aRt personality research: A tutorial on network analysis of personality data in R. Journal of Research in Personality, 54, 13–29. doi: 10.1016/j.jrp.2014.07.003
   Web of Science ®Google Scholar
• Cramer, A. O. J., van Borkulo, C. D., Giltay, E. J., van der Maas, H. L. J., Kendler, K. S., Scheffer, M., … Branchi, I. (2016). Major depression as a complex dynamic system. PLoS ONE, 11(12), e0167490. doi: 10.1371/journal.pone.0167490
   PubMed Web of Science ®Google Scholar
• Cramer, A. O. J., Waldorp, L., van der Maas, H., & Borsboom, D. (2010). Comorbidity: A network perspective. Behavioral and Brain Sciences, 33(2–3), 137–150. doi: 10.1017/S0140525X09991567
   PubMed Web of Science ®Google Scholar
• Csárdi, G., & Nepusz, T. (2006). The Igraph Software Package for Complex Network Research. InterJournal, Complex Systems, 1695. Retrieved from http://igraph.org
   Google Scholar
• Dalege, J., Borsboom, D., van Harreveld, F., van den Berg, H., Conner, M., & van der Maas, H. L. J. (2015). Toward a formalized account of attitudes: The Causal Attitude Network (CAN) model. Psychological Review, 123(1), 2–22. doi: 10.1037/a0039802
   PubMed Web of Science ®Google Scholar
• Danaher, P., Wang, P., & Witten, D. M. (2014). The joint graphical lasso for inverse covariance estimation across multiple classes. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 76(2), 373–397. doi:10.1111/rssb.12033.
   PubMed Web of Science ®Google Scholar
• David, S. J., Marshall, A. J., Evanovich, E. K., & Mumma, H. (2018). Intraindividual dynamic network analysis – implications for clinical assessment. Journal of Psychopathology and Behavioral Assessment, 40, 235–248. doi: 10.1007/s10862-017-9632-8
   PubMed Web of Science ®Google Scholar
• De Schryver, M., Vindevogel, S., Rasmussen, A. E., & Cramer, A. O. J. (2015). Unpacking constructs: A network approach for studying war exposure, daily stressors and post-traumatic stress disorder. Frontiers in Psychology, 6, 4. doi: 10.3389/fpsyg.2015.01896
   PubMed Web of Science ®Google Scholar
• Efron, B. (1979). Bootstrap methods: Another look at the jackknife. The Annals of Statistics, 7(1), 1–26.
   Web of Science ®Google Scholar
• Engel, G. L. (1980). The clinical application of the biopsychosocial model. American Journal of Psychiatry, 137, 535–544. doi: 10.1176/ajp.137.5.535
   PubMed Web of Science ®Google Scholar
• Epskamp, S. (2018). Regularized Gaussian psychological networks: Brief report on the performance of extended BIC model selection. Retrieved from https://arxiv.org/abs/1606.05771
   Google Scholar
• Epskamp, S., Borsboom, D., & Fried, E. I. (2018a). Estimating psychological networks and their accuracy: A tutorial paper. Behavior Research Methods, 50(1), 195–212. doi: 10.3758/s13428-017-0862-1
   PubMed Web of Science ®Google Scholar
• Epskamp, S., Cramer, A., Waldorp, L., Schmittmann, V. D., & Borsboom, D. (2012). Qgraph: Network visualizations of relationships in psychometric data. Journal of Statistical Software, 48(1), 1–18. doi: 10.18637/jss.v048.i04
   Web of Science ®Google Scholar
• Epskamp, S., & Fried, E. I. (In Press). A tutorial on estimating regularized psychological networks. Psychological Methods, doi: 10.1037/met0000167
   Web of Science ®Google Scholar
• Epskamp, S., Kruis, J., Marsman, M., & Marinazzo, D. (2017). Estimating psychopathological networks: Be careful what you wish for. PLOS ONE, 12(6), e0179891.
   PubMed Web of Science ®Google Scholar
• Epskamp, S., Maris, G., Waldorp, L., & Borsboom, D. (In Press). Network psychometrics. In P. Irwing, D. Hughes, & T. Booth (Eds.), Handbook of psychometrics. New York, NY, USA: Wiley.
   Google Scholar
• Epskamp, S., van Borkulo, C. D., van der Veen, M. N., Servaas, M. N., Isvoranu, A.-M., Riese, H., & Cramer, A. O. J. (2018b). Personalized network modeling in psychopathology: The importance of contemporaneous and temporal connections. Clinical Psychological Science, 6(3), 416–427. doi: 10.1177/2167702617744325
   PubMed Web of Science ®Google Scholar
• Estrada, E., & Knight, P. A. (2015). A first course in network theory. Oxford: Oxford University Press.
   Google Scholar
• Fan, J., Feng, Y., & Wu, Y. (2009). Network exploration via the adaptive LASSO and SCAD penalties. The Annals of Applied Statistics, 3(2), 521–541. doi: 10.1214/08-AOAS215
   PubMed Web of Science ®Google Scholar
• Finegood, D. T., Merth, T. D. N., & Rutter, H. (2010). Implications of the foresight obesity system map for solutions to childhood obesity. Obesity, 18(Supplement1), S13–S16.
   PubMedGoogle Scholar
• Forbes, M. K., Wright, A. G. C., Markon, K. E., & Krueger, R. F. (2017). Evidence that psychopathology symptom networks have limited replicability. Journal of Abnormal Psychology, 126(7), 969–988. doi: 10.1037/abn0000276
   PubMed Web of Science ®Google Scholar
• Foygel, R., & Drton, M. (2010). Extended Bayesian information criteria for Gaussian graphical models. Advances in Neural Information Processing Systems, 23, 24th Annual Conference on Neural Information Processing Systems 2010, NIPS 2010.
   Google Scholar
• Foygel Barber, R., & Drton, M. (2015). High-dimensional ising model selection with Bayesian information criteria. Electronic Journal of Statistics, 9(1), 567–607. doi: 10.1214/154957804100000000
   Web of Science ®Google Scholar
• Freeman, L. C. (1978). Centrality in social networks conceptual clarification. Social Networks, 1(3), 215–239. doi: 10.1016/0378-8733(78)90021-7
   Web of Science ®Google Scholar
• Fried, E. I. (2016). R tutorial: how to identify communities of items in networks. Retrieved from http://psych-networks.com/r-tutorial-identify-communities-items-networks/
   Google Scholar
• Fried, E. I., & Cramer, A. O. J. (2017). Moving forward: Challenges and directions for psychopathological network theory and methodology. Perspectives on Psychological Science, 12(6), 999–1020. doi: 10.17605/OSF.IO/BNEK
   Web of Science ®Google Scholar
• Friedman, J., Hastie, T., & Tibshirani, R. (2008). Sparse inverse covariance estimation with the graphical lasso. Biostatistics (Oxford, England), 9(3), 432–441. doi: 10.1093/biostatistics/kxm045
   PubMed Web of Science ®Google Scholar
• Fruchterman, T. M. J., & Reingold, E. M. (1991). Graph drawing by force-directed placement. Software: Practice and Experience, 21(11), 1129–1164. doi: 10.1002/spe.4380211102
   Web of Science ®Google Scholar
• Granger, C. W. J. (1969). Investigating causal relations by econometric models and cross-spectral methods. Econometrica, 37(3), 424–438. doi: 10.2307/1912791
   Web of Science ®Google Scholar
• Greenland, S., Pearl, J., & Robins, J. M. (1999). Causal diagrams for epidemiologic research. Epidemiology, 10, 37–48.
   PubMed Web of Science ®Google Scholar
• Guo, J., Levina, E., Michailidis, G., & Zhu, J. (2011). Joint estimation of multiple graphical models. Biometrika, 98(1), 1–15. doi: 10.1093/biomet/asq060
   PubMed Web of Science ®Google Scholar
• Hagger, M. S., Chatzisarantis, N. L. D., & Biddle, S. J. H. (2002). A meta-analytic review of the theories of reasoned action and planned behavior in physical activity: Predictive validity and the contribution of additional variables. Journal of Sport & Exercise Psychology, 24(1), 3–32.
   Web of Science ®Google Scholar
• Haslbeck, J. M. B., & Waldorp, L. J. (2016). Structure estimation for mixed graphical models in high dimensional data. Retrieved from https://arxiv.org/abs/1510.05677
   Google Scholar
• Isvoranu, A. M., van Borkulo, C. D., Boyette, L., Wigman, J. T. W., Vinkers, C. H., Borsboom, D., … GROUP Investigators. (2017). A network approach to psychosis: Pathways between childhood trauma and psychotic symptoms. Schizophrenia Bulletin, 43(1), 187–196. doi: 10.1093/schbul/sbw055
   PubMed Web of Science ®Google Scholar
• Kelly, H. H. (1983). Perceived causal structures. In J. Jaspars, F. D. Fincham, & M. Hewstone (Eds.), Attribution theory and research: Conceptual, developmental and social dimensions (pp. 343–369). London: Academic Press.
   Google Scholar
• Kossakowski, J. J., Epskamp, S., Kieffer, J. M., van Borkulo, C. D., Rhemtulla, M., & Borsboom, D. (2016). The application of a network approach to health-related quality of life (HRQoL): Introducing a new method for assessing hrqol in healthy adults and cancer patient. Quality of Life Research, 25, 781–792. doi: 10.1007/s11136-015-1127-z
   PubMed Web of Science ®Google Scholar
• Krämer, N., Schäfer, J., & Boulesteix, A. L. (2009). Regularized estimation of large-scale gene association networks using graphical Gaussian models. BMC Bioinformatics, 10, 384. doi: 10.1186/1471-2105-10-384
   PubMed Web of Science ®Google Scholar
• Kroeze, R., van der Veen, D. C., Servaas, M. N., Bastiaansen, J. A., Oude Voshaar, R. C., Borsboom, D., … Riese, H. (2017). Personalized feedback on symptom dynamics of psychopathology: A proof-of-principle study. Journal for Person-Oriented Research, 3, 1–10.
   Google Scholar
• Langley, D. J., Wijn, R., Epskamp, S., & Van Bork, R. (2015). Should I get that Jab? Exploring Influence to encourage vaccination via online social media. ECIS 2015 Research-in-Progress Papers, Paper 64.
   Google Scholar
• Lauritzen, S. L. (1996). Graphical models. Oxford, UK: Clarendon Press.
   Google Scholar
• Lawton, R., Conner, M., & McEachan, R. (2009). Desire or reason: Predicting health behaviors from affective and cognitive attitudes. Health Psychology, 28, 56–65. doi: 10.1037/a0013424
   PubMed Web of Science ®Google Scholar
• Lehman, B. J., David, D. M., & Gruber, J. A. (2017). Rethinking the biopsychosocial model of health: Understanding health as a dynamic system. Social and Personality Psychology Compass, 11(8), e12282. doi: 10.1111/spc3.12328
   Web of Science ®Google Scholar
• Leigh Brown, A. J., Lycett, S. J., Weinert, L., Hughes, G. H., Fearnhill, E., & Dunn, D. T. (2011). Transmission network parameters estimated from HIV sequences for a nationwide epidemic. The Journal of Infectious Diseases, 204, 1463–1469. doi: 10.1093/infdis/jir550
   PubMed Web of Science ®Google Scholar
• Liu, H., Lafferty, J. D., & Wasserman, L. (2009). The nonparanormal: Semiparametric estimation of high dimensional undirected graphs. The Journal of Machine Learning Research, 10, 2295–2328.
   Web of Science ®Google Scholar
• MacCallum, R. C., Wegener, D. T., Uchino, B. N., & Fabrigar, L. R. (1993). The problem of equivalent models in applications of covariance structure analysis. Psychological Bulletin, 114(1), 185–199. doi: 10.1037/0033-2909.114.1.185
   PubMed Web of Science ®Google Scholar
• McEachan, R. R. C., Conner, M., Taylor, N., & Lawton, R. J. (2011). Prospective prediction of health-related behaviors with the theory of planned behavior: A meta-analysis. Health Psychology Review, 5, 97–144. doi: 10.1080/17437199.2010.521684
   Web of Science ®Google Scholar
• Milgram, S. (1967). The small-world problem. Psychology Today, 2, 60–67.
   Google Scholar
• Mõttus, R., & Allerhand, M. (2017). Why do traits come together? The underlying trait and network approaches. In V. Zeigler-Hill, & T. Shackelford (Eds.), SAGE handbook of personality and individual differences: Volume 1. The science of personality and individual differences (pp. 1–22). London: SAGE.
   Google Scholar
• Noar, S. M., & Zimmerman, R. S. (2005). Health behavior theory and cumulative knowledge regarding health behaviors: Are we moving in the right direction? Health Education Research, 20, 275–290. doi: 10.1093/her/cyg113
   PubMed Web of Science ®Google Scholar
• Opsahl, T., Agneessens, F., & Skvoretz, J. (2010). Node centrality in weighted networks: Generalizing degree and shortest paths. Social Networks, 32(3), 245–251. doi: 10.1016/j.socnet.2010.03.006
   Web of Science ®Google Scholar
• Pastor-Satorras, R., & Vespignani, A. (2001). Epidemic spreading in scale-free networks. Physics Review Letters, 86, 3200–3203.
   PubMed Web of Science ®Google Scholar
• Pearl, J. (2000). Causality: Models, reasoning, and inference. New York, NY: Cambridge University Press.
   Google Scholar
• R Core Team. (2017). R: A language and environment for statistical computing [Computer software manual]. Vienna, Austria. Retrieved from https://www.R-project.org/
   Google Scholar
• Rhemtulla, M., Fried, E. I., Aggen, S. H., Tuerlinckx, F., Kendler, K. S., & Borsboom, D. (2016). Network analysis of substance abuse and dependence symptoms. Drug and Alcohol Dependence, 161, 230–237. doi: 10.1016/j.drugalcdep.2016.02.005
   PubMed Web of Science ®Google Scholar
• Richetin, J., Preti, E., Costantini, G., De Panfilis, C., & Mazza, M. (2017). The centrality of affective instability and identity in borderline personality disorder: Evidence from network analysis. PLOS one, 12(10), e0186695. doi: 10.1371/journal.pone.0186695
   PubMed Web of Science ®Google Scholar
• Santos, H. P., Jr., Kossakowski, J. J., Schwartz, T. A., Beeber, L., & Fried, E. I. (2018). Longitudinal network structure of depression symptoms and self-efficacy in low-income mothers. PLoS ONE, 13(1), e0191675. doi: 10.1371/journal.pone.0191675
   PubMed Web of Science ®Google Scholar
• Saramäki, J., Kivelä, M., Onnela, J., Kaski, K., & Kertész, J. (2007). Generalizations of the clustering coeffic ient to weighted complex networks. Physical Review E, 75(2), 27–105. doi: 10.1103/PhysRevE.75.027105
   Web of Science ®Google Scholar
• Schmittmann, V. D., Cramer, A. O. J., Waldorp, L. J., Epskamp, S., Kievit, R. A., & Borsboom, D. (2013). Deconstructing the construct: A network perspective on psychological phenomena. New Ideas in Psychology, 31, 43–53. doi: 10.1016/j.newideapsych.2011.02.007
   Web of Science ®Google Scholar
• Sniehotta, F. F., Presseau, J., & Araújo-Soares, V. (2014). Time to retire the theory of planned behaviour. Health Psychology Review, 8(1), 1–7. doi: 10.1080/17437199.2013.869710
   PubMed Web of Science ®Google Scholar
• Spirtes, P., Glymour, C., & Scheines, R. (2000). Causation, prediction, and search (2nd ed.). Cambridge, MA: MIT Press.
   Google Scholar
• Steinley, D., Hoffman, M., Brusco, M. J., & Sher, K. J. (2017). A method for making inferences in network analysis: Comment on Forbes, Wright, Markon, and Krueger (2017). Journal of Abnormal Psychology, 126(7), 1000–1010. doi: 10.1037/abn0000308
   PubMed Web of Science ®Google Scholar
• Suls, J., & Rothman, A. (2004). Evolution of the biopsychosocial model: Prospects and challenges for health psychology. Health Psychology, 23, 119–125. doi: 10.1037/0278-6133.23.2.119
   PubMed Web of Science ®Google Scholar
• Tibshirani, R. (1996). Regression shrinkage and selection via the lasso. Journal of the Royal Statistical Society. Series B (Methodological), 58, 267–288.
   Web of Science ®Google Scholar
• Valente, T. W. (2012). Network interventions. Science, 337(6090), 49–53. doi: 10.1126/science.1217330
   PubMed Web of Science ®Google Scholar
• Van Borkulo, C. D. (2018). Network comparison test: Permutation-based test of differences in strength of networks. Retrieved from github.com/cvborkulo/ NetworkComparisonTest
   Google Scholar
• van Borkulo, C. D., Borsboom, D., Epskamp, S., Blanken, T. F., Boschloo, L., Schoevers, R. A., & Waldorp, L. J. (2014). A new method for constructing networks from binary data. Scientific Reports, 4(5918), 1–10. doi: 10.1038/srep05918
   Web of Science ®Google Scholar
• van Borkulo, C. D., Boschloo, L., Borsboom, D., Penninx, B. W. J. H., Waldorp, L. J., & Schoevers, R. A. (2015). Association of symptom network structure with the course of depression. JAMA Psychiatry, 72(12), 1219–1226. doi: 10.1001/jamapsychiatry.2015.2079
   PubMed Web of Science ®Google Scholar
• van der Maas, H. L., Dolan, C. V., Grasman, R. P., Wicherts, J. M., Huizenga, H. M., & Raijmakers, M. E. (2006). A dynamical model of general intelligence: The positive manifold of intelligence by mutualism. Psychological Review, 113(4), 842–861. doi: 10.1037/0033-295X.113.4.842
   PubMed Web of Science ®Google Scholar
• Ware, J. E., Jr., & Sherbourne, C. D. (1992). The MOS 36-item short-form health survey (SF-36): I. Conceptual framework and item selection. Medical Care, 30, 473–483.
   PubMed Web of Science ®Google Scholar
• Watts, D. J., & Strogatz, S. H. (1998). Collective dynamics of “small-world” networks. Nature, 393(6684), 440–442. doi: 10.1038/30918
   PubMed Web of Science ®Google Scholar
• Wetzels, R., & Wagenmakers, E.-J. (2012). A default Bayesian hypothesis test for correlations and partial correlations. Psychonomic Bulletin & Review, 19, 1057–1064. doi: 10.3758/s13423-012-0295-x
   PubMed Web of Science ®Google Scholar
• Wild, B., Eichler, M., Friederich, H.-C., Hartmann, M., Zipfel, S., & Herzog, W. (2010). A graphical vector autoregressive modeling approach to the analysis of electronic diary data. BMC Medical Research Methodology, 10(28), 1–13. doi: 10.1186/1471-2288-10-28
   PubMedGoogle Scholar