{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:48:01Z","timestamp":1792788481465,"version":"4.5.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1011759","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,1,18]],"date-time":"2024-01-18T00:00:00Z","timestamp":1705536000000}}],"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2024,1,5]],"date-time":"2024-01-05T00:00:00Z","timestamp":1704412800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009125","name":"National Center for Theoretical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009125","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Taiwan MOE Yushan Fellow Program","award":["NTU-112V1034-1"],"award-info":[{"award-number":["NTU-112V1034-1"]}]},{"DOI":"10.13039\/100020595","name":"National Science and Technology Council","doi-asserted-by":"publisher","award":["112-2621-M-002-020"],"award-info":[{"award-number":["112-2621-M-002-020"]}],"id":[{"id":"10.13039\/100020595","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Abrupt changes in system states and dynamical behaviors are often observed in natural systems; such phenomena, named regime shifts, are explained as transitions between alternative steady states (more generally, attractors). Various methods have been proposed to detect regime shifts from time series data, but a generic detection method with theoretical linkage to underlying dynamics is lacking. Here, we provide a novel method named Nested-Library Analysis (NLA) to retrospectively detect regime shifts using empirical dynamic modeling (EDM) rooted in theory of attractor reconstruction. Specifically, NLA determines the time of regime shift as the cutting point at which sequential reduction of the library set (i.e., the time series data used to reconstruct the attractor for forecasting) optimizes the forecast skill of EDM. We illustrate this method on a chaotic model of which changing parameters present a critical transition. Our analysis shows that NLA detects the change point in the model system and outperforms existing approaches based on statistical characteristics. In addition, NLA empirically detected a real-world regime shift event revealing an abrupt change of Pacific Decadal Oscillation index around the mid-1970s. Importantly, our method can be easily generalized to various systems because NLA is equation-free and requires only a single time series.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1011759","type":"journal-article","created":{"date-parts":[[2024,1,5]],"date-time":"2024-01-05T13:43:54Z","timestamp":1704462234000},"page":"e1011759","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Detecting shifts in nonlinear dynamics using Empirical Dynamic Modeling with Nested-Library Analysis"],"prefix":"10.1371","volume":"20","author":[{"given":"Yong-Jin","family":"Huang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9817-2956","authenticated-orcid":true,"given":"Chun-Wei","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chih-hao","family":"Hsieh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,1,5]]},"reference":[{"key":"pcbi.1011759.ref001","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1146\/annurev.ecolsys.35.021103.105711","article-title":"Regime shifts, resilience, and biodiversity in ecosystem management.","volume":"35","author":"C Folke","year":"2004","journal-title":"Annu Rev Ecol Evol Syst"},{"key":"pcbi.1011759.ref002","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.ecolecon.2012.09.003","article-title":"Regime shifts and management","volume":"84","author":"A-S Cr\u00e9pin","year":"2012","journal-title":"Ecological Economics"},{"issue":"6295","key":"pcbi.1011759.ref003","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1126\/science.aad8745","article-title":"Climate-driven regime shift of a temperate marine ecosystem","volume":"353","author":"T Wernberg","year":"2016","journal-title":"Science"},{"issue":"18","key":"pcbi.1011759.ref004","doi-asserted-by":"crossref","first-page":"2657","DOI":"10.1002\/hyp.7835","article-title":"Nitrate concentrations and fluxes in the River Thames over 140 years (1868\u20132008): are increases irreversible?","volume":"24","author":"N Howden","year":"2010","journal-title":"Hydrological Processes"},{"issue":"6","key":"pcbi.1011759.ref005","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1111\/j.1365-2486.2008.01814.x","article-title":"Reorganization of a large marine ecosystem due to atmospheric and anthropogenic pressure: a discontinuous regime shift in the Central Baltic Sea","volume":"15","author":"C M\u00f6llmann","year":"2009","journal-title":"Global Change Biology"},{"issue":"1","key":"pcbi.1011759.ref006","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1146\/annurev.es.04.110173.000245","article-title":"Resilience and stability of ecological systems","volume":"4","author":"CS Holling","year":"1973","journal-title":"Annual review of ecology and systematics"},{"issue":"6856","key":"pcbi.1011759.ref007","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/35098000","article-title":"Catastrophic shifts in ecosystems","volume":"413","author":"M Scheffer","year":"2001","journal-title":"Nature"},{"issue":"12","key":"pcbi.1011759.ref008","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1016\/j.tree.2003.09.002","article-title":"Catastrophic regime shifts in ecosystems: linking theory to observation","volume":"18","author":"M Scheffer","year":"2003","journal-title":"Trends in ecology & evolution"},{"issue":"1659","key":"pcbi.1011759.ref009","doi-asserted-by":"crossref","first-page":"20130279","DOI":"10.1098\/rstb.2013.0279","article-title":"A holistic view of marine regime shifts. 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