Browse select publications produced by Icelabbers on this page by year or tag using the filters below, or type in an author name to search for publications by that author.
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Uszko, Wojciech; Diehl, Sebastian; Wickman, Jonas Fitting functional response surfaces to data: a best practice guide Journal Article Ecosphere, 11 (4), pp. e03051, 2020. Abstract | Links | BibTeX | Tags: data transformation, functional response, heteroscedasticity, Hill exponent, ingestion rate, parameter correlation, parameter estimation, prey density, temperature, type III Holmberg, Martin Pandemier och Epidemier - ett tvärvetenskapligt perspektiv Book 1, 2020, ISBN: 9789144135359. BibTeX | Tags: Bota, Andras; Holmberg, Martin; Gardner, Lauren; Rosvall, Martin Socio-economic and environmental patterns behind H1N1 spreading in Sweden Journal Article medRxiv, 2020. Abstract | Links | BibTeX | Tags: Franklin, O; Harrison, S P; Dewar, R; Farrior, C E; Brännström, Åke; Dieckmann, U; Pietsch, S; Falster, D; Cramer, W; Loreau, M; Wang, H; Mäkelä, A; Rebel, K T; Meron, E; Schymanski, S J; Rovenskaya, E; Stocker, B D; Zaehle, S; Manzoni, S; van Oijen, M; Wright, I J; Ciais, P; van Bodegom, P M; Peñuelas, J; Hofhansl, F; Terrer, C; Soudzilovskaia, N A; Midgley, G; Prentice, I C Organizing principles for vegetation dynamics Journal Article Nat Plants, 6 (5), pp. 444–453, 2020, ([DOI:hrefhttps://dx.doi.org/10.1038/s41477-020-0655-x10.1038/s41477-020-0655-x] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/3239388232393882]). BibTeX | Tags: Joshi, J; Brännström, Åke; Dieckmann, U Emergence of social inequality in the spatial harvesting of renewable public goods Journal Article PLoS Comput. Biol., 16 (1), pp. e1007483, 2020, ([PubMed Central:hrefhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974303PMC6974303] [DOI:hrefhttps://dx.doi.org/10.1371/journal.pcbi.100748310.1371/journal.pcbi.1007483] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/1822176118221761]). BibTeX | Tags: Sjodin, H; Johansson, A F; Brannstrom, A; Farooq, Z; Kriit, H K; Wilder-Smith, A; Astrom, C; Thunberg, J; Soderquist, M; Rocklov, J COVID-19 healthcare demand and mortality in Sweden in response to non-pharmaceutical mitigation and suppression scenarios Journal Article Int J Epidemiol, 2020, ISSN: 1464-3685 (Electronic)
0300-5771 (Linking). Liu, Y; Rocklov, J What is the reproductive number of yellow fever? Journal Article J Travel Med, 2020, ISSN: 1708-8305 (Electronic)
1195-1982 (Linking). DiSera, L; Sjodin, H; Rocklov, J; Tozan, Y; Sudre, B; Zeller, H; Munoz, A G The Mosquito, the Virus, the Climate: An Unforeseen Reunion in 2018 Journal Article Geohealth, 4 (8), pp. e2020GH000253, 2020, ISSN: 2471-1403 (Electronic)
2471-1403 (Linking). Tozan, Y; Sjodin, H; Munoz, A G; Rocklov, J Transmission dynamics of dengue and chikungunya in a changing climate: do we understand the eco-evolutionary response? Journal Article Expert Rev Anti Infect Ther, pp. 1-7, 2020, ISSN: 1744-8336 (Electronic)
1478-7210 (Linking). Rocklov, J; Gayle, A A Data science and machine learning, mathematical and statistical methods Journal Article Int J Epidemiol, 2020, ISSN: 1464-3685 (Electronic)
0300-5771 (Linking). Myint, Phyo E E; Sereemaspun, A; Rocklov, J; Nithikathkul, C Int J Environ Res Public Health, 17 (11), 2020, ISSN: 1660-4601 (Electronic)
1660-4601 (Linking). Rocklov, J; Dubrow, R Author Correction: Climate change: an enduring challenge for vector-borne disease prevention and control Journal Article Nat Immunol, 21 (6), pp. 695, 2020, ISSN: 1529-2916 (Electronic)
1529-2908 (Linking). Rocklov, J; Dubrow, R Climate change: an enduring challenge for vector-borne disease prevention and control Journal Article Nat Immunol, 21 (5), pp. 479-483, 2020, ISSN: 1529-2916 (Electronic)
1529-2908 (Linking). Sjodin, H; Wilder-Smith, A; Osman, S; Farooq, Z; Rocklov, J Only strict quarantine measures can curb the coronavirus disease (COVID-19) outbreak in Italy, 2020 Journal Article Euro Surveill, 25 (13), 2020, ISSN: 1560-7917 (Electronic)
1025-496X (Linking). Rocklov, J; Sjodin, H High population densities catalyse the spread of COVID-19 Journal Article J Travel Med, 27 (3), 2020, ISSN: 1708-8305 (Electronic)
1195-1982 (Linking). Rocklov, J; Sjodin, H; Wilder-Smith, A COVID-19 outbreak on the Diamond Princess cruise ship: estimating the epidemic potential and effectiveness of public health countermeasures Journal Article J Travel Med, 27 (3), 2020, ISSN: 1708-8305 (Electronic)
1195-1982 (Linking). Liu, Y; Gayle, A A; Wilder-Smith, A; Rocklov, J The reproductive number of COVID-19 is higher compared to SARS coronavirus Journal Article J Travel Med, 27 (2), 2020, ISSN: 1708-8305 (Electronic)
1195-1982 (Linking). Liu, Y; Lillepold, K; Semenza, J C; Tozan, Y; Quam, M B M; Rocklov, J Reviewing estimates of the basic reproduction number for dengue, Zika and chikungunya across global climate zones Journal Article Environ Res, 182 , pp. 109114, 2020, ISSN: 1096-0953 (Electronic)
0013-9351 (Linking). Calatayud, Joaquín; Andivia, Enrique; Escuderoa, Adrián; Melián, Carlos J; Bernardo-Madrid, Rubén; Stoffel, Markus; Aponte, Cristina; Medina, Nagore G; Molina-Venegas, Rafael; Arnan, Xavier; Rosvall, Martin; Neuman, Magnus; Noriega, Jorge Ari; Alves-Martins, Fernanda; Draper, Isabel; Luzuriaga, Arantzazu; Ballesteros-Cánovas, Juan Antonio; Morales-Molino, César; Ferrandis, Pablo; Herrero, Asier; Pataro, Luciano; Juen, Leandro; Cea, Alex; Madrigal-González, Jaime Positive associations among rare species and their persistence in ecological assemblages Journal Article Nature Ecology and Evolution, 4 , pp. 40-45, 2019. Abstract | Links | BibTeX | Tags: Calatayud, Rosvall Calatayud, Joaquín; Bernardo-Madrid, Rubén; Neuman, Magnus; Rojas, Alexis; Rosvall, Martin Exploring the solution landscape enables more reliable network community detection Journal Article Phys. Rev. E, 100 , pp. 052308, 2019.
title = {Fitting functional response surfaces to data: a best practice guide},
author = {Wojciech Uszko and Sebastian Diehl and Jonas Wickman},
url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.3051},
doi = {10.1002/ecs2.3051},
year = {2020},
date = {2020-01-01},
journal = {Ecosphere},
volume = {11},
number = {4},
pages = {e03051},
abstract = {Abstract Describing how resource consumption rates depend on resource density, conventionally termed “functional responses,” is crucial to understanding the population dynamics of trophically interacting organisms. Yet, accurately determining the functional response for any given pair of predator and prey remains a challenge. Moreover, functional responses are potentially complex surfaces in multidimensional space, where resource density is only one of several factors determining consumption rates. We explored how three sources of error can be addressed in the design and statistical analysis of functional response experiments: ill-chosen spacing of prey densities, heteroscedastic variance in consumption rates, and non-independence of parameters of the function describing prey consumption in relation to prey density and additional environmental factors. We generated extensive, virtual data sets that simulated feeding experiments in which both prey density and environmental temperature were varied, and for which the true, deterministic functional response surface was known and realistic variance had been added. We compared eight different methods of functional response fitting, one of which stood out as best performing. We subsequently tested several conclusions from the simulation study against experimental data of zooplankton feeding on algae across a broad range of temperatures. We summarize our main findings in three best practice guidelines for the experimental estimation of functional response surfaces, of which the second is the most important: (1) space prey densities logarithmically, starting from very low densities; (2) log-transform prey consumption data prior to fitting; and (3) fit a multivariate functional response surface to all data (including all prey densities and other factors, in our case temperature) in a single step. We also observed that functional response surfaces were fitted more accurately and precisely than their component parameters. The latter occurred because parameter estimates were non-independent, which is an inevitable feature of fitting complex nonlinear functions to data: A given response surface can often be described with near-equal accuracy by multiple parameter combinations. We therefore conclude that fitted functional response models perform better at optimizing the fit of the overall response surface than at determining how component parameters, such as the attack rate or handling time, depend on environmental factors such as temperature.},
keywords = {data transformation, functional response, heteroscedasticity, Hill exponent, ingestion rate, parameter correlation, parameter estimation, prey density, temperature, type III},
pubstate = {published},
tppubtype = {article}
}
title = {Pandemier och Epidemier - ett tvärvetenskapligt perspektiv},
author = {Martin Holmberg},
isbn = {9789144135359},
year = {2020},
date = {2020-01-01},
pages = {155},
edition = {1},
institution = {Umeå University, Department of culture and media studies},
keywords = {},
pubstate = {published},
tppubtype = {book}
}
title = {Socio-economic and environmental patterns behind H1N1 spreading in Sweden},
author = {Andras Bota and Martin Holmberg and Lauren Gardner and Martin Rosvall},
url = {https://www.medrxiv.org/content/early/2020/04/24/2020.03.18.20038349},
doi = {10.1101/2020.03.18.20038349},
year = {2020},
date = {2020-01-01},
journal = {medRxiv},
publisher = {Cold Spring Harbor Laboratory Press},
abstract = {The first influenza pandemic in our century started in 2009, spreading from Mexico to the rest of the world, infecting a noticeable fraction of the world population. The outbreak reached Europe in late April, and eventually, almost all countries had confirmed H1N1 cases. On 6 May, Swedish authorities reported the first confirmed influenza case. By the time the pandemic ended, more than 10 thousand people were infected in the country. In this paper, we aim to discover critical socio-economic, travel, and environmental factors contributing to the spreading of H1N1 in Sweden covering six years between 2009 and 2015, focusing on the onset and 2. the peak of the epidemic phase in each municipality. We apply the Generalized Inverse Infection Method (GIIM) to identify these factors. GIIM represents an epidemic spreading process on a network of nodes corresponding to geographical objects, connected by links indicating travel routes, and transmission probabilities assigned to the links guiding the infection process. The GIIM method uses observations on a real-life outbreak as a training dataset to estimate these probabilities and construct a simulated outbreak matching the training data as close as possible. Our results show that the influenza outbreaks considered in this study are mainly driven by the largest population centers in the country. Also, changes in temperature have a noticeable effect. Other socio-economic factors contribute only moderately to the epidemic peak and have a negligible effect on the epidemic onset. We also demonstrate that by training our model on the 2009 outbreak, we can predict the timing of the epidemic onset in the following five seasons with good accuracy. The model proposed in this paper provides a real-time decision support tool advising on resource allocation and surveillance. Furthermore, while this study only considers H1N1 outbreaks, the model can be adapted to other influenza strains or diseases with a similar transmission mechanism.Competing Interest StatementThe authors have declared no competing interest.Funding StatementAndras Bota was supported by the Olle Engkvist Byggmästare Foundation. Martin Rosvall was supported by the Swedish Research Council, grant 2016-00796.Author DeclarationsAll relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.YesAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesData available on request from the authors},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Organizing principles for vegetation dynamics},
author = {O Franklin and S P Harrison and R Dewar and C E Farrior and Åke Brännström and U Dieckmann and S Pietsch and D Falster and W Cramer and M Loreau and H Wang and A Mäkelä and K T Rebel and E Meron and S J Schymanski and E Rovenskaya and B D Stocker and S Zaehle and S Manzoni and M van Oijen and I J Wright and P Ciais and P M van Bodegom and J Peñuelas and F Hofhansl and C Terrer and N A Soudzilovskaia and G Midgley and I C Prentice},
year = {2020},
date = {2020-01-01},
journal = {Nat Plants},
volume = {6},
number = {5},
pages = {444--453},
note = {[DOI:hrefhttps://dx.doi.org/10.1038/s41477-020-0655-x10.1038/s41477-020-0655-x] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/3239388232393882]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Emergence of social inequality in the spatial harvesting of renewable public goods},
author = {J Joshi and Åke Brännström and U Dieckmann},
year = {2020},
date = {2020-01-01},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {1},
pages = {e1007483},
note = {[PubMed Central:hrefhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974303PMC6974303] [DOI:hrefhttps://dx.doi.org/10.1371/journal.pcbi.100748310.1371/journal.pcbi.1007483] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/1822176118221761]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {COVID-19 healthcare demand and mortality in Sweden in response to non-pharmaceutical mitigation and suppression scenarios},
author = {H Sjodin and A F Johansson and A Brannstrom and Z Farooq and H K Kriit and A Wilder-Smith and C Astrom and J Thunberg and M Soderquist and J Rocklov},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32954400},
doi = {10.1093/ije/dyaa121},
issn = {1464-3685 (Electronic)
0300-5771 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Int J Epidemiol},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {What is the reproductive number of yellow fever?},
author = {Y Liu and J Rocklov},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32889541},
doi = {10.1093/jtm/taaa156},
issn = {1708-8305 (Electronic)
1195-1982 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {J Travel Med},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {The Mosquito, the Virus, the Climate: An Unforeseen Reunion in 2018},
author = {L DiSera and H Sjodin and J Rocklov and Y Tozan and B Sudre and H Zeller and A G Munoz},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32864539},
doi = {10.1029/2020GH000253},
issn = {2471-1403 (Electronic)
2471-1403 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Geohealth},
volume = {4},
number = {8},
pages = {e2020GH000253},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Transmission dynamics of dengue and chikungunya in a changing climate: do we understand the eco-evolutionary response?},
author = {Y Tozan and H Sjodin and A G Munoz and J Rocklov},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32741233},
doi = {10.1080/14787210.2020.1794814},
issn = {1744-8336 (Electronic)
1478-7210 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Expert Rev Anti Infect Ther},
pages = {1-7},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Data science and machine learning, mathematical and statistical methods},
author = {J Rocklov and A A Gayle},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32594118},
doi = {10.1093/ije/dyaa111},
issn = {1464-3685 (Electronic)
0300-5771 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Int J Epidemiol},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Discovery of Carcinogenic Liver Fluke Metacercariae in Second Intermediate Hosts and Surveillance on Fish-Borne Trematode Metacercariae Infections in Mekong Region of Myanmar},
author = {E E Phyo Myint and A Sereemaspun and J Rocklov and C Nithikathkul},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32526911},
doi = {10.3390/ijerph17114108},
issn = {1660-4601 (Electronic)
1660-4601 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Int J Environ Res Public Health},
volume = {17},
number = {11},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Author Correction: Climate change: an enduring challenge for vector-borne disease prevention and control},
author = {J Rocklov and R Dubrow},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32350458},
doi = {10.1038/s41590-020-0692-7},
issn = {1529-2916 (Electronic)
1529-2908 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Nat Immunol},
volume = {21},
number = {6},
pages = {695},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Climate change: an enduring challenge for vector-borne disease prevention and control},
author = {J Rocklov and R Dubrow},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32313242},
doi = {10.1038/s41590-020-0648-y},
issn = {1529-2916 (Electronic)
1529-2908 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Nat Immunol},
volume = {21},
number = {5},
pages = {479-483},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Only strict quarantine measures can curb the coronavirus disease (COVID-19) outbreak in Italy, 2020},
author = {H Sjodin and A Wilder-Smith and S Osman and Z Farooq and J Rocklov},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32265005},
doi = {10.2807/1560-7917.ES.2020.25.13.2000280},
issn = {1560-7917 (Electronic)
1025-496X (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Euro Surveill},
volume = {25},
number = {13},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {High population densities catalyse the spread of COVID-19},
author = {J Rocklov and H Sjodin},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32227186},
doi = {10.1093/jtm/taaa038},
issn = {1708-8305 (Electronic)
1195-1982 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {J Travel Med},
volume = {27},
number = {3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {COVID-19 outbreak on the Diamond Princess cruise ship: estimating the epidemic potential and effectiveness of public health countermeasures},
author = {J Rocklov and H Sjodin and A Wilder-Smith},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32109273},
doi = {10.1093/jtm/taaa030},
issn = {1708-8305 (Electronic)
1195-1982 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {J Travel Med},
volume = {27},
number = {3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {The reproductive number of COVID-19 is higher compared to SARS coronavirus},
author = {Y Liu and A A Gayle and A Wilder-Smith and J Rocklov},
url = {https://www.ncbi.nlm.nih.gov/pubmed/32052846},
doi = {10.1093/jtm/taaa021},
issn = {1708-8305 (Electronic)
1195-1982 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {J Travel Med},
volume = {27},
number = {2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Reviewing estimates of the basic reproduction number for dengue, Zika and chikungunya across global climate zones},
author = {Y Liu and K Lillepold and J C Semenza and Y Tozan and M B M Quam and J Rocklov},
url = {https://www.ncbi.nlm.nih.gov/pubmed/31927301},
doi = {10.1016/j.envres.2020.109114},
issn = {1096-0953 (Electronic)
0013-9351 (Linking)},
year = {2020},
date = {2020-01-01},
journal = {Environ Res},
volume = {182},
pages = {109114},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Positive associations among rare species and their persistence in ecological assemblages},
author = {Joaquín Calatayud and Enrique Andivia and Adrián Escuderoa and Carlos J. Melián and Rubén Bernardo-Madrid and Markus Stoffel and Cristina Aponte and Nagore G. Medina and Rafael Molina-Venegas and Xavier Arnan and Martin Rosvall and Magnus Neuman and Jorge Ari Noriega and Fernanda Alves-Martins and Isabel Draper and Arantzazu Luzuriaga and Juan Antonio Ballesteros-Cánovas and César Morales-Molino and Pablo Ferrandis and Asier Herrero and Luciano Pataro and Leandro Juen and Alex Cea and Jaime Madrigal-González },
doi = {10.1038/s41559-019-1053-5},
year = {2019},
date = {2019-12-16},
journal = {Nature Ecology and Evolution},
volume = {4},
pages = {40-45},
abstract = {According to the competitive exclusion principle, species with low competitive abilities should be excluded by more efficient competitors; yet, they generally remain as rare species. Here, we describe the positive and negative spatial association networks of 326 disparate assemblages, showing a general organization pattern that simultaneously supports the primacy of competition and the persistence of rare species. Abundant species monopolize negative associations in about 90% of the assemblages. On the other hand, rare species are mostly involved in positive associations, forming small network modules. Simulations suggest that positive interactions among rare species and microhabitat preferences are the most probable mechanisms underpinning this pattern and rare species persistence. The consistent results across taxa and geography suggest a general explanation for the maintenance of biodiversity in competitive environments.},
keywords = {Calatayud, Rosvall},
pubstate = {published},
tppubtype = {article}
}
title = {Exploring the solution landscape enables more reliable network community detection},
author = {Joaquín Calatayud and Rubén Bernardo-Madrid and Magnus Neuman and Alexis Rojas and Martin Rosvall},
url = {https://link.aps.org/doi/10.1103/PhysRevE.100.052308},
doi = {10.1103/PhysRevE.100.052308},
year = {2019},
date = {2019-11-01},
journal = {Phys. Rev. E},
volume = {100},
pages = {052308},
publisher = {American Physical Society},
keywords = {Rojas},
pubstate = {published},
tppubtype = {article}
}