| 1. |
- Håkansson, Nina, et al.
(författare)
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Generating structure specific networks
- 2010
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Ingår i: Advances in Complex Systems. - : World Scientific Publishing Company. - 0219-5259. ; 13:2, s. 239-250
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Tidskriftsartikel (refereegranskat)abstract
- Theoretical exploration of network structure significance requires a range of different networks for comparison. Here, we present a new method to construct networks in a spatial setting that uses spectral methods in combination with a probability distribution function. Nearly all previous algorithms for network construction have assumed randomized distribution of links or a distribution dependent on the degree of the nodes. We relax those assumptions. Our algorithm is capable of creating spectral networks along a gradient from random to highly clustered or diverse networks. Number of nodes and link density are specified from start and the structure is tuned by three parameters (gamma, sigma, kappa). The structure is measured by fragmentation, degree assortativity, clustering and group betweenness of the networks. The parameter gamma regulates the aggregation in the spatial node pattern and sigma and kappa regulates the probability of link forming.
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| 2. |
- Lindström, Tom, et al.
(författare)
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A spectral and Bayesian approach for analysis of fluctuations and synchrony in ecological datasets
- 2012
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Ingår i: Methods in Ecology and Evolution. - : Wiley-Blackwell. - 2041-210X. ; 3:6, s. 1019-1027
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Tidskriftsartikel (refereegranskat)abstract
- Autocorrelation within ecological time series and synchrony between them may provide insight into the main drivers of observed dynamics. We here present methods that analyse autocorrelation and synchrony in ecological datasets using a spectral approach combined with Bayesian inference. To exemplify, we implement the method on dendrochronological data of the pedunculate oak (Quercus robur). The data consist of 110 years of growth of 10 live trees and seven trees that died during a synchronized oak death in Sweden in c. 2002-2007. We find that the highest posterior density is found for a noise colour of tree growth of gamma approximate to 0.95 (i.e. pink noise) with little difference between trees, suggesting climatic variation as a driving factor. This is further supported by the presence of synchrony, which we estimate based on phase-shift analysis. We conclude that the synchrony is time-scale dependent with higher synchrony at larger time-scales. We further show that there is no difference between the growth patterns of the alive and dead tree groups. This suggests that the trees were driven by the same factors prior to the synchronized death. We argue that this method is a promising approach for linking theoretical models with empirical data.
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| 3. |
- Lindström, Tom, et al.
(författare)
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Estimation of distance related probability of animal movements between holdings and implications for disease spread modeling
- 2009
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Ingår i: Preventive Veterinary Medicine. - : Elsevier. - 0167-5877 .- 1873-1716. ; 91:2-4, s. 85-94
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Tidskriftsartikel (refereegranskat)abstract
- Between holding contacts are more common over short distances and this may have implications for the dynamics of disease spread through these contacts. A reliable estimation of how contacts depend on distance is therefore important when modeling livestock diseases. In this study, we have developed a method for analyzing distant dependent contacts and applied it to animal movement data from Sweden. The data were analyzed with two competing models. The first model assumes that contacts arise from a purely distance dependent process. The second is a mixture model and assumes that, in addition, some contacts arise independent of distance. Parameters were estimated with a Bayesian Markov Chain Monte Carlo (MCMC) approach and the model probabilities were compared. We also investigated possible between model differences in predicted contact structures, using a collection of network measures. We found that the mixture model was a much better model for the data analyzed. Also, the network measures showed that the models differed considerably in predictions of contact structures, which is expected to be important for disease spread dynamics. We conclude that a model with contacts being both dependent on, and independent of, distance was preferred for modeling the example animal movement contact data.
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| 4. |
- Lindström, Tom, 1977-, et al.
(författare)
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Splitting the tail of the displacement kernel shows the unimportance of kurtosis
- 2008
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Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 89:7, s. 1784-1790
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Tidskriftsartikel (refereegranskat)abstract
- Animals disperse in space through different movement behaviors, resulting in different displacement distances. This is often described with a displacement kernel where the long-distance dispersers are within the tail of the kernel. A displacement with a large proportion of long-distance dispersers may have impact on different aspects of spatial ecology such as invasion speed, population persistence, and distribution. It is, however, unclear whether the kurtosis of the kernel plays a major role since a fatter tail also influences the variance of the kernel. We modeled displacement in landscapes with different amounts and configurations of habitats and handled kurtosis and variance separately to study how these affected population distribution and transition time. We conclude that kurtosis is not important for any of these aspects of spatial ecology. The variance of the kernel, on the other hand, was of great importance to both population distribution and transition time. We argue that separating variance and kurtosis can cast new light on the way in which long-distance dispersers are important in ecological processes. Consequences for empirical studies are discussed.
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| 5. |
- Lindström, Tom, et al.
(författare)
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The shape of the spatial kernel and its implications for biological invasions in patchy environments
- 2011
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Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : Royal Society. - 0962-8452 .- 1471-2954. ; 278:1711, s. 1564-1571
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Tidskriftsartikel (refereegranskat)abstract
- Ecological and epidemiological invasions occur in a spatial context. In the study presented we tested how these processes relate to the distance dependence of spread or dispersal between spatial entities such as habitat patches or infective units. The distance dependence was described by a spatial kernel which can be characterized by its shape, quantified by kurtosis, and width, quantified by the kernel variance. We also introduced a method to analyze or generate non randomly distributed infective units or patches as point pattern landscapes. The method is based on Fourier transform and consists of two measures in the spectral representation; Continuity that relates to autocorrelation and Contrast that refers to difference in density of patches, or infective units, in different areas of the landscape. The method was also used to analyze some relevant empirical data where our results are expected to have implications for ecological or epidemiological studies. We analyzed distributions of large old trees (Quercus and Ulmus) as well as the distributions of farms (both cattle and pig) in Sweden. We tested the invasion speed in generated landscapes with different amount of Continuity and Contrast. The results showed that kurtosis, i.e. the kernel shape, was not important for predicting the invasion speed in randomly distributed patches or infective units. However, depending on the assumptions of dispersal, it may be highly important when the distribution of patches or infective units deviates from randomness, in particular when the Contrast is high. We conclude that speed of invasions and spread of diseases depends on its spatial context through the spatial kernel intertwined to the spatial structure. This implies high demands on the empirical data; it requires knowledge of both shape and width of the spatial kernel as well as spatial structure of patches or infective units.
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| 6. |
- Nöremark, Maria, et al.
(författare)
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Spatial and temporal investigations of reported movements, births and deaths of cattle and pigs in Sweden
- 2009
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Ingår i: Acta Veterinaria Scandinavica. - : Springer Science and Business Media LLC. - 0044-605X .- 1751-0147. ; 51:37
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Tidskriftsartikel (refereegranskat)abstract
- Background: Livestock movements can affect the spread and control of contagious diseases and new data recording systems enable analysis of these movements. The results can be used for contingency planning, modelling of disease spread and design of disease control programs. Methods: Data on the Swedish cattle and pig populations during the period July 2005 until June 2006 were obtained from databases held by the Swedish Board of Agriculture. Movements of cattle and pigs were investigated from geographical and temporal perspectives, births and deaths of cattle were investigated from a temporal perspective and the geographical distribution of holdings was also investigated. Results: Most movements of cattle and pigs were to holdings within 100 km, but movements up to 1200 km occurred. Consequently, the majority of movements occurred within the same county or to adjacent counties. Approximately 54% of the cattle holdings and 45% of the pig holdings did not purchase any live animals. Seasonal variations in births and deaths of cattle were identified, with peaks in spring. Cattle movements peaked in spring and autumn. The maximum number of holdings within a 3 km radius of one holding was 45 for cattle and 23 for pigs, with large variations among counties. Missing data and reporting bias ( digit preference) were detected in the data. Conclusion: The databases are valuable tools in contact tracing. However since movements can be reported up to a week after the event and some data are missing they cannot replace other methods in the acute phase of an outbreak. We identified long distance transports of cattle and pigs, and these findings support an implementation of a total standstill in the country in the case of an outbreak of foot-and-mouth disease. The databases contain valuable information and improvements in data quality would make them even more useful.
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