A GIS-based approach to spatio-temporal analysis of environmental pollution in urban areas: A case study of Prague's environment extended by LIDAR data

Environmental pollution of urban areas is one of key factors that state authorities and local agencies have to consider in the decision-making process. To find a compromise among many criteria, spatial analysis extended by geostatistical methods and dynamic models has to be carried out. In this case, spatial analysis includes processing of a wide range of air, water and soil pollution data and possibly noise assessment and waste management data. Other spatial inputs consist of data from remote sensing and GPS field measurements. Integration and spatial data management are carried out within the framework of a geographic information system (GIS). From a modeling point of view, GIS is used mainly for the preprocessing and postprocessing of data to be displayed in digital map layers and visualized in 3D scenes. Moreover, for preprocessing and postprocessing, deterministic and geostatistical methods (IDW, ordinary kriging) are used for spatial interpolation; geoprocessing and raster algebra are used in multi-criteria evaluation and risk assessment methods. GIS is also used as a platform for spatio-temporal analyses or for building relationships between the GIS database and stand-alone modeling tools. A case study is presented illustrating the application of spatial analysis to the urban areas of Prague. This involved incorporating environmental data from monitoring networks and field measurements into digital map layers. Extra data inputs were used to represent the 3D concentration fields of air pollutants (ozone, NO₂) measured by differential absorption LIDAR. ArcGIS was used to provide spatial data management and analysis, extended by modeling tools developed internally in the ArcObjects environment and external modules developed with MapObjects. Ordinary kriging methods were employed to predict ozone concentrations in selected 3D locations together with estimates of variability. Higher ozone concentrations were found above crossroads with their heavy traffic than above the surrounding areas. Ozone concentrations also varied with height above the digital elevation model. Processed data, spatial analysis and models are integrated within the framework of the GIS project, providing an approach that state and local authorities can use to address environmental protection issues.     

Social network analysis and valid Markov chain Monte Carlo tests of null models

Analyses of animal social networks derived from group-based associations often rely on randomisation methods developed in ecology (Manly, Ecology 76:1109–1115, 1995) and made available to the animal behaviour community through implementation of a pair-wise swapping algorithm by Bejder et al. (Anim Behav 56:719–725, 1998). We report a correctable flaw in this method and point the reader to a wider literature on the subject of null models in the ecology literature. We illustrate the importance of correcting the method using a toy network and use it to make a preliminary analysis of a network of associations among eagle rays.

Diurnal rhythm of the bioluminescent field in the ocean epipelagic zone

Characteristics of the diurnal rhythm of the bioluminescence field are analyzed on the basis of experimental data obtained in the region around Kamchatka peninsula (50°31′N; 163°50′E). The feasibility of reconstructing the nocturnal structure of the bioluminescence field by measurements made at other times of the day has been demonstrated. Diurnal rhythm parameters for the bioluminescent field of several other studied areas of the ocean have been defined. The temporal parameters feature linear latitudinal dependence. At the equator the boundaries of morning and evening transition periods are 05:06 to 07:30 and 17:48 to 19:54 hrs, respectively. In the Barents Sea in spring these boundaries are 02:42 to 04:06 and 19:48 to 21:12 hrs. Boundary times of diurnal rhythm do not deviate from the linear regression by more than 10%. Received: 21 August 1998 / Accepted 4 March 1999     

A simple random path method for the analysis of flow networks

The path of a particle through an ecosystem is modelled as a Markov chain. For a given flow network, powers of the transition matrix are used to calculate the distribution of the particles over the network after each transition. The method may be applied for the definition and calculation of trophic levels in food webs. The algorithm yields the trophic level distribution of species, the species composition of trophic levels, and the path length distribution of output flows. In addition, the network can be described as a linear chain, with the throughflows at each step identified. Data from several ecosystems are analyzed by the method, showing that surprising insights may result.     

Accounting for multiple testing in the analysis of spatio-temporal environmental data

The statistical analysis of environmental data from remote sensing and Earth system simulations often entails the analysis of gridded spatio-temporal data, with a hypothesis test being performed for each grid cell. When the whole image or a set of grid cells are analyzed for a global effect, the problem of multiple testing arises. When no global effect is present, we expect $$ alpha $$% of all grid cells to be false positives, and spatially autocorrelated data can give rise to clustered spurious rejections that can be misleading in an analysis of spatial patterns. In this work, we review standard solutions for the multiple testing problem and apply them to spatio-temporal environmental data. These solutions are independent of the test statistic, and any test statistic can be used (e.g., tests for trends or change points in time series). Additionally, we introduce permutation methods and show that they have more statistical power. Real-world data are used to provide examples of the analysis, and the performance of each method is assessed in a simulation study. Unlike other simulation studies, our study compares the statistical power of the presented methods in a comprehensive simulation study. In conclusion, we present several statistically rigorous methods for analyzing spatio-temporal environmental data and controlling the false positives. These methods allow the use of any test statistic in a wide range of applications in environmental sciences and remote sensing.     

Effects of tour boats on dolphin activity examined with sensitivity analysis of Markov chains

In Patagonia, Argentina, watching dolphins, especially dusky dolphins (Lagenorhynchus obscurus), is a new tourist activity. Feeding time decreases and time to return to feeding after feeding is abandoned and time it takes a group of dolphins to feed increase in the presence of boats. Such effects on feeding behavior may exert energetic costs on dolphins and thus reduce an individual's survival and reproductive capacity or maybe associated with shifts in distribution. We sought to predict which behavioral changes modify the activity pattern of dolphins the most. We modeled behavioral sequences of dusky dolphins with Markov chains. We calculated transition probabilities from one activity to another and arranged them in a stochastic matrix model. The proportion of time dolphins dedicated to a given activity (activity budget) and the time it took a dolphin to resume that activity after it had been abandoned (recurrence time) were calculated. We used a sensitivity analysis of Markov chains to calculate the sensitivity of the time budget and the activity-resumption time to changes in behavioral transition probabilities. Feeding-time budget was most sensitive to changes in the probability of dolphins switching from traveling to feeding behavior and of maintaining feeding behavior. Thus, an increase in these probabilities would be associated with the largest reduction in the time dedicated to feeding. A reduction in the probability of changing from traveling to feeding would also be associated with the largest increases in the time it takes dolphins to resume feeding. To approach dolphins when they are traveling would not affect behavior less because presence of the boat may keep dolphins from returning to feeding. Our results may help operators of dolphin-watching vessels minimize negative effects on dolphins.     

Interpolation performance of a spatio-temporal model with spatially varying coefficients: application to PM<Subscript>10</Subscript> concentrations in Rio de Janeiro

In this work we present a Bayesian analysis in linear regression models with spatially varying coefficients for modeling and inference in spatio-temporal processes. This kind of model is particularly appealing in situations where the effect of one or more explanatory processes on the response present substantial spatial heterogeneity. We describe for this model how to make inference about the regression coefficients and response processes under two scenarios: when the explanatory processes are known throughout the study region, and when they are known only at the sampling locations. Using a simulation experiment we investigate how parameter inference and interpolation performance are affected by some features of the data and prior distribution that is used. The proposed methodology is used to model the dataset on PM₁₀ levels in the metropolitan region of Rio de Janeiro presented in Paez and Gamerman (2003).     

Multivariate Bayesian analysis of atmosphere–ocean general circulation models

Numerical experiments based on atmosphere–ocean general circulation models (AOGCMs) are one of the primary tools in deriving projections for future climate change. Although each AOGCM has the same underlying partial differential equations modeling large scale effects, they have different small scale parameterizations and different discretizations to solve the equations, resulting in different climate projections. This motivates climate projections synthesized from results of several AOGCMs’ output. We combine present day observations, present day and future climate projections in a single highdimensional hierarchical Bayes model. The challenging aspect is the modeling of the spatial processes on the sphere, the number of parameters and the amount of data involved. We pursue a Bayesian hierarchical model that separates the spatial response into a large scale climate change signal and an isotropic process representing small scale variability among AOGCMs. Samples from the posterior distributions are obtained with computer-intensive MCMC simulations. The novelty of our approach is that we use gridded, high resolution data covering the entire sphere within a spatial hierarchical framework. The primary data source is provided by the Coupled Model Intercomparison Project (CMIP) and consists of 9 AOGCMs on a 2.8 by 2.8 degree grid under several different emission scenarios. In this article we consider mean seasonal surface temperature and precipitation as climate variables. Extensions to our model are also discussed.     

Effect of modified magnetic field on the ocean migration of maturing chum salmon, Oncorhynchus keta

To investigate the role of magnetic compass orientation in oceanic migrating chum salmon, Oncorhynchus keta, an ultrasonic telemetry study was carried out in the western North Pacific off the coast of Kushiro, Hokkaido. Four salmon were fitted with a tag which generated an artificial magnetic field and modified the geomagnetic field around the head of the fish. Initially, the free-ranging salmon with stomach-implanted ultrasonic transmitters were tracked for a period of several hours before the magnetic field was altered for a period of 16 h. The generator produced an alternating magnetic field intensity of about 6 gauss, with polarity which reversed every 11.25 min. There was no observable effect on the horizontal and vertical movements of the salmon when the magnetic field was modified. However, it was noted that salmon slowed their swimming speed significantly before changing direction, regardless of whether the fish were swimming under the normal geomagnetic field or whether they were swimming under the modified field. Received: 6 April 1997 / Accepted: 29 April 1997     

Detecting pattern in biological stressor response relationships using model based cluster analysis

Environmental monitoring of aquatic systems is needed to estimate the quality of the systems, to evaluate standards and to study stressor–response relationships. Monitoring programs often focus on the collection of biological, chemical and physical measures of the system. An important concern is the effect of chemical and physical stressors on the biological community. Evaluation of relationships may be difficult as the extent of the relationship is not known. From a management perspective, interest is on what factors affect the biological community and where these factors have an influence. The focus of this paper is on the use of regression based cluster analysis as a tool for finding relationships between a single biological response and a suite of environmental stressors. The approach to cluster analysis uses a penalized regression classification likelihood and Markov Chain Model Composition Monte Carlo. This approach allows for simultaneous development of regression models and clustering of the regression models. The method is applied to the analysis of a data set describing stressors/response relationship in Ohio.     

Bayesian hierarchical spatio-temporal modelling of trends and future projections in the ocean wave climate with a \text{ CO }_2 regression component

Bad weather and rough seas continue to be a major cause for ship losses and is thus a significant contributor to the risk to maritime transportation. This stresses the importance of taking severe sea state conditions adequately into account, with due treatment of the uncertainties involved, in ship design and operation in order to enhance safety. Hence, there is a need for appropriate stochastic models describing the variability of sea states. These should also incorporate realistic projections of future return levels of extreme sea states, taking into account long-term trends related to climate change and inherent uncertainties. The stochastic ocean wave model presented in this paper exploits the flexible framework of Bayesian hierarchical space-time models. It allows modelling of complex dependence structures in space and time and incorporation of physical features and prior knowledge, yet at the same time remains intuitive and easily interpreted. Furthermore, by taking a Bayesian approach, the uncertainties of the model parameters are also taken into account. A regression component with $\text{ CO }_2$ as an explanatory variable has been introduced in order to extract long-term trends in the data. The model has been fitted by monthly maximum significant wave height data for an area in the North Atlantic ocean. The different components of the model will be outlined in the paper, and the results will be discussed. Furthermore, a discussion of possible extensions to the model will be given.     

A hierarchical analysis of terrestrial ecosystem model Biome-BGC: Equilibrium analysis and model calibration

The increasing complexity of ecosystem models represents a major difficulty in tuning model parameters and analyzing simulated results. To address this problem, this study develops a hierarchical scheme that simplifies the Biome-BGC model into three functionally cascaded tiers and analyzes them sequentially. The first-tier model focuses on leaf-level ecophysiological processes; it simulates evapotranspiration and photosynthesis with prescribed leaf area index (LAI). The restriction on LAI is then lifted in the following two model tiers, which analyze how carbon and nitrogen is cycled at the whole-plant level (the second tier) and in all litter/soil pools (the third tier) to dynamically support the prescribed canopy. In particular, this study analyzes the steady state of these two model tiers by a set of equilibrium equations that are derived from Biome-BGC algorithms and are based on the principle of mass balance. Instead of spinning-up the model for thousands of climate years, these equations are able to estimate carbon/nitrogen stocks and fluxes of the target (steady-state) ecosystem directly from the results obtained by the first-tier model. The model hierarchy is examined with model experiments at four AmeriFlux sites. The results indicate that the proposed scheme can effectively calibrate Biome-BGC to simulate observed fluxes of evapotranspiration and photosynthesis; and the carbon/nitrogen stocks estimated by the equilibrium analysis approach are highly consistent with the results of model simulations. Therefore, the scheme developed in this study may serve as a practical guide to calibrate/analyze Biome-BGC; it also provides an efficient way to solve the problem of model spin-up, especially for applications over large regions. The same methodology may help analyze other similar ecosystem models as well.     

Interaction of ocean acidification and temperature; the high cost of survival in the brittlestar Ophiura ophiura

This study has demonstrated an interaction between the effect of increased ocean acidity and temperature (40 days exposure) on a number of key physiological parameters in the ophiuroid brittlestar, Ophiura ophiura. Metabolic upregulation is seen in the low pH treatments when combined with low temperature. However, this is far outweighed by the response to elevated temperature (+4.5°C). In the high temperature/low pH treatments treatments (where calcite is undersaturated) there appears to be an energetic trade-off likely in order to maintain net calcification where dissolution of calcium carbonate may occur. This energy deficit results in a ~30% reduction in the rate of arm regeneration at pH 7.3 which is predicted to be reached by the year 2300. This understanding of how O. ophiura responds to ocean acidification, taking into account an interactive effect of temperature, suggests that fitness and survival may indirectly be reduced through slower recovery from arm damage.     

Coral recruitment: a spatio-temporal analysis along the coastline of Eilat,northern Red Sea

Recruitment rates of stony corals to artificial substrates were monitored for 2 years at 20 sites along the coast of Eilat, northern Red Sea, to compare with those recorded at other coral reef locations and to assess variation in recruitment at several spatial scales. Coral recruitment was low compared to that observed on the Great Barrier Reef in Australia, but was similar to levels reported from other high-latitude reef locations. Pocilloporids were the most abundant coral recruits in all seasons. Recruitment was twofold higher during the first year than during the second year of study. There was considerable spatial variability, with the largest proportion of variance, apart from the error term, attributable to differences between sites, at a scale of 10² m. Spearmans ranked correlation showed consistency in spatial patterns of recruitment of pocilloporid corals between years, but not of acroporid corals. During spring, when only the brooding pocilloporid coral Stylophora pistillata reproduces at this locality, most coral recruitment occurred at central and southern sites adjacent to well-developed coral reefs. During summer, recruitment patterns varied significantly between years, with wide variation in the recruitment of broadcasting acroporid corals at northern sites located distant from coral reefs. Settlement was low at all sites during autumn and winter. This work is the first detailed analysis of coral recruitment patterns in the Red Sea, and contributes to the understanding of the spatial and temporal scales of variation in this important reef process.Communicated by O. Kinne, Oldendorf/Luhe     

Throughflow analysis: A stochastic approach

Ecological network analysis (ENA), predicated on systems theory and Leontiev input–output analysis, is a method widely used in ecology to reveal ecosystem properties. An important ecosystem property computed in ENA is throughflows, the amount of matter/energy leaving each compartment of the ecosystem. Throughflows are analyzed via a matrix representing their relationships to the driving input at the boundary. Network particle tracking (NPT) builds on ENA to offer a Lagrangian particle method that describes the activity of the ecosystem at the microscopic level. This paper introduces a Lagrangian throughflow analysis methodology using NPT and shows that the NPT throughflow matrix, , agrees with the conventional ENA throughflow matrix, , for ecosystems at steady-state with donor-controlled flows. The matrix is computed solely from the pathways (particles’ histories) generated by NPT simulations and its average over multiple runs of the algorithm with longer simulation time agrees with the Eulerian matrix (Law of Large Numbers). While the traditional NEA throughflow analysis is mostly used with steady-state ecosystem models, the Lagrangian throughflow analysis that we propose can be used with non-steady-state models and paves the way for the development of dynamic throughflow analysis.     

Using social network analysis tools in ecology: Markov process transition models applied to the seasonal trophic network dynamics of the Chesapeake Bay

Ecosystem components interact in complex ways and change over time due to a variety of both internal and external influences (climate change, season cycles, human impacts). Such processes need to be modeled dynamically using appropriate statistical methods for assessing change in network structure. Here we use visualizations and statistical models of network dynamics to understand seasonal changes in the trophic network model described by Baird and Ulanowicz [Baird, D., Ulanowicz, R.E., 1989. Seasonal dynamics of the Chesapeake Bay ecosystem. Ecol. Monogr. 501 (59), 329–364] for the Chesapeake Bay (USA). Visualizations of carbon flow networks were created for each season by using a network graphic analysis tool (NETDRAW). The structural relations of the pelagic and benthic compartments (nodes) in each seasonal network were displayed in a two-dimensional space using spring-embedder analyses with nodes color-coded for habitat associations (benthic or pelagic). The most complex network was summer, when pelagic species such as sea nettles, larval fishes, and carnivorous fishes immigrate into Chesapeake Bay and consume prey largely from the plankton and to some extent the benthos. Winter was the simplest of the seasonal networks, and exhibited the highest ascendency, with fewest nodes present and with most of the flows shifting to the benthic bacteria and sediment POC compartments. This shift in system complexity corresponds with a shift from a pelagic- to benthic-dominated system over the seasonal cycle, suggesting that winter is a mostly closed system, relying on internal cycling rather than external input. Network visualization tools are useful in assessing temporal and spatial changes in food web networks, which can be explored for patterns that can be tested using statistical approaches. A simulation-based continuous-time Markov Chain model called SIENA was used to determine the dynamic structural changes in the trophic network across phases of the annual cycle in a statistical as opposed to a visual assessment. There was a significant decrease in outdegree (prey nodes with reduced link density) and an increase in the number of transitive triples (a triad in which i chooses j and h, and j also chooses h, mostly connected via the non-living detritus nodes in position i), suggesting the Chesapeake Bay is a simpler, but structurally more efficient, ecosystem in the winter than in the summer. As in the visual analysis, this shift in system complexity corresponds with a shift from a pelagic to a more benthic-dominated system from summer to winter. Both the SIENA model and the visualization in NETDRAW support the conclusions of Baird and Ulanowicz [Baird, D., Ulanowicz, R.E., 1989. Seasonal dynamics of the Chesapeake Bay ecosystem. Ecol. Monogr. 501 (59), 329–364] that there was an increase in the Chesapeake Bay ecosystem's ascendancy in the winter. We explain such reduced complexity in winter as a system response to lowered temperature and decreased solar energy input, which causes a decline in the production of new carbon, forcing nodes to go extinct; this causes a change in the structure of the system, making it simpler and more efficient than in summer. It appears that the seasonal dynamics of the trophic structure of Chesapeake Bay can be modeled effectively using the SIENA statistical model for network change.     

A multiscale hierarchical Markov transition matrix model for generating and analyzing thematic raster maps

A model is described for generating hierarchically scaled spatial pattern as represented in a thematic raster map. The model involves a series of Markov transition matrices, one for each level in the scaling hierarchy. In full generality, the model allows the transition matrices to be different at each level, potentially making available a large number of parameters for landscape characterization. The model is self-similar when the transition matrices are all equal. A method is presented for fitting the model to data that take the form of a single-resolution thematic raster map. Explicit analytic solutions are obtained for the fitted parameters. The fitting method is based on a relationship between the hierarchical transitions in the model and spatial transitions at varying distance scales in the data map, a categorical analogy of the geostatistical variogram.     

A Bayesian hierarchical framework for calibrating aquatic biogeochemical models

Model practitioners increasingly place emphasis on rigorous quantitative error analysis in aquatic biogeochemical models and the existing initiatives range from the development of alternative metrics for goodness of fit, to data assimilation into operational models, to parameter estimation techniques. However, the treatment of error in many of these efforts is arguably selective and/or ad hoc. A Bayesian hierarchical framework enables the development of robust probabilistic analysis of error and uncertainty in model predictions by explicitly accommodating measurement error, parameter uncertainty, and model structure imperfection. This paper presents a Bayesian hierarchical formulation for simultaneously calibrating aquatic biogeochemical models at multiple systems (or sites of the same system) with differences in their trophic conditions, prior precisions of model parameters, available information, measurement error or inter-annual variability. Our statistical formulation also explicitly considers the uncertainty in model inputs (model parameters, initial conditions), the analytical/sampling error associated with the field data, and the discrepancy between model structure and the natural system dynamics (e.g., missing key ecological processes, erroneous formulations, misspecified forcing functions). The comparison between observations and posterior predictive monthly distributions indicates that the plankton models calibrated under the Bayesian hierarchical scheme provided accurate system representations for all the scenarios examined. Our results also suggest that the Bayesian hierarchical approach allows overcoming problems of insufficient local data by “borrowing strength” from well-studied sites and this feature will be highly relevant to conservation practices of regions with a high number of freshwater resources for which complete data could never be practically collected. Finally, we discuss the prospect of extending this framework to spatially explicit biogeochemical models (e.g., more effectively connect inshore with offshore areas) along with the benefits for environmental management, such as the optimization of the sampling design of monitoring programs and the alignment with the policy practice of adaptive management.     

Effects of ocean acidification, temperature and nutrient regimes on the appendicularian Oikopleura dioica: a mesocosm study

Increasing pCO₂ is hypothesized to induce shifts in plankton communities toward smaller cells, reduced carbon export rates and increased roles of gelatinous zooplankton. Appendicularians, among the most numerous pan-global “gelatinous” zooplankton, continuously produce filter-feeding houses, shortcutting marine food webs by ingesting submicron particles, and their discarded houses contribute significantly to carbon fluxes. We present a first mesocosm-scale study on the effects of temperature, pCO₂ and bloom structures on the appendicularian, Oikopleura dioica. There were effects of temperature and nutrients on phytoplankton communities. No shifts in functional phytoplankton groups, nor changes in particle sizes/morphotypes, known to impact appendicularian feeding, were observed under manipulated pCO₂ conditions. However, appendicularian abundance was positively correlated with increased pCO₂, temperature and nutrient levels, consistent with hypotheses concerning gelatinous zooplankton in future oceans. This suggests appendicularians will play more important roles in marine pelagic communities and vertical carbon transport under projected ocean acidification and elevated temperature scenarios.