Habitat classification modeling with incomplete data: pushing the habitat envelope.

Habitat classification models (HCMs) are invaluable tools for species conservation, land-use planning, reserve design, and metapopulation assessments, particularly at broad spatial scales. However, species occurrence data are often lacking and typically limited to presence points at broad scales. This lack of absence data precludes the use of many statistical techniques for HCMs. One option is to generate pseudo-absence points so that the many available statistical modeling tools can bb used. Traditional techniques generate pseudo-absence points at random across broadly defined species ranges, often failing to include biological knowledge concerning the species-habitat relationship. We incorporated biological knowledge of the species-habitat relationship into pseudo-absence points by creating habitat envelopes that constrain the region from which points were randomly selected. We define a habitat envelope as an ecological representation of a species, or species feature's (e.g., nest) observed distribution (i.e., realized niche) based on a single attribute, or the spatial intersection of multiple attributes. We created HCMs for Northern Goshawk (Accipiter gentilis atricapillus) nest habitat during the breeding season across Utah forests with extant nest presence points and ecologically based pseudo-absence points using logistic regression. Predictor variables were derived from 30-m USDA Landfire and 250-m Forest Inventory and Analysis (FIA) map products. These habitat-envelope-based models were then compared to null envelope models which use traditional practices for generating pseudo-absences. Models were assessed for fit and predictive capability using metrics such as kappa, threshold-independent receiver operating characteristic (ROC) plots, adjusted deviance (D(adj)2), and cross-validation, and were also assessed for ecological relevance. For all cases, habitat envelope-based models outperformed null envelope models and were more ecologically relevant, suggesting that incorporating biological knowledge into pseudo-absence point generation is a powerful tool for species habitat assessments. Furthermore, given some a priori knowledge of the species-habitat relationship, ecologically based pseudo-absence points can be applied to any species, ecosystem, data resolution, and spatial extent.     

Estimating the spatio-temporal risk of disease epidemics using a bioclimatic niche model

There are presently few tools available for estimating epidemic risks from forest pathogens, and hence informing pro-active disease management. In this study we demonstrated that a bioclimatic niche model can be used to examine questions of epidemic risk in temperate eucalypt plantations. The bioclimatic niche model, CLIMEX, was used to identify regional variation in climate suitability for Mycosphaerella leaf disease (MLD), a major cause of foliage damage in temperate eucalypt plantations around the world. Using historical observations of MLD damage, we were able to convert the relative score of climatic suitability generated by CLIMEX into a severity ranking ranging from low to high, providing for the first time a direct link between risk and impact, and allowing us to explore disease severity in a way meaningful to forest managers. We determined that the ‘Compare Years’ function in CLIMEX could be used for site-specific risk assessment to identify severity, frequency and seasonality of MLD epidemics. We explored appropriate scales of risk assessment for forest managers. Applying the CLIMEX model of MLD using a 0.25° or coarser grid size to areas of sharp topographic relief frequently misrepresented the risk posed by MLD, because considerable variation occurred between individual forest sites encompassed within a single grid cell. This highlighted the need for site-specific risk assessment to address many questions pertinent to managing risk in plantations.     

Ecological Uses of Vertebrate Indicator Species: A Critique

Abstract: Plant and animal species have been used for decades as indicators of air and water quality and agricultural and range conditions. Increasingly, vertebrates are used to assess population trends and habitat quality for other species. In this paper we review the conceptual bases, assumptions, and published guidelines for selection and use of vertebrates as ecological indicators. We conclude that an absence of precise definitions and procedures, confounded criteria used to select species, and discordance with ecological literature severely weaken the effectiveness and credibility of using vertebrates as ecological indicators. In many cases the use of ecological indicator species is inappropriate, but when necessary, the following recommendations will make their use more rigorous: (1) clearly state assessment goals, (2) use indicators only when other assessment options are unavailable, (3) choose indicator species by explicitly defined criteria that are in accord with assessment goals, (4) include all species that fulfill stated selection criteria (5) know the biology of the indicator in detail, and treat the indicator as a formal estimator in conceptual and statistical models, (6) identify and define sources of subjectivity when selecting monitoring and intetpreting indicator species, (7) submit assessment design, methods of data collection and statistical analysis, interpretations, and recommendations to peer review and (8) direct research at developing an overall strategy for monitoring wildlife that accounts for natural variability in population attributes and incorporates concepts from landscape ecology.     

The crucial role of the accessible area in ecological niche modeling and species distribution modeling

Using known occurrences of species and correlational modeling approaches has become a common paradigm in broad-scale ecology and biogeography, yet important aspects of the methodology remain little-explored in terms of conceptual basis. Here, we explore the conceptual and empirical reasons behind choice of extent of study area in such analyses, and offer practical, but conceptually justified, reasoning for such decisions. We assert that the area that has been accessible to the species of interest over relevant time periods represents the ideal area for model development, testing, and comparison.     

Qualitative modeling and monitoring of selected ecosystem functions

This paper proposes three qualitative models that were applied for modeling of Small Water Cycle violation in ecosystem of Trebon region, South Bohemia. SWC refers to the behavior of the local ecosystem (e.g., the Trebon region), in which the volume of water that comes into the ecosystem is evaporated and falls back into this system. SWC is characterized by early morning dues and frequent small rain precipitation. In the Trebon Biosphere Reserve characterized by wetlands, forests and agriculture land, the evaporated water rises quickly inside the zone and does not have time to recondense before it is transported outside the ecosystem to the distant mountains, where it condenses spontaneously in the rising air streams.The essential pre-model for developing our qualitative models is the database model implemented in the MS SQL environment. The data in this model were collected for last five years and contain information about SWC violation and about the landscape stability development. The database system is used for standard reports, for correlating digital and graphic runs from associated meteorological stations, and for computing the evapotranspiration at the points where the stations are located and also at approximate inter-points.In parallel, and in addition to this standard use of the database model, the data was applied in the development of qualitative models (state model, model for the detection of unexpected situations and matroid model). This transformation and compression of the data was done with help of experienced experts and with the help of special mathematical operations. Qualitative models introduced in this paper overcome experience with quantitative models namely in these items: (1) They provide compression of information contained in large volumes of numerical data. (2) On the contrary of individual quantitative modeling qualitative models enable to describe the function and properties of the whole ecosystem. (3) Conclusions from qualitative models are in many cases better than are the generalizations of results from quantitative models.The first goal of the paper is to model situations associated with violations of the Small Water Cycle (SWC) in this ecosystem, and to contribute to acceptable solutions. The second goal of the paper is to investigate temporary models for the stability of the landscape development and to propose qualitative models for software support for integrated environmental modeling.     

Two-phase modeling of sediment clouds

A sediment cloud release in stagnant ambient fluid occurs in many engineering applications. Examples include land reclamation and disposal of dredged materials. The detailed modeling of the distinct characteristics of both the solid and fluid phases of the sediment cloud is hitherto unavailable in the literature despite their importance in practice. In this paper, the two-phase mixing characteristics of the sediment cloud are investigated both experimentally and theoretically. Experiments were carried out to measure the transient depth penetration and the lateral spread of the sediment cloud and its entrained fluid using the laser induced fluorescence technique, with a range of particle sizes frequently encountered in the field (modeled at laboratory scale). A two-phase model of the sediment cloud that provides detailed predictions of the mixing characteristics of the individual phases is also proposed. The entrained fluid characteristics are solved by an integral model accounting for the buoyancy loss (due to particle separation) in each time step. The flow field induced by the sediment cloud is approximated by a Hill’s spherical vortex centered at the centroid and with the size of the entrained fluid. The particle equation of motion under the effect of the induced flow governs each computational particle. A random walk model using the hydrodynamic diffusion coefficient is used to account for the random fluctuation of particles in the dispersive regime. Overall, the model predictions of the two-phase mixing characteristics are in good agreement with the experimental data for a wide range of release conditions.     

Boosted trees for ecological modeling and prediction

Accurate prediction and explanation are fundamental objectives of statistical analysis, yet they seldom coincide. Boosted trees are a statistical learning method that attains both of these objectives for regression and classification analyses. They can deal with many types of response variables (numeric, categorical, and censored), loss functions (Gaussian, binomial, Poisson, and robust), and predictors (numeric, categorical). Interactions between predictors can also be quantified and visualized. The theory underpinning boosted trees is presented, together with interpretive techniques. A new form of boosted trees, namely, "aggregated boosted trees" (ABT), is proposed and, in a simulation study, is shown to reduce prediction error relative to boosted trees. A regression data set is analyzed using ABT to illustrate the technique and to compare it with other methods, including boosted trees, bagged trees, random forests, and generalized additive models. A software package for ABT analysis using the R software environment is included in the Appendices together with worked examples.     

不同土地利用方式及开垦时间对岩溶山区土壤养分空间分布的影响

采集贵州普定典型岩溶山区7种土地利用方式和3个不同开垦时间(27 a、39 a、48 a)的0～10 cm、10～20 cm、20～40 cm土壤样品,进行室内理化分析.结果显示,林地土壤有机质、全氮、碱解氮累积量较多,玉米黄豆地含量最少.林地土壤0～10 cm层有机质、全氮、碱解氮分别比玉米黄豆地高271.0%、317.7%、246.1%.林地和撂荒地对土壤养分循环较为有利.林地开垦为农业用地后,土壤有机质、全氮、碱解氮含量明显下降,全磷、有效磷、全钾含量没有明显变化,有效钾含量增多.开垦39 a的0～10 cm层土壤有机质、全氮、全磷、有效磷、有效钾含量高于开垦27 a和48 a土壤的含量,碱解氮低于开垦27 a和48 a土壤的含量;开垦27 a的土壤全钾含量高于开垦39 a和48 a土壤的含量.开垦时间长或短对土壤养分含量的影响未表现特殊规律性,可能受到其他因素的影响.     

Spatial surplus production modeling of Atlantic tunas and billfish

We formulate and simulation-test a spatial surplus production model that provides a basis with which to undertake multispecies, multi-area, stock assessment. Movement between areas is parameterized using a simple gravity model that includes a "residency" parameter that determines the degree of stock mixing among areas. The model is deliberately simple in order to (1) accommodate nontarget species that typically have fewer available data and (2) minimize computational demand to enable simulation evaluation of spatial management strategies. Using this model, we demonstrate that careful consideration of spatial catch and effort data can provide the basis for simple yet reliable spatial stock assessments. If simple spatial dynamics can be assumed, tagging data are not required to reliably estimate spatial distribution and movement. When applied to eight stocks of Atlantic tuna and billfish, the model tracks regional catch data relatively well by approximating local depletions and exchange among high-abundance areas. We use these results to investigate and discuss the implications of using spatially aggregated stock assessment for fisheries in which the distribution of both the population and fishing vary over time.     

A macroeconomic analysis of regional environmental modeling and planning

Alterations in the institutional structure of a region through exogenous investment can be viewed as a tool for regional adjustments in environmental quality. Two models are presented: an expanded Metzler interregional model that incorporates regional disamenities into the multiplier structure and a regional migration model for estimating regional disamenities. The underlying suggestion of the regional environmental trade model is that a concept of aggregate efficiency should be established for the allocation of large exogenous investment expenditures across regions. An example estimation is presented for the Southwest. Revised regional multipliers that include disamenity levels are calculated and the investment decisions with and without disamenity effects are considered. The example estimations suggest that failure to include disamenity corrections in regional multipliers will lead to greater regional inequality in welfare.     

Indigenous Uses, Population Density, and Conservation of Threatened Medicinal Plants in Protected Areas of the Indian Himalayas

Abstract:  For 10 years I monitored the population density of threatened medicinal plant species in seven protected areas in the Indian Himalayas. I also documented the indigenous uses of threatened medicinal plants through interviews with 138 herbal healers (83 Tibetan healers and 55 Ayurvedic healers) residing in the buffer zone villages of these protected areas. To assess the population status of threatened medicinal plant species, I sampled the 10 major habitat types in the protected areas. In all, I found 60 threatened medicinal plant species during the study period, of which 54 species occurred in the sampling plots. Twenty-two percent of threatened medicinal plant species were critically endangered, 16% were endangered, and 27% were vulnerable. Thirty-two threatened medicinal plant species were endemic to the Himalayan region. The density of threatened medicinal plant species varied with protected areas. The Valley of Flowers protected area had the highest number of threatened medicinal plant species. The "moist" habitat type was richest in these species among all 10 habitat types sampled. Arnebia euchroma (Royle ex Benth.) Johnston and Ephedra gerardiana Wall. ex Stapf. were the most common threatened medicinal plant species. The indigenous groups of healers used these threatened species in curing about 45 different ailments. Based on my findings, I believe that to ensure the long-term sustainability of threatened medicinal plants, medicinal-plant conservation areas should be established.     

Hydrodynamic modeling of Edmonton storm-water ponds

Environmental Fluid Mechanics - Computational models often are applied to simulate water quality for management of natural and constructed aquatic systems. As part of a larger study, a...     

The empirical modeling of an ecosystem

The authors have endeavored to create a verified a-posteriori model of a planktonic ecosystem. Verification of an empirically derived set of first-order, quadratic differential equations proved elusive due to the sensitivity of the model system to changes in initial conditions. Efforts to verify a similarly derived set of linear differential equations were more encouraging, yielding reasonable behavior for half of the ten ecosystem compartments modeled. The well-behaved species models gave indications as to the rate-controlling process in the ecosystem.     

Relating environmental modeling to policy issues and decisions

This paper describes a linear program-based computer model which has been developed to identify the most effective spending patterns for environmental cleanup based on public preferences and spending limitations. The inputs to the model include the costs of removing each residual studied from its various sources. The objective function is the total “value of removal”. The factor added for each residual consists of a value for the residual multiplied by the quantity or fraction removed.Results of the analysis relate to and support current and projected policy decisions by the U.S. Environmental Protection Agency (EPA) for air and water programs. In addition, the results of the analysis suggest that EPA undertake a redirection of the Nation's resources among residual control programs.     

Concentrations of Potentially Toxic Metals in Urban Soils of Seville: Relationship with Different Land Uses

Fifty-two samples of surface soils were taken in the urban area of Seville, to assess the possible influence of different land uses on their metal contents and their relationship with several soil properties. The samples corresponded to five categories or land uses: agricultural, parks, ornamental gardens, riverbanks, and roadsides. Sequential extraction of metal according to the procedure proposed by the former Community Bureau of Reference (BCR) was carried out, and pseudo-total (aqua regia soluble) metal contents were determined. Lower organic C, total N and available P and K contents were found in riverbank samples, probably due to the lack of manuring of those sites, left in a natural status. In contrast, significantly higher electrical conductivity was found in those sites, due to the tidal influence of the nearby Atlantic Ocean. Other land uses did not show significant differences in the general properties. Concentrations of Cu, Pb and Zn, both aqua-regia soluble and sequentially extracted, were clearly higher in soils from ornamental gardens, whereas the concentrations in the riverbank samples were slightly lower than the other categories. In contrast, other metals (Cd, Cr, Fe, Mn, Ni) were uniformly distributed throughout all land uses. A strong statistical association is found among the concentrations of Cu, Pb, Zn and organic C, suggesting that the larger contents of these metals in ornamental gardens are partly due to organic amendments added to those sites more frequently than to other kinds of sites. Considering the conclusions of previous studies, heavy traffic can also contribute to those `urban’ metals in urban soils. Periodic monitoring of the concentrations of urban metals in busy city centres and of the quality of amendments added to soils of recreational areas are recommended.     

3S与在线监测技术在环境模型研究中的应用

结合环境信息系统的研究现状和研究实例，首先分析了3S和在线监测技术与环境模型研究结合的必要性，并分析指出了3S、在线监测技术在环境模型研究中潜在的应用范围，然后剖析了3S技术与环境模型研究结合的三阶水平，最后介绍了3S在环境规划模型研究中的理想结合框架。     

Joint use of data and modeling in coastal wave transformation

In the framework of a research project entitled ??BRISA??BReaking waves and Induced SAnd transport??, a methodology was devised to characterize the waves joining together in-situ measurements and numerical wave propagation models. With this goal in mind, a number of in-situ measurements were made, for selected positions in front of Praia de Faro (South Portugal), during four days (25th to 28th March, 2009) by using different types of equipments (e.g., resistive wave gauges, pressure sensors, currentmeters and a new prototype pore pressure sensor using optical fibre). Wave records were obtained simultaneously offshore (at a water depth of 11.7?m below mean sea level, MSL) and at the surf and swash zones. The data processing and analysis were made by applying classical time domain techniques. Numerical simulations of the wave propagation between offshore and inshore for the measurement period were performed with two numerical models, a 1D model based on linear theory and a nonlinear Boussinesq-type model, COULWAVE, both forced by the measured offshore wave conditions of 27th March 2009. Comparisons between numerical results and field data for the pressure sensors placed in the surf and swash zones were made and discussed. This approach enables to evaluate the performance of those models to simulate those specific conditions, but also to validate the models by gaining confidence on their use in other conditions.     

Occupancy estimation and modeling with multiple states and state uncertainty

The distribution of a species over space is of central interest in ecology, but species occurrence does not provide all of the information needed to characterize either the well-being of a population or the suitability of occupied habitat. Recent methodological development has focused on drawing inferences about species occurrence in the face of imperfect detection. Here we extend those methods by characterizing occupied locations by some additional state variable (e.g., as producing young or not). Our modeling approach deals with both detection probabilities <1 and uncertainty in state classification. We then use the approach with occupancy and reproductive rate data from California Spotted Owls (Strix occidentalis occidentalis) collected in the central Sierra Nevada during the breeding season of 2004 to illustrate the utility of the modeling approach. Estimates of owl reproductive rate were larger than na?ve estimates, indicating the importance of appropriately accounting for uncertainty in detection and state classification.