Leaf‐litter breakdown in pasture and deciduous woodland streams: a comparison among three European regions

1. Human land‐use has altered catchments on a large scale in most parts of the world, with one of the most profound changes relevant for streams and rivers being the widespread clearance of woody riparian vegetation to make way for livestock grazing pasture. Increasingly, environmental legislation, such as the EU Water Framework Directive (EU WFD), calls for bioassessment tools that can detect such anthropogenic impacts on ecosystem functioning. 2. We conducted a large‐scale field experiment in 30 European streams to quantify leaf‐litter breakdown, a key ecosystem process, in streams whose riparian zones and catchments had been cleared for pasture compared with those in native deciduous woodland. The study encompassed a west–east gradient, from Ireland to Switzerland to Romania, with each of the three countries representing a distinct region. We used coarse‐mesh and fine‐mesh litter bags (10 and 0.5 mm, respectively) to assess total, microbial and, by difference, macroinvertebrate‐mediated breakdown. 3. Overall, total breakdown rates did not differ between land‐use categories, but in some regions macroinvertebrate‐mediated breakdown was higher in deciduous woodland streams, whereas microbial breakdown was higher in pasture streams. This result suggests that overall ecosystem functioning is maintained by compensatory increases in microbial activity in pasture streams. 4. We suggest that simple coefficients of breakdown rates on their own often might not be powerful enough as a bioassessment tool for detecting differences related to land‐use such as riparian vegetation removal. However, shifts in the relative contributions to breakdown by microbial decomposers versus invertebrate detritivores, as revealed by the ratios of their associated breakdown rate coefficients, showed clear responses to land‐use.     

Time‐Dependent Predictive Accuracy in the Presence of Competing Risks

Summary Competing risks arise naturally in time‐to‐event studies. In this article, we propose time‐dependent accuracy measures for a marker when we have censored survival times and competing risks. Time‐dependent versions of sensitivity or true positive (TP) fraction naturally correspond to consideration of either cumulative (or prevalent) cases that accrue over a fixed time period, or alternatively to incident cases that are observed among event‐free subjects at any select time. Time‐dependent (dynamic) specificity (1–false positive (FP)) can be based on the marker distribution among event‐free subjects. We extend these definitions to incorporate cause of failure for competing risks outcomes. The proposed estimation for cause‐specific cumulative TP/dynamic FP is based on the nearest neighbor estimation of bivariate distribution function of the marker and the event time. On the other hand, incident TP/dynamic FP can be estimated using a possibly nonproportional hazards Cox model for the cause‐specific hazards and riskset reweighting of the marker distribution. The proposed methods extend the time‐dependent predictive accuracy measures of Heagerty, Lumley, and Pepe (2000, Biometrics 56, 337–344) and Heagerty and Zheng (2005, Biometrics 61, 92–105).     

Competing Risks and Time‐Dependent Covariates

Time‐dependent covariates are frequently encountered in regression analysis for event history data and competing risks. They are often essential predictors, which cannot be substituted by time‐fixed covariates. This study briefly recalls the different types of time‐dependent covariates, as classified by Kalbfleisch and Prentice [The Statistical Analysis of Failure Time Data, Wiley, New York, 2002] with the intent of clarifying their role and emphasizing the limitations in standard survival models and in the competing risks setting. If random (internal) time‐dependent covariates are to be included in the modeling process, then it is still possible to estimate cause‐specific hazards but prediction of the cumulative incidences and survival probabilities based on these is no longer feasible. This article aims at providing some possible strategies for dealing with these prediction problems. In a multi‐state framework, a first approach uses internal covariates to define additional (intermediate) transient states in the competing risks model. Another approach is to apply the landmark analysis as described by van Houwelingen [Scandinavian Journal of Statistics 2007, 34 , 70–85] in order to study cumulative incidences at different subintervals of the entire study period. The final strategy is to extend the competing risks model by considering all the possible combinations between internal covariate levels and cause‐specific events as final states. In all of those proposals, it is possible to estimate the changes/differences of the cumulative risks associated with simple internal covariates. An illustrative example based on bone marrow transplant data is presented in order to compare the different methods.     

Impact of climatic variability on parameters used in typology and ecological quality assessment of surface waters—implications on the Water Framework Directive

In most cases the negative impacts of climate change to aquatic ecosystems cannot be mitigated by measures in the river basin management. Ignoring climate change by the Water Framework Directive may have strong implications for the typology and quality assessment systems used for water bodies. As a result of climate change, water bodies, especially those located near the type boundaries may change their type. Compared to typology characteristics, water quality parameters are even more labile and may be easily affected by climate change. The paper exemplifies that the anticipated deterioration of water quality within the time frame relevant for WFD implementation may be large enough to endanger the fulfillment of the set water quality objectives. The review of the river basin characterization every six years, as required by the WFD, might also include re-evaluation of reference conditions according to the changes observed at pristine reference sites. As a consequence, the restoration targets (i.e., the good ecological status) would also need to be evaluated periodically.     

Parametric regression on cumulative incidence function

We propose parametric regression analysis of cumulative incidence function with competing risks data. A simple form of Gompertz distribution is used for the improper baseline subdistribution of the event of interest. Maximum likelihood inferences on regression parameters and associated cumulative incidence function are developed for parametric models, including a flexible generalized odds rate model. Estimation of the long-term proportion of patients with cause-specific events is straightforward in the parametric setting. Simple goodness-of-fit tests are discussed for evaluating a fixed odds rate assumption. The parametric regression methods are compared with an existing semiparametric regression analysis on a breast cancer data set where the cumulative incidence of recurrence is of interest. The results demonstrate that the likelihood-based parametric analyses for the cumulative incidence function are a practically useful alternative to the semiparametric analyses.     

Performance of bottom ramps to mitigate gravel habitat bottlenecks in a channelized lowland river

The long‐term performance of measures to restore in‐stream habitat in gravel bed rivers is uncertain in the presence of impoundments, land use pressures, and fine sediment inputs. The goal of this study was to evaluate the longer‐term performance of five bottom ramps, designed to facilitate fish passage, and constructed similarly to artificial riffles to provide compensatory gravel riverbed habitat for benthic invertebrates and lithophilic, coarse‐substrate‐preferring fish in a channelized lowland river. Bottom ramp age did not significantly influence habitat conditions indicated by a lack of correlations with the percentage of fine sediment less than 2 mm, the organic content of the substrate, and the years since construction. A significant decrease in the relative abundances of coarse‐substrate‐preferring benthic invertebrates corresponding to project construction age was found, but there were no significant differences in the density of rheophilic, fast‐flow‐preferring or lithophilic fish species among sites. This study presents substantial evidence that similarly constructed bottom ramps in comparable environmental settings provided sufficient habitat for sensitive benthic invertebrates and fish to be present for over 13 years. However, a sudden decrease in habitat suitability cannot be excluded in the long‐term if there is a fine sediment deposition threshold, which results in ramps becoming full. Nevertheless, bottom ramps are recommended as effective measures to enhance longitudinal connectivity, fish passage, and gravel habitat provision in channelized lowland rivers.     

Assessing eutrophication in the Portuguese continental Exclusive Economic Zone within the European Marine Strategy Framework Directive

This study reports the state and causes of eutrophication in the Portuguese continental Exclusive Economic Zone (EEZ), during a 14-year period (1995–2008), following the European Marine Strategy Framework Directive (MSFD) and using the trophic index TRIX for an integrated evaluation of indicators of eutrophication, and identifies areas where monitoring is needed to improve the eutrophication assessment. A non-continuous dataset for the 8 indicators specified by the MSFD for eutrophication assessment was used, including published and grey data. Eutrophication indicators were validated and thresholds reviewed, considering regional differences. The diatom:flagellate ratio was found a poor indicator of eutrophication as shifts in the diatom:flagellate ratio naturally occur associated with alternating water column turbulence and upwelling, and stratification, and therefore, could not be associated with anthropogenic nutrient enrichment effects. Assessment areas were, as a whole, classified as non-problem areas concerning eutrophication. Although nutrient enrichment was observed in coastal waters, related to river plume influence, nutrient enrichment direct and indirect effects were generally not detectable, possibly due to water column dispersion and mixing processes. Only occasionally, mild eutrophication was found in specific areas under the influence of major river (Douro, Vouga and Guadiana) plumes, associated with high nutrient and phytoplankton biomass levels and seagrass decline, which indicates the need for directed monitoring on eutrophication in those areas.     

A note on including time-dependent covariate in regression model for competing risks data

Recently, regression analysis of the cumulative incidence function has gained interest in competing risks data analysis, through the model proposed by Fine and Gray (JASA 1999; 94: 496-509). In this note, we point out that inclusion of time-dependent covariates in this model can lead to serious bias. We illustrate the problems arising in such a context, using bone marrow transplant data as a working example and numerical simulations. Practical advices are given, preventing the misuse of this model.