National Institute of Water and Atmospheric Research

About: National Institute of Water and Atmospheric Research is a facility organization based out in Auckland, New Zealand. It is known for research contribution in the topics: Population & Benthic zone. The organization has 2608 authors who have published 6103 publications receiving 267813 citations. The organization is also known as: NIWA & Taihoro Nukurangi.

Novel methods improve prediction of species' distributions from occurrence data

Abstract: Prediction of species' distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence-only data to fit models, and independent presence-absence data to evaluate the predictions. Along with well-established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species' distributions. These include machine-learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species' occurrence data. Presence-only data were effective for modelling species' distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve.

Species Distribution Models: Ecological Explanation and Prediction Across Space and Time

Abstract: Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes, sometimes requiring extrapolation in space and time. SDMs are now widely used across terrestrial, freshwater, and marine realms. Differences in methods between disciplines reflect both differences in species mobility and in “established use.” Model realism and robustness is influenced by selection of relevant predictors and modeling method, consideration of scale, how the interplay between environmental and geographic factors is handled, and the extent of extrapolation. Current linkages between SDM practice and ecological theory are often weak, hindering progress. Remaining challenges include: improvement of methods for modeling presence-only data and for model selection and evaluation; accounting for biotic interactions; and assessing model uncertainty.

A working guide to boosted regression trees

Abstract: Summary 1 Ecologists use statistical models for both explanation and prediction, and need techniques that are flexible enough to express typical features of their data, such as nonlinearities and interactions 2 This study provides a working guide to boosted regression trees (BRT), an ensemble method for fitting statistical models that differs fundamentally from conventional techniques that aim to fit a single parsimonious model Boosted regression trees combine the strengths of two algorithms: regression trees (models that relate a response to their predictors by recursive binary splits) and boosting (an adaptive method for combining many simple models to give improved predictive performance) The final BRT model can be understood as an additive regression model in which individual terms are simple trees, fitted in a forward, stagewise fashion 3 Boosted regression trees incorporate important advantages of tree-based methods, handling different types of predictor variables and accommodating missing data They have no need for prior data transformation or elimination of outliers, can fit complex nonlinear relationships, and automatically handle interaction effects between predictors Fitting multiple trees in BRT overcomes the biggest drawback of single tree models: their relatively poor predictive performance Although BRT models are complex, they can be summarized in ways that give powerful ecological insight, and their predictive performance is superior to most traditional modelling methods 4 The unique features of BRT raise a number of practical issues in model fitting We demonstrate the practicalities and advantages of using BRT through a distributional analysis of the short-finned eel ( Anguilla australis Richardson), a native freshwater fish of New Zealand We use a data set of over 13 000 sites to illustrate effects of several settings, and then fit and interpret a model using a subset of the data We provide code and a tutorial to enable the wider use of BRT by ecologists

Global observed changes in daily climate extremes of temperature and precipitation

Abstract: A suite of climate change indices derived from daily temperature and precipitation data, with a primary focus on extreme events, were computed and analyzed. By setting an exact formula for each index and using specially designed software, analyses done in different countries have been combined seamlessly. This has enabled the presentation of the most up-to-date and comprehensive global picture of trends in extreme temperature and precipitation indices using results from a number of workshops held in data-sparse regions and high-quality station data supplied by numerous scientists world wide. Seasonal and annual indices for the period 1951-2003 were gridded. Trends in the gridded fields were computed and tested for statistical significance. Results showed widespread significant changes in temperature extremes associated with warming, especially for those indices derived from daily minimum temperature. Over 70% of the global land area sampled showed a significant decrease in the annual occurrence of cold nights and a significant increase in the annual occurrence of warm nights. Some regions experienced a more than doubling of these indices. This implies a positive shift in the distribution of daily minimum temperature throughout the globe. Daily maximum temperature indices showed similar changes but with smaller magnitudes. Precipitation changes showed a widespread and significant increase, but the changes are much less spatially coherent compared with temperature change. Probability distributions of indices derived from approximately 200 temperature and 600 precipitation stations, with near-complete data for 1901-2003 and covering a very large region of the Northern Hemisphere midlatitudes (and parts of Australia for precipitation) were analyzed for the periods 1901-1950, 1951-1978 and 1979-2003. Results indicate a significant warming throughout the 20th century. Differences in temperature indices distributions are particularly pronounced between the most recent two periods and for those indices related to minimum temperature. An analysis of those indices for which seasonal time series are available shows that these changes occur for all seasons although they are generally least pronounced for September to November. Precipitation indices show a tendency toward wetter conditions throughout the 20th century.

Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data

Abstract: Most methods for modeling species distributions from occurrence records require additional data representing the range of environmental conditions in the modeled region. These data, called background or pseudo-absence data, are usually drawn at random from the entire region, whereas occurrence collection is often spatially biased toward easily accessed areas. Since the spatial bias generally results in environmental bias, the difference between occurrence collection and background sampling may lead to inaccurate models. To correct the estimation, we propose choosing background data with the same bias as occurrence data. We investigate theoretical and practical implications of this approach. Accurate information about spatial bias is usually lacking, so explicit biased sampling of background sites may not be possible. However, it is likely that an entire target group of species observed by similar methods will share similar bias. We therefore explore the use of all occurrences within a target group as biased background data. We compare model performance using target-group background and randomly sampled background on a comprehensive collection of data for 226 species from diverse regions of the world. We find that target-group background improves average performance for all the modeling methods we consider, with the choice of background data having as large an effect on predictive performance as the choice of modeling method. The performance improvement due to target-group background is greatest when there is strong bias in the target-group presence records. Our approach applies to regression-based modeling methods that have been adapted for use with occurrence data, such as generalized linear or additive models and boosted regression trees, and to Maxent, a probability density estimation method. We argue that increased awareness of the implications of spatial bias in surveys, and possible modeling remedies, will substantially improve predictions of species distributions.