Andrew K. Skidmore

Bio: Andrew K. Skidmore is an academic researcher from University of Twente. The author has contributed to research in topics: Normalized Difference Vegetation Index & Canopy. The author has an hindex of 84, co-authored 529 publications receiving 29944 citations. Previous affiliations of Andrew K. Skidmore include Wageningen University and Research Centre & ITC Enschede.

Collinearity: a review of methods to deal with it and a simulation study evaluating their performance

Abstract: Collinearity refers to the non independence of predictor variables, usually in a regression-type analysis. It is a common feature of any descriptive ecological data set and can be a problem for parameter estimation because it inflates the variance of regression parameters and hence potentially leads to the wrong identification of relevant predictors in a statistical model. Collinearity is a severe problem when a model is trained on data from one region or time, and predicted to another with a different or unknown structure of collinearity. To demonstrate the reach of the problem of collinearity in ecology, we show how relationships among predictors differ between biomes, change over spatial scales and through time. Across disciplines, different approaches to addressing collinearity problems have been developed, ranging from clustering of predictors, threshold-based pre-selection, through latent variable methods, to shrinkage and regularisation. Using simulated data with five predictor-response relationships of increasing complexity and eight levels of collinearity we compared ways to address collinearity with standard multiple regression and machine-learning approaches. We assessed the performance of each approach by testing its impact on prediction to new data. In the extreme, we tested whether the methods were able to identify the true underlying relationship in a training dataset with strong collinearity by evaluating its performance on a test dataset without any collinearity. We found that methods specifically designed for collinearity, such as latent variable methods and tree based models, did not outperform the traditional GLM and threshold-based pre-selection. Our results highlight the value of GLM in combination with penalised methods (particularly ridge) and threshold-based pre-selection when omitted variables are considered in the final interpretation. However, all approaches tested yielded degraded predictions under change in collinearity structure and the ‘folk lore’-thresholds of correlation coefficients between predictor variables of |r| >0.7 was an appropriate indicator for when collinearity begins to severely distort model estimation and subsequent prediction. The use of ecological understanding of the system in pre-analysis variable selection and the choice of the least sensitive statistical approaches reduce the problems of collinearity, but cannot ultimately solve them.

Where is positional uncertainty a problem for species distribution modelling

Abstract: Species data held in museum and herbaria, survey data and opportunistically observed data are a substantial information resource. A key challenge in using these data is the uncertainty about where an observation is located. This is important when the data are used for species distribution modelling (SDM), because the coordinates are used to extract the environmental variables and thus, positional error may lead to inaccurate estimation of the species–environment relationship. The magnitude of this effect is related to the level of spatial autocorrelation in the environmental variables. Using local spatial association can be relevant because it can lead to the identification of the specific occurrence records that cause the largest drop in SDM accuracy. Therefore, in this study, we tested whether the SDM predictions are more affected by positional uncertainty originating from locations that have lower local spatial association in their predictors. We performed this experiment for Spain and the Netherlands, using simulated datasets derived from well known species distribution models (SDMs). We used the K statistic to quantify the local spatial association in the predictors at each species occurrence location. A probabilistic approach using Monte Carlo simulations was employed to introduce the error in the species locations. The results revealed that positional uncertainty in species occurrence data at locations with low local spatial association in predictors reduced the prediction accuracy of the SDMs. We propose that local spatial association is a way to identify the species occurrence records that require treatment for positional uncertainty. We also developed and present a tool in the R environment to target observations that are likely to create error in the output from SDMs as a result of positional uncertainty.

Narrow band vegetation indices overcome the saturation problem in biomass estimation

Abstract: Remotely sensed vegetation indices such as NDVI, computed using the red and near infrared bands have been used to estimate pasture biomass. These indices are of limited value since they saturate in dense vegetation. In this study, we evaluated the potential of narrow band vegetation indices for characterizing the biomass of Cenchrus ciliaris grass measured at high canopy density. Three indices were tested: Modified Normalized Difference Vegetation Index (MNDVI), Simple Ratio (SR) and Transformed Vegetation Index (TVI) involving all possible two band combinations between 350 nm and 2500 nm. In addition, we evaluated the potential of the red edge position in estimating biomass at full canopy cover. Results indicated that the standard NDVI involving a strong chlorophyll absorption band in the red region and a near infrared band performed poorly in estimating biomass (R 2=0.26). The MNDVIs involving a combination of narrow bands in the shorter wavelengths of the red edge (700–750 nm) and longer wavelengths of...

Effects of fire and herbivory on the stability of savanna ecosystems

Abstract: Savanna ecosystems are characterized by the co-occurrence of trees and grass- es. In this paper, we argue that the balance between trees and grasses is, to a large extent, determined by the indirect interactive effects of herbivory and fire. These effects are based on the positive feedback between fuel load (grass biomass) and fire intensity. An increase in the level of grazing leads to reduced fuel load, which makes fire less intense and, thus, less damaging to trees and, consequently, results in an increase in woody vegetation. The system then switches from a state with trees and grasses to a state with solely trees. Similarly, browsers may enhance the effect of fire on trees because they reduce woody biomass, thus indirectly stimulating grass growth. This consequent increase in fuel load results in more intense fire and increased decline of biomass. The system then switches from a state with solely trees to a state with trees and grasses. We maintain that the interaction between fire and herbivory provides a mechanistic explanation for observed discontinuous changes in woody and grass biomass. This is an alternative for the soil degradation mechanism, in which there is a positive feedback between the amount of grass biomass and the amount of water that infiltrates into the soil. The soil degradation mechanism predicts no discontinuous chang- es, such as bush encroachment, on sandy soils. Such changes, however, are frequently ob- served. Therefore, the interactive effects of fire and herbivory provide a more plausible explanation for the occurrence of discontinuous changes in savanna ecosystems.

The global distribution and burden of dengue

Abstract: Dengue is a systemic viral infection transmitted between humans by Aedes mosquitoes. For some patients, dengue is a life-threatening illness. There are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread. The contemporary worldwide distribution of the risk of dengue virus infection and its public health burden are poorly known. Here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. We then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. We predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanization. Using cartographic approaches, we estimate there to be 390 million (95% credible interval 284-528) dengue infections per year, of which 96 million (67-136) manifest apparently (any level of disease severity). This infection total is more than three times the dengue burden estimate of the World Health Organization. Stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. The most notable differences are discussed. These new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. We anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help to guide improvements in disease control strategies using vaccine, drug and vector control methods, and in their economic evaluation.

Collinearity: a review of methods to deal with it and a simulation study evaluating their performance

Abstract: Collinearity refers to the non independence of predictor variables, usually in a regression-type analysis. It is a common feature of any descriptive ecological data set and can be a problem for parameter estimation because it inflates the variance of regression parameters and hence potentially leads to the wrong identification of relevant predictors in a statistical model. Collinearity is a severe problem when a model is trained on data from one region or time, and predicted to another with a different or unknown structure of collinearity. To demonstrate the reach of the problem of collinearity in ecology, we show how relationships among predictors differ between biomes, change over spatial scales and through time. Across disciplines, different approaches to addressing collinearity problems have been developed, ranging from clustering of predictors, threshold-based pre-selection, through latent variable methods, to shrinkage and regularisation. Using simulated data with five predictor-response relationships of increasing complexity and eight levels of collinearity we compared ways to address collinearity with standard multiple regression and machine-learning approaches. We assessed the performance of each approach by testing its impact on prediction to new data. In the extreme, we tested whether the methods were able to identify the true underlying relationship in a training dataset with strong collinearity by evaluating its performance on a test dataset without any collinearity. We found that methods specifically designed for collinearity, such as latent variable methods and tree based models, did not outperform the traditional GLM and threshold-based pre-selection. Our results highlight the value of GLM in combination with penalised methods (particularly ridge) and threshold-based pre-selection when omitted variables are considered in the final interpretation. However, all approaches tested yielded degraded predictions under change in collinearity structure and the ‘folk lore’-thresholds of correlation coefficients between predictor variables of |r| >0.7 was an appropriate indicator for when collinearity begins to severely distort model estimation and subsequent prediction. The use of ecological understanding of the system in pre-analysis variable selection and the choice of the least sensitive statistical approaches reduce the problems of collinearity, but cannot ultimately solve them.