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      A comparison of absolute performance of different correlative and mechanistic species distribution models in an independent area

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          Abstract

          To investigate the comparative abilities of six different bioclimatic models in an independent area, utilizing the distribution of eight different species available at a global scale and in Australia. Global scale and Australia. We tested a variety of bioclimatic models for eight different plant species employing five discriminatory correlative species distribution models ( SDMs) including Generalized Linear Model ( GLM), MaxEnt, Random Forest ( RF), Boosted Regression Tree ( BRT), Bioclim, together with CLIMEX ( CL) as a mechanistic niche model. These models were fitted using a training dataset of available global data, but with the exclusion of Australian locations. The capabilities of these techniques in projecting suitable climate, based on independent records for these species in Australia, were compared. Thus, Australia is not used to calibrate the models and therefore it is as an independent area regarding geographic locations. To assess and compare performance, we utilized the area under the receiver operating characteristic ( ROC) curves ( AUC), true skill statistic ( TSS), and fractional predicted areas for all SDMs. In addition, we assessed satisfactory agreements between the outputs of the six different bioclimatic models, for all eight species in Australia. The modeling method impacted on potential distribution predictions under current climate. However, the utilization of sensitivity and the fractional predicted areas showed that GLM, MaxEnt, Bioclim, and CL had the highest sensitivity for Australian climate conditions. Bioclim calculated the highest fractional predicted area of an independent area, while RF and BRT were poor. For many applications, it is difficult to decide which bioclimatic model to use. This research shows that variable results are obtained using different SDMs in an independent area. This research also shows that the SDMs produce different results for different species; for example, Bioclim may not be good for one species but works better for other species. Also, when projecting a “large” number of species into novel environments or in an independent area, the selection of the “best” model/technique is often less reliable than an ensemble modeling approach. In addition, it is vital to understand the accuracy of SDMs' predictions. Further, while TSS, together with fractional predicted areas, are appropriate tools for the measurement of accuracy between model results, particularly when undertaking projections on an independent area, AUC has been proved not to be. Our study highlights that each one of these models ( CL, Bioclim, GLM, MaxEnt, BRT, and RF) provides slightly different results on projections and that it may be safer to use an ensemble of models.

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          The meaning and use of the area under a receiver operating characteristic (ROC) curve.

          A representation and interpretation of the area under a receiver operating characteristic (ROC) curve obtained by the "rating" method, or by mathematical predictions based on patient characteristics, is presented. It is shown that in such a setting the area represents the probability that a randomly chosen diseased subject is (correctly) rated or ranked with greater suspicion than a randomly chosen non-diseased subject. Moreover, this probability of a correct ranking is the same quantity that is estimated by the already well-studied nonparametric Wilcoxon statistic. These two relationships are exploited to (a) provide rapid closed-form expressions for the approximate magnitude of the sampling variability, i.e., standard error that one uses to accompany the area under a smoothed ROC curve, (b) guide in determining the size of the sample required to provide a sufficiently reliable estimate of this area, and (c) determine how large sample sizes should be to ensure that one can statistically detect differences in the accuracy of diagnostic techniques.
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            Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine.

            The clinical performance of a laboratory test can be described in terms of diagnostic accuracy, or the ability to correctly classify subjects into clinically relevant subgroups. Diagnostic accuracy refers to the quality of the information provided by the classification device and should be distinguished from the usefulness, or actual practical value, of the information. Receiver-operating characteristic (ROC) plots provide a pure index of accuracy by demonstrating the limits of a test's ability to discriminate between alternative states of health over the complete spectrum of operating conditions. Furthermore, ROC plots occupy a central or unifying position in the process of assessing and using diagnostic tools. Once the plot is generated, a user can readily go on to many other activities such as performing quantitative ROC analysis and comparisons of tests, using likelihood ratio to revise the probability of disease in individual subjects, selecting decision thresholds, using logistic-regression analysis, using discriminant-function analysis, or incorporating the tool into a clinical strategy by using decision analysis.
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              Random forest: a classification and regression tool for compound classification and QSAR modeling.

              A new classification and regression tool, Random Forest, is introduced and investigated for predicting a compound's quantitative or categorical biological activity based on a quantitative description of the compound's molecular structure. Random Forest is an ensemble of unpruned classification or regression trees created by using bootstrap samples of the training data and random feature selection in tree induction. Prediction is made by aggregating (majority vote or averaging) the predictions of the ensemble. We built predictive models for six cheminformatics data sets. Our analysis demonstrates that Random Forest is a powerful tool capable of delivering performance that is among the most accurate methods to date. We also present three additional features of Random Forest: built-in performance assessment, a measure of relative importance of descriptors, and a measure of compound similarity that is weighted by the relative importance of descriptors. It is the combination of relatively high prediction accuracy and its collection of desired features that makes Random Forest uniquely suited for modeling in cheminformatics.
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                Author and article information

                Journal
                Ecol Evol
                Ecol Evol
                10.1002/(ISSN)2045-7758
                ECE3
                Ecology and Evolution
                John Wiley and Sons Inc. (Hoboken )
                2045-7758
                27 July 2016
                August 2016
                : 6
                : 16 ( doiID: 10.1002/ece3.2016.6.issue-16 )
                : 5973-5986
                Affiliations
                [ 1 ] Ecosystem Management School of Environmental and Rural ScienceUniversity of New England Armidale NSW 2351Australia
                [ 2 ] Department of Natural ResourcesIsfahan University of Technology IsfahanIran
                Author notes
                [*] [* ] Correspondence

                Farzin Shabani, Ecosystem Management, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.

                Tel: 612 6773 5878;

                Fax: 612 6773 2769;

                E‐mail: fshaban2@ 123456une.edu.au

                Article
                ECE32332
                10.1002/ece3.2332
                4983607
                27547370
                e6849ae2-7df3-4c82-9acd-36e8e9164437
                © 2016 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 21 January 2016
                : 27 June 2016
                : 29 June 2016
                Page count
                Pages: 14
                Categories
                Original Research
                Original Research
                Custom metadata
                2.0
                ece32332
                August 2016
                Converter:WILEY_ML3GV2_TO_NLMPMC version:4.9.4 mode:remove_FC converted:14.08.2016

                Evolutionary Biology
                bioclimatic model,correlative model,fundamental niche,mechanistic niche model,modeling methods,realized niche,species distribution model

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