Vijay Barve

Bio: Vijay Barve is an academic researcher from Florida Museum of Natural History. The author has contributed to research in topics: Butterfly & Biodiversity informatics. The author has an hindex of 10, co-authored 36 publications receiving 1510 citations. Previous affiliations of Vijay Barve include University of Florida & University of Kansas.

Discovering and developing primary biodiversity data from social networking sites

Abstract: An ever-increasing need exists for fine-scale biodiversity occurrence records for a broad variety of research applications in biodiversity and science more generally. Even though large-scale data aggregators like GBIF serve such data in large quantities, major gaps and biases still exist, both in taxonomic coverage and in spatial coverage. To address these gaps, in this dissertation, I explored social networking sites (SNS) as a rich potential source of additional biodiversity occurrence records. In my first chapter, I explored the idea of discovering, extracting, and organizing massive numbers of biodiversity occurrence records now available on SNSs. I presented a proof-of-concept with Flickr as the SNS and Snowy Owls (Bubo scandiacus) and Monarch Butterflies (Danaus plexippus) as target species. The methods presented in this chapter can easily be used for any other SNS, region, or species group. These approaches are broadly applicable to animal and plant groups that are photographed, and that can be identified from photographs with some degree of confidence (e.g., birds, butterflies, cetaceans, orchids, dragonflies, amphibians, and plants). SNS thus offer a rich new source of biodiversity data. To understand the strengths and weaknesses of biodiversity data, we need effective tools by which to explore and visualize these data. I developed a suite of such tools in an R package called bdvis, which is described in chapter two. The package allows

A practical guide to MaxEnt for modeling species' distributions: what it does, and why inputs and settings matter

Abstract: The MaxEnt software package is one of the most popular tools for species distribution and environmental niche modeling, with over 1000 published applications since 2006. Its popularity is likely for two reasons: 1) MaxEnt typically outperforms other methods based on predictive accuracy and 2) the software is particularly easy to use. MaxEnt users must make a number of decisions about how they should select their input data and choose from a wide variety of settings in the software package to build models from these data. The underlying basis for making these decisions is unclear in many studies, and default settings are apparently chosen, even though alternative settings are often more appropriate. In this paper, we provide a detailed explanation of how MaxEnt works and a prospectus on modeling options to enable users to make informed decisions when preparing data, choosing settings and interpreting output. We explain how the choice of background samples reflects prior assumptions, how nonlinear functions of environmental variables (features) are created and selected, how to account for environmentally biased sampling, the interpretation of the various types of model output and the challenges for model evaluation. We demonstrate MaxEnt’s calculations using both simplified simulated data and occurrence data from South Africa on species of the flowering plant family Proteaceae. Throughout, we show how MaxEnt’s outputs vary in response to different settings to highlight the need for making biologically motivated modeling decisions.

Making better Maxent models of species distributions: complexity, overfitting and evaluation

Abstract: Aim Models of species niches and distributions have become invaluable to biogeographers over the past decade, yet several outstanding methodological issues remain. Here we address three critical ones: selecting appropriate evaluation data, detecting overfitting, and tuning program settings to approximate optimal model complexity. We integrate solutions to these issues for Maxent models, using the Caribbean spiny pocket mouse, Heteromys anomalus, as an example. Location North-western South America. Methods We partitioned data into calibration and evaluation datasets via three variations of k-fold cross-validation: randomly partitioned, geographically structured and masked geographically structured (which restricts background data to regions corresponding to calibration localities). Then, we carried out tuning experiments by varying the level of regularization, which controls model complexity. Finally, we gauged performance by quantifying discriminatory ability and overfitting, as well as via visual inspections of maps of the predictions in geography. Results Performance varied among data-partitioning approaches and among regularization multipliers. The randomly partitioned approach inflated estimates of model performance and the geographically structured approach showed high overfitting. In contrast, the masked geographically structured approach allowed selection of high-performing models based on all criteria. Discriminatory ability showed a slight peak in performance around the default regularization multiplier. However, regularization levels two to four times higher than the default yielded substantially lower overfitting. Visual inspection of maps of model predictions coincided with the quantitative evaluations. Main conclusions Species-specific tuning of model parameters can improve the performance of Maxent models. Further, accurate estimates of model performance and overfitting depend on using independent evaluation data. These strategies for model evaluation may be useful for other modelling methods as well.

Uses and misuses of bioclimatic envelope modeling

Abstract: Bioclimatic envelope models use associations between aspects of climate and species' occurrences to estimate the conditions that are suitable to maintain viable populations. Once bioclimatic envelopes are characterized, they can be applied to a variety of questions in ecology, evolution, and conservation. However, some have questioned the usefulness of these models, because they may be based on implausible assumptions or may be contradicted by empirical evidence. We review these areas of contention, and suggest that criticism has often been misplaced, resulting from confusion between what the models actually deliver and what users wish that they would express. Although improvements in data and methods will have some effect, the usefulness of these models is contingent on their appropriate use, and they will improve mainly via better awareness of their conceptual basis, strengths, and limitations.