Workshops

We are hosting three workshops at IBS Évora on Tuesday, 20th. Each workshop has limited numbers of places available so make sure you finalize your registration soon at www.ibs2018.uevora.pt/registration/. If limited numbers of participants apply for a particular workshop, we might have to cancel it depending on availability of conference funds. In such case, participants already enrolled in canceled workshops will be offered the chance to attend other workshops or have their workshop fee reimbursed. The following workshops were selected following an open call for proposals:

Workshop #1 – BioGIS: Biodiversity Geographic Information System

Organisers: Prof. Alejandro Rozenfeld^1,2,*, Mr. Louis Hansen³, Prof. Carsten Rahbek³ & Prof. Miguel B. Araújo^4,5

Institutions: ¹CONICET, Argentina; ²INTELYMEC-CIFICEN Buenos Aires, Argentina ,³Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark; ⁴Spanish Research Council (CSIC) at the National Museum of Natural Sciences in Madrid, Spain; ⁵University of Èvora, Portugal

Contact: alejandro.rozenfeld@gmail.com

BioGIS is a platform for visual inspection and analyses of large biodiversity data sets. It is a fully fledged geographical information system with functions that until recently were only available in WORLDMAP (a computer program developed by Paul Williams at the Natural History Museum and that was discontinued in the late 90s). Analytical functions include species richness, dispersal field and rarity analysis, spatial turnover (beta diversity), temporal turnover, spatiotemporal turnover, and overlays of 1-D, 2-D, and 3-D scores on maps. The program allows importing data in several formats, including shape files, raster files, and data matrices of several kinds (thus being able to smoothly communicate with BIOMOD, BIOENSEMBLES, and other modelling software). The program is being developed as part of a partnership involving Alejandro Rozenfeld, Carsten Rahbek, and Miguel B. Araújo. BioGIS constitutes a multiplatform, object oriented and stand-alone analytical tool developed on MATLAB. It combines efficient management of big matrices and graphical capabilities to perform complex analysis and deploy results onto maps at multiple scales. It’s been mainly developed as an analytical tool-box environment to help researchers and get them inspired to formulate new questions on ecology and biogeography. It is a full-day workshop organized into three sessions. In the first session, the whole system will be extensively explained. In the second session, a full tutorial will be demonstrated stressing the system with different data set formats. In the third session, we will help participants to apply BioGIS on their own data sets.

Workshop #2 – Applications of NicheA for Research in Biogeography 

 

Organizers: Luis E. Escobar, Virginia Tech, VA, USA. (ecoguate2003@gmail.com) and Huijie Qiao, Chinese Academy of Sciences, Beijing, China (huijieqiao@gmail.com)

The full-day hands-on workshop will include a variety of analysis in environmental space, from basic to advanced biogeographic applications, including visualization of backgrounds and occurrences in environmental dimensions, projections to future climates, and generation of virtual species. NicheA is free, open-source software, available under the GNU Lesser General Public License, that was published in late 2016 and hast at least 15 scientific citations to date. The software is available at http://nichea.sourceforge.net/.  The ecological niche has been a central concept in modern biogeography. G. Evelyn Hutchinson presented a formalization of niche concepts more than 50 yr ago, proposing relationships between ecological niches and geographic spaces (which he called ‘biotopes’); this linkage is known as the Hutchinsonian duality. However, tools for visualizing, exploring, and analyzing distributions of species in these linked spaces have remained limited. In this workshop, participants will learn the theory behind the Hutchinsonian duality and methods to link environmental with geographic space. The workshop will be focused on the installation, features, and application of Niche Analyst (NicheA), a toolkit developed to work on the environmental space following the Hutchinsonian approach of an n-multidimensional space occupied by the species. Furthermore, NicheA is a toolkit including several independent functions with which to analyze the complexity of ecological niche models. Such functions can be arranged, exported, and imported in the form of a workflow. By merging different functions via this tool, users can analyze diverse problems creatively, without the limitations of single- function applications. Thus, NicheA is a workbench at which users can address a variety of questions related to species’ ecological niches and geographic distributions. Because ecological niche modeling is a rapidly-developing field that is seeing impressive research use in addressing various questions in ecology, the workshop will  range a variety of topics from basic background generation, ecological niche models based on ellipsoids and polyhedrons, and displays of models from other software (e.g., Maxent, GARP), to more advanced topics like niche similarity estimations, model workflows, and generation of virtual species and environments. Finally, although NicheA has the capability for developing complex analyses under multivariate environmental scenarios; the user-friendly interface makes this software an ideal resource for teaching in ecology.

Reference: Qiao, H., Peterson, A. T., Campbell, L. P., Soberón, J., Ji, L., & Escobar, L. E. (2016). NicheA: Creating virtual species and ecological niches in multivariate environmental scenarios. Ecography, 39, 805–813. https://doi.org/10.1111/ecog.01961

Workshop #3 – sdm: a reproducible and extensible R package for species distribution modelling

Organisers: Dr. Babak Naimi1* & Prof. Miguel B. Araújo2,3

Institutions: 1University of ETH, Switzerland; 2Spanish Research Council (CSIC) at the National Museum of Natural Sciences in Madrid, Spain; 3University of Èvora, Portugal

Contact: naimi.b@gmail.com

sdm is a comprehensive modelling and simulation framework that enables fitting of individual and community-based species distribution models, while supporting markedly different modelling methods including correlative, process-based (mechanistic), agent-based, and cellular automata. It generates ensembles of models, and several options for evaluation of model results and projection of species potential distributions in space and time. The generic design of sdm is object-oriented making it flexible and amenable to efficient handling of errors. The object-oriented design also makes it easily extended by users wanting to support additional models and/or procedures for any of the main steps in species distribution modelling. sdm employs high performance computing solutions to speed up modelling, and also provides a graphical user interface (GUI) making it friendly even for users who are not familiar with R. The sdm package is developed by the organisers of this workshop, and published as a cover paper in the journal of Ecography (Naimi and Araujo, 2016). The workshop includes two sessions. In the first session, the package will be introduced and its capabilities will be demonstrated. In the second session, the participants have the opportunity to practice on their own laptops and just get quickly started working with the sdm package. It is recommended that the participants have the latest version of R and rstudio installed on their laptops.

Reference:

Naimi, B. & Araújo, M.B. (2016) sdm: a reproducible and extensible R platform for species distribution modelling. Ecography. 39: 368–375. DOI: 10.1111/ecog.01881