| Discussion Forum
Strategies for Successful Publication
in Peer Reviewed Journals | Moderator: Nick Gotelli Panelists: Ulises Balza, Andressa Cabral, Simon Darroch, Marta Jarzyna, Mark Lomolino, Pablo Marquet, Toby Pennington, Susanne Renner, Alexandria Shupinski Date: Thursday, November 12, 16:00 UTC Description: Peer-reviewed publications are an essential element for success in the sciences. How can you improve your chances of success when you submit your manuscript? Collectively, the entire TIBS board has decades of experience as Editors, Associate Editors, Subject Matter Editors, Reviewers, and Authors for a range of journals that publish papers in biogeography and macroecology. We want to share our suggestions and experiences with you to help you improve your submissions. We will have an open discussion to answer your questions, which you can submit anonymously before the meeting or ask during the discussion. Potential topics we will cover include: - Pipeline and Timeline For Peer-Reviewed Journals
- Selecting A Journal
- The Importance Of The Abstract, Cover Letter, and Suggested Reviewers
- Formatting And Preparing Your Manuscript
- Dealing With Reviewer Criticisms
- The Future Of Peer-Reviewed Publications
Open to all participants and free to TIBS members. | | Fees
TIBS members: Free; registration is open now!
Non-members: $10USD; registration is open now!
| | | | Training Course
Strategic Coding Practices: Reproducible Coding For Large Open-Ended Projects | Moderator: Dr. Nicholas J. Gotelli Dates Day 1: Wednesday, October 14, 14:00-16:00 UTC + 17:00–19:00 UTC Day 2: Thursday, October 15, 14:00-16:00 UTC Description: Most researchers know how to write a script of computer code to execute a relatively simple set of instructions. But this kind of coding quickly becomes slow, inefficient, and not reproducible for real-world projects, which may have many different data sets and interacting components. This workshop will teach you how to structure and organize your code into modular units that are flexible and easy to use, no matter how large or complex your project eventually becomes. Although the workshop is taught in R, the principles can and should be applied when working with any scripting language. This strategy of high-level coding is pre-adapted for working with AI: you can “code” the project, and AI can “write the code” for your functions. Although we will be doing a modest amount of coding in the workshop, participants could still get a lot of benefit from the presentation just from listening; doing the in-workshop coding is not essential for learning the basic approach. - Format: Remote, with live coding exercises using the RStudio platform
- Expected Background: Moderate skill in R coding using the RStudio editor
- Required: Personal computer (Linux, Windows, or Mac OS) with current versions of R and RStudio; internet access
- Total time: 6 hours spread over two days
- Maximum attendees: 50
| | Fees
TIBS members: $20USD; registration is open now!
Non-members: $70USD; registration is open now!
| | | | Training Course
Take your species distribution models to the next level with Bayesian non-parametric regression trees | Moderator: Dr A. Márcia Barbosa Dates: Day 1: Tuesday, December 15, 14:00-16:30 UTC Day 2: Wednesday, December 16, 14:00-16:30 UTC Day 3: Thursday, December 17, 14:00-16:30 UTC Description: Bayesian Additive Regression Trees (BART) are a powerful machine learning technique with very promising applications in ecology and biogeography in general, and in species distribution modelling (SDM) in particular. BART can produce highly accurate predictions without overfitting to noise or to particular cases in the data. Notably, unlike most SDM methods, BART generally shows a well-balanced performance regarding both main aspects of predictive accuracy: discrimination (i.e., distinguishing presence from absence localities) and calibration (i.e., having predicted probabilities reflect gradual occurrence frequencies across space and environment). Moreover, the Bayesian framework inherently handles prediction uncertainty, and it has a built-in complexity penalty with very sensible defaults, freeing the user from arbitrary or intensively cross-validated parameter choices. This workshop will take participants through a worked example, from essential data preparation to model output analysis, using sample data and annotated R scripts. These scripts can be adapted on-the-spot by participants to work on any species’ presence-only (e.g. from GBIF) or presence-(pseudo)absence data and predictor variables (but mind that computation time can be very large for large datasets). We’ll prepare species occurrence and environmental data, compute and evaluate BART distribution models, identify influential predictors, map prediction uncertainty, plot partial response curves with Bayesian credible intervals, and map relative presence probability regarding particular predictors. All sessions include both theoretical lectures and hands-on practice with R. - Format: Live online lessons on Zoom, with a Slack space for workshop materials, questions and discussion.
- Expected Background: This workshop requires familiarity with R at the user level; Basic knowledge about species distribution (or ecological niche) models.
- Required: A computer with recent versions of R, RStudio, and R packages ‘embarcadero’ and ‘terra’ already installed; A good enough internet connection for live video sessions, and preferably a webcam for enhanced interactivity.
- Total time: 7.5 hours spread over three days
- Maximum attendees: 20
| | Fees
TIBS members: $80USD; registration is open now!
Non-members: $120USD; registration opens November 1.
| | | | Training Course
Beyond binary maps: fuzzy logic for threshold-free estimates of diversity, similarity and change | Moderator: Dr A. Márcia Barbosa Dates Day 1: Tuesday, February 16, 14:00-16:30 UTC Day 2: Wednesday, February 17, 14:00-16:30 UTC Description:Species have continually changing distributions, and they occur with varying frequency across space. Categorical occurrence maps, whether observed or model-derived, are thus incomplete and oversimplified representations of species’ actual distributions. Moreover, categorical occurrence derived from model predictions normally relies on largely arbitrary but outcome-determining user-specified thresholds. Analyses that build on such categorical maps, such as most indices of diversity, overlap, (dis)similarity and change, thus omit important gradations in species occurrence and can be visibly conditioned by threshold choice. Fuzzy logic is a simple tool to eliminate the need for such thresholds and formally incorporate the location uncertainty and gradual variations that characterize natural biodiversity patterns. This workshop will show how fuzzy logic can be easily integrated into biogeographical analyses to improve the depiction and combination of species distribution patterns, with applications in macroecological interactions, global change, biotic regionalization and other biodiversity studies. We will use presence-(pseudo)absence models that produce presence probability values (e.g. generalized linear and generalized additive models; tree-based classification and regression methods), which can be converted to favourability or fuzzy membership values. We will see how these values allow direct comparison and combination of gradual distribution patterns across species, regions and time periods; and how common indices of diversity, overlap and (dis)similarity can also be generalized to work with fuzzy (degree of) occurrence values. This allows the use of presence probability models without depending on thresholds to force them into binary predictions, thus avoiding the compounded effects of threshold choice on results and conclusions. The workshop includes concise theoretical lessons explaining the concepts behind the described procedures, and practical hands-on sessions where participants put these procedures into practice using R. Note that we will not cover data preparation and model building; We will provide some already-made species distribution models as examples for participants to work with. Participants are also encouraged to bring their own presence-(pseudo)absence data and presence probability predictions, for different (ecologically related) species or time periods. - Format: Live online lessons on Zoom, with a Slack space for workshop materials, questions and discussion.
- Expected Background: This workshop requires familiarity with R at the user level and basic knowledge about species distribution (or ecological niche) models.
- Required: A computer with recent versions of R, RStudio, and R packages ‘fuzzySim’ and ‘terra’ already installed; A good enough internet connection for live video sessions, and preferably a webcam for enhanced interactivity.
- Total time: 5 hours spread over two days
- Maximum attendees: 20
| | Fees
TIBS members: $80USD; registration is open now!
Non-members: $120USD; registration opens November 1.
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