NicheToolBox

Luis Osorio Olvera\(^{1,2}\)

What I am going to talk about

  • What is ntbox?
  • What does ntbox do?
  • Innovation
  • Where to get ntbox?
  • How to find help?
  • An example of use

What is NicheToolBox?

NicheToolBox is an R package with tools for modeling species niches and distributions. It comes with a Graphical User Interface (GUI) developed in the shiny framework.

What is NicheToolBox?

ntbox can be used either its Graphical User Interface or via R commands.

ntbox potential

As NicheToolBox is developed in R, it is posible to incorporate all the functions available in other packages.

Get environmental data

Snow

Forest

Mountains

Mountains

Interactive way to visualize GBIF data


Mountains

Extrapolation risk assessment

  • Mobility-Oriented Parity (MOP)(Owens et al. 2012)
  • Extrapolation Detection tool (ExDet)(Mesgaran, Cousens, and Webber 2014)
    • Univariate extrapolation
    • Multivariate extrapolation
  • Multivariate Environmental Similarity Surfaces (MESS)(Elith, Kearney, and Phillips 2010)

Model calibration & selection protocol in E-space

  • Significance
    • Partial ROC test (Peterson, Papes, and Soberon 2008)
  • Performance
    • Model performance is computed as omission rates
    • It determines if a given point lie inside or outside of the ellipsoid model.

Model calibration & selection protocol in E-space

Mountains \[omission=\frac{10}{200}=0.05\]

The evaluation in environmental space makes the process of model calibration and selection faster than methods that need to create a continuos map first and then transform it into a binary map in order to compute omission rates (Osorio-Olvera et al. 2020).

Model cal & sel protocol in E-space

## -----------------------------------------------------------------------------------------
##      **** Starting model selection process ****
## -----------------------------------------------------------------------------------------
## 
## A total number of 56 models will be created for combinations of 8 variables taken by 3 
## 
## A total number of 56 models will be created for combinations of 8 variables taken by 5 
## 
## A total number of 28 models will be created for combinations of 8 variables taken by 6 
## 
## -----------------------------------------------------------------------------------------
##   **A total number of 140 models will be tested **
## 
## -----------------------------------------------------------------------------------------
##   11 models passed omr_criteria for train data
##   15 models passed omr_criteria for test data
##   3 models passed omr_criteria for train and test data

Model selection protocol in E-space

fitted_vars nvars om_rate_train om_rate_test pval_proc env_bg_aucratio
bio01,bio07,bio12 3 0.0672269 0.0392157 0 1.732222
bio01,bio02,bio07 3 0.0504202 0.0392157 0 1.677287
bio01,bio02,bio03 3 0.0672269 0.0588235 0 1.625080
bio01,bio03,bio12 3 0.0756303 0.0392157 0 1.723496
bio01,bio07,bio14 3 0.0756303 0.0588235 0 1.740715

Tools to see the Huchinsonian duality

Where to get it?

NicheToolBox is on GitHub and can be installed via devtools

https://github.com/luismurao/ntbox

How to find help?

How to cite

Luis Osorio-Olvera, Soberón J.,Falconi F., Peterson AT., Lira-Noriega, Contreas-Díaz R., Martínez Meyer E., Barve V., Barve N. (2020). ntbox: From Getting Biodiversity Data to Evaluating Species Distribution Models in a Friendly GUI Environment. R package version 0.4.6.0.https://github.com/luismurao/ntbox

References

Elith, Jane, Michael Kearney, and Steven Phillips. 2010. “The art of modelling range-shifting species.” Methods Ecol. Evol. 1 (4): 330–42.

Mesgaran, Mohsen B., Roger D. Cousens, and Bruce L. Webber. 2014. “Here be dragons: a tool for quantifying novelty due to covariate range and correlation change when projecting species distribution models.” Edited by Janet Franklin. Divers. Distrib. 20 (10): 1147–59. https://doi.org/10.1111/ddi.12209.

Osorio-Olvera, Luis, C. Yañez-Arenas, E. Martínez-Meyer, and A. T. Peterson. 2020. “Relationships between population densities and niche?centroid distances in North American birds.” Ecol. Lett. 23: 555–64. https://doi.org/10.1111/ele.13453.

Owens, H, L Campbell, L Dornak, E Saupe, N Barve, J Soberon, K Ingenloff, A Lira-Noriega, C Hensz, and C Myers. 2012. “Constraints on Interpretation of Ecological Niche Models by Limited Environmental Ranges on Calibration Areas: Software Script Appendix.”

Peterson, A. Townsend, Monica Papes, and Jorge Soberon. 2008. “Rethinking receiver operating characteristic analysis applications in ecological niche modeling.” Ecol. Modell. 213 (1): 63–72.