This repository provides the ecological niche modeling community with access to the DesktopGARP 1.1.3 Rule-set Writing and Mapping Application. This application runs the original 1.1.3 DesktopGARP version with the addition of writing the rule-sets from the experiment as a text file and producing a map for each model of how rules are applied to the landscape. The rule-set is the set of if/then logic strings relating environmental conditions to presence/absence. These rules are then fitted or mapped to landscape, with each rule assigning presence or absence. This function can be used to visualize how specific rules match specific locations. This was illustrated in detail in Blackburn (2006) and Joyner (2010). Rule-set exploraration was detailed first in McNyset (2005), then used in specific analyses in Mullins et al. (2011) and Barro et al. (2016). Most recently, the rule-sets were evaluated to compare environmental conditions supporting different Culicoides midges in Florida (Sloyer et al. 2019).
These additional tools have been described in the literature in several papers:
Barro, A. S., M. Fegan, B. Moloney, K. Porter, J. Muller, S. Warner, and J. K. Blackburn. 2016. Redefining the Australian Anthrax Belt: Modeling the Ecological Niche and Predicting the Geographic Distribution of Bacillus anthracis. PLOS Negl Trop Dis 10:e0004689.
Blackburn, J. 2006, April. Evaluating the spatial ecology of anthrax in North America: Examining epidemiological components across multiple geographic scales using a GIS-based approach. Doctoral dissertation, Louisiana State University, Baton Rouge.
Blackburn, J. K., K. M. McNyset, A. Curtis, and M. E. Hugh-Jones. 2007. Modeling the geographic distribution of Bacillus anthracis, the causative agent of anthrax disease, for the contiguous United States using predictive ecologic niche modeling. American Journal of Tropical Medicine and Hygiene 77:1103–1110.
Mullins, J., M., L. Lukhnova, A. Aikimbayev, Y. Pazilov, M. Van Ert, and J. K. Blackburn. 2011. Ecological Niche Modelling of the Bacillus anthracis A1. a sub-lineage in Kazakhstan. BMC ecology 11:32.
Joyner, T. A. 2010. Ecological niche modeling of a zoonosis: a case study using anthrax and climate change in Kazakhstan. MS, UNIVERSITY OF FLORIDA, Gainesville.
McNyset, K. M. 2005. Use of ecological niche modelling to predict distributions of freshwater fish species in Kansas. Ecology of Freshwater Fish 14:243–255.
Sloyer, K. E., N. D. Burkett-Cadena, A. Yang, J. L. Corn, S. L. Vigil, B. L. McGregor, S. M. Wisely, and J. K. Blackburn. 2019. Ecological niche modeling the potential geographic distribution of four Culicoides species of veterinary significance in Florida, USA. PloS one 14:e0206648.
We thank R. Scachetti-Pereira for developing the DesktopGARP algorithm implementation 1.1.3 with the rule-set writing and mapping functions.
Tutorial for installing DesktopGARP 1.1.3 are here in a YouTube video: https://youtu.be/zaUAgjeoAS8
Tutorial for populating a GARP experiment is found here in a YouTube video: https://youtu.be/vIzRiXA2aOE
Additional DesktopGARP tools from the UF SEER Lab are available from C.G. Haase: https://github.com/cghaase/GARPTools