DOI: 10.5061/dryad.t4b8gtj1x
title: GapAnalysis: An R package to calculate conservation indicators using spatial information

description: Effective assessments of the current status of biodiversity conservation
 are needed to support planning, policy, and action, from local to global
 levels. Of particular use would be well documented, reproducible methods
 based on openly accessible data and tools. Such methods should provide an
 accurate estimate of the state of conservation of diversity, identifying
 gaps in current conservation systems, while providing a benchmark against
 which to measure success, including determining when conservation goals
 have been met. Here we introduce GapAnalysis, an open source R package
 developed to support the assessment of the state of conservation of taxa,
 both ex situ (in genebanks, botanic gardens, and other repositories) and
 in situ (in protected natural areas). The eco-geographic variation
 maintained in conservation repositories and that present within protected
 natural areas is compared with the full extent of eco-geographic variation
 predicted within species’ native ranges. Eco-geographic conservation gaps
 are identified, and taxa are then prioritized for further action. The
 package enables users to quickly determine conservation status, gaps, and
 priorities for as few as one to as many as thousands of taxa, for any wild
 flora or fauna for which occurrence data and species distribution models
 are available. To demonstrate the use of GapAnalysis, we provide case
 studies for wild plant taxa in the genera Capsicum L. and Cucurbita L,
 with an accompanying online R tutorial for three of the Cucurbita species.
description: The methods for compiling the occurrence data, performing species
 distribution modeling, and conducting GapAnalysis for these taxa are
 described in full in Khoury et al. (2019a, b). In short, occurrence data
 were drawn from biodiversity and conservation repository databases and
 from the authors’ own botanical explorations. Duplicates and non-wild
 records were removed, taxonomic names were standardized, and records were
 classified as H (reference) or G (<i>ex situ </i>sample) as
 per the definitions described in this paper (see Input data). Species
 distributions were produced with the MaxEnt algorithm (Phillips et al.
 2017) using 26 climatic and topographic predictors (Jarvis et al, 2008,
 Fick and Hijmans 2017) at a spatial resolution of 2.5 arc-minutes,
 employing a subset of variables as well as number and location of
 pseudo-absences specific to each taxon. The occurrence data, models, and
 full results are available at Khoury et al. (2019c, d). A GapAnalysis R
 tutorial for three of the <i>Cucurbita</i> species is provided
 in the usage section of the GapAnalysis GitHub repository (https://github.com/CIAT-DAPA/GapAnalysis) and included as an example in the R package itself. Note that the three-species R package tutorial uses a lower spatial resolution for efficiency (10 arc-min vs. 2.5 arc-min), and hence the GapAnalysis results differ from those described below and in Khoury et al. (2019a, b). <strong>References</strong> Jarvis A., Reuter, H. I., Nelson, A. and Guevara, E. 2008. Hole-filled seamless SRTM data V4, International Center for Tropical Agriculture (CIAT), http://srtm.csi.cgiar.org Khoury, C. K., Carver, D., Barchenger, D. W., Barboza, G., van Zonneweld, M., Jarret, R., Bohs, L., Kantar, M. B., Uchanski, M., Mercer, K., Nabhan, G. P., Bosland, P. W. and Greene, S. L. 2019a. Modeled distributions and conservation status of the wild relatives of chile peppers (<i>Capsicum</i> L). - Diversity and Distributions 26(2): 209-225. doi: 10.1111/DDI.13008. Khoury, C. K., Carver, D., Kates, H. R., Achicanoy, H. A., van Zonneweld, M., Thomas, E., Heinitz, C., Jarret, R., Labate, J. A., Reitsma, K., Nabhan, G. P. and Greene, S. L. 2019b. Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (<i>Cucurbita</i> L.). - Plants, People, Planet 2(3): 269-283. doi: 10.1002/ppp3.10085. Phillips, S. J., Anderson, R. P., Dudik, M., Schapire, R. E. and Blair, M. E. 2017. Opening the black box: an open-source release of Maxent. - Ecography<i> </i>40: 887-893.