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Data_and_code

dataset
posted on 28.03.2018 by Bo Dalsgaard, Jonathan Kennedy, Benno Simmons, Andrea Baquero, Ana Martín González, Allan Timmermann, Pietro Maruyama, Jimmy McGuire, Jeff Ollerton, William Sutherland, Carsten Rahbek
To run the extinction models, first download the Stochastic Coextinction Model code from the Supplementary Information of Vieira and Almeida-Neto (2015) (see references). The script netcascade (April 2014).R is required for the analyses in this paper. The supplementary information contains three scripts: 1. Main.R – This script runs simulations on the 8 networks to calculate PE, SE and VE for each species in each network. 2. IterativeNodeDeletion.R – A wrapper around netcascade (April 2014).R that calls netcascade() repeatedly to iteratively remove species from the network. 3. IterNodeDelMultiSim.R – A wrapper around IterativeNodeDeletion.R that runs IterativeNodeDeletion() multiple times to account for the stochasticity in the netcascade() algorithm. And four datasets: 1. data/rvalues.csv – The expert-assigned dependency categories for each plant species in each network used to determine R values 2. data/webs – Folder containing the 8 interaction matrices 3. data/phylogeny - contains (1) a set of 1000 phylogenies for the 13 Caribbean hummingbird species that were analysed (Caribbean_Phylogenies_.nex), (2) the maximum clade credibility (MCC) phylogeny (Caribbean_MCC_Phylogeny.nex) 4. data/traits - species-level data for body mass and bill length If you use the extinction modelling code please cite the following two papers: 1. Dalsgaard et al. (in press) Trait evolution, resource specialisation and vulnerability to plant extinctions among Antillean hummingbirds. Proceedings of the Royal Society B. 2. Vieira, M.C. and Almeida‐Neto, M., 2015. A simple stochastic model for complex coextinctions in mutualistic networks: robustness decreases with connectance. Ecology Letters, 18(2), pp.144-152. doi: 10.1111/ele.12394 If you use the data please cite: Dalsgaard et al. (in press) Trait evolution, resource specialisation and vulnerability to plant extinctions among Antillean hummingbirds. Proceedings of the Royal Society B. References: Vieira, M.C. and Almeida‐Neto, M., 2015. A simple stochastic model for complex coextinctions in mutualistic networks: robustness decreases with connectance. Ecology Letters, 18(2), pp.144-152. doi: 10.1111/ele.12394

History

dc.type.embargo

untilArticleAppears

dc.format.extent

181151, 2196

dc.identifier.uri

http://hdl.handle.net/10255/dryad.172080

dc.coverage.spatial

Caribbean, West Indies

Licence

Exports