README.md

In clementviolet/omnivor: Ecological Networks Analysis

omnivor

The goal of omnivor is to set up a friendly-user environement for networks analysis in ecology.

Installation

You can install the released version of omnivor from github with:

# install.packages("devtools")
devtools::install_github("clementviolet/omnivor")

Licence

This project is licensed under the GPL-3 Licence - see the LICENSE.md file for details.

To do

Package structure :

• [ ] Adopt a POO structure ;
• [ ] Use pkgdown ;
• [ ] Add dataset ;
• [ ] Create a vignette.

List of metrics to be added first (Dunne (2009) and, Vermaat et al. (2009)) :

• [x] Connectance ;
• [ ] Connectance (bipartite network)
• [x] Species richness (number of node) ;
• [x] Linkage density ;
• [x] Clustering coefficient ;
• [x] Characteristic path length ;
• [x] Mean food chain length ;
• [x] Prey-averaged trophic level ;
• [x] Shortest trophic level ;
• [x] Short-weighted trophic level averaged ;
• [x] Percentage of top species in a web ;
• [x] Percentage of basal species in a web ;
• [x] Percentage of intermediate species ;
• [x] Percentage of canibal species in a web ;
• [x] Percentage of omnivores in a web ;
• [x] Normalized standard deviation of generality ;
• [x] Normalized standard deviation of vulnerability ;
• [x] Normalized standard deviation of links ;
• [ ] Mean across taxa of the maximum trophic similarity of each taxon to other taxa

List of other metrics to include (Delmas et al. (2019)) :

• [ ] To be continued…

Others :

• [ ] Other trophic length metrics (Wiliams and Martinez (2004))

clementviolet/omnivor documentation built on Aug. 16, 2019, 12:05 a.m.