NOS web interface permits to compute the node overlap and segregation measures (Ɲ̄) introduced by Strona and Veech (2015). Please refer to the original article and to Strona et al. (2017) for details on the measures and on their computation. Using the interface is very simple. The first step is that of providing a network. The correct format of the network is that of a comma separated list of edges (i.e. links between nodes) with no header (i.e. without column names), such as:
Note that nodes can be indicated by numbers, letters, and alphanumeric strings. It is important, however, that node names do not include spaces, punctuation marks and special characters.
There are three possible ways to provide a network to NOS, namely:
- by pasting it in the text-box, below the "PASTE YOUR NETWORK HERE" line;
- by uploading a text file using the "Choose file" button below the "OR UPLOAD A TEXT FILE FOR YOUR NETWORK" line;
for both options, alongside the network, you may provide a network listing all potential interactions between nodes, in order to add ecological realism to the analysis. Please, refer to Strona and Veech (2017) for further details on this aspect. Of course, node names should be consistent between the network of observed interactions and that of potential ones.
- or you can have NOS generate a network with predefined structure.
For this last option, you will have to set to "YES" the radio button next to the line "GENERATE AND ANALYZE A NETWORK WITH PREDEFINED STRUCTURE".
Then you will have to choose the desired kind of structure ("OVERLAP", "SEGREGATION" or "MODULARITY").
In the case of "MODULARITY", you may also set the desired number of modules (default is 2; possible values are integers between 2 and 5).
In all cases, you may change the number of nodes in the network (up to 99 nodes are allowed), and the degree of randomness (a value between 0 and 9), that is how much network structure departs from perfect overlap, segregation or modularity.
After you have provided NOS a network in correct format, you may can modify the default analysis setting.
By default, NOS consider a network as 'DIRECTED UNIMODE' (e.g. a food-web). However, you may change the option "SPECIFY THE KIND OF YOUR NETWORK" to "UNDIRECTED" (e.g. a species co-occurrence network), or to "DIRECTED BIPARTITE" (e.g. a host-parasite or a plant-pollinator network).
Then, in case you have not provided a network of potential interactions, you can ask NOS to generate one by identifying potential trophic links based on network structure. If you want to select this option, set the radiobutton below "COMPUTE POTENTIAL NETWORK BASED ON ESTIMATION OF TROPHIC LEVEL" to 'YES'. If you do this, the network will be treated as "DIRECTED UNIMODE" (i.e. as a food-web) regardless of your previous selection to the "SPECIFY THE KIND OF YOUR NETWORK" option.
There are three possible criteria that NOS can use to evaluate node trophic levels based on the distance (in terms of steps in the network) between a node and a basal resource, namely "Shortest Path", "Chain Averaged Path", and "Longest Path". Please refer to Williams and Martinez (2004) for details on this aspect.
There are also two possible rules that NOS can use to identify potential interactions based on the estimated trophic levels. The first rule, named "Threshold Rule" assumes that a species (Sp1) consumes another species (Sp2) if trophic level (TL) of Sp1 is higher than that of Sp2.
The second rule, named "Step Rule", assumes that Sp1 consumes Sp2 if:
TL(Sp2) +a ≤ TL(Sp1) < TL(Sp2) + b
The two parameters a and b (default to 1) are used to define how different can be the trophic level of a consumer and those of its resources. By using low values of a and b, one can avoid to have potential interactions between, for example, a top predator and a plant. Please refer to Strona et al. (2017) for further information on this aspect.
Additionally, you can choose wheter or not to "EXCLUDE CANNIBALISTIC INTERACTIONS (I.E. SELF LINKS) FROM COMPUTATION". When this option is set to 'YES' (which is the default value), the overlap in shared neighbors between a pair of nodes is computed by excluding the two nodes from the respective sets of potential neighbors (see Strona and Veech 2015)).
Finally, you can "SELECT THE FRACTION OF PAIRWISE COMPARISONS TO BE PERFORMED". This should be a real number between 0 and 1. Although Strona et al. 2017 showed that a small fraction of performed comparisons is enough to provide a reliable measure of Ɲ̄, we recommend that you keep the default value of 1, and that you use lower values only for exploratory analyses, or in case your network is exceedingly large.
This, together with the references listed at the bottom of this page, should be enough to start using NOS. However, for any doubt or question, feel free to contact the authors at:
Cazelles, K., Araújo, M. B., Mouquet, N., Gravel, D. (2016). A theory for species co-occurrence in interaction networks. Theoretical Ecology, 9(1), 39-48.
Strona, G., Veech, J. A. (2015). A new measure of ecological network structure based on node overlap and segregation. Methods in Ecology and Evolution, 6(8), 907-915.
Strona, G., & Veech, J. A. (2017). Forbidden versus permitted interactions: Disentangling processes from patterns in ecological network analysis. Ecology and Evolution, doi: 10.1002/ece3.3102.
Strona, G., Matthews T. J., Kortsch S., Veech, J. A. (2017). A software suite to compute node overlap and segregation (Ɲ̄) in ecological networks.
Williams, R. J., Martinez, N. D. (2004). Limits to trophic levels and omnivory in complex food webs: theory and data. The American Naturalist, 163(3), 458-468.