foodwebWoodward: Broadstone Stream seasonal food webs

In dynsbm: Dynamic Stochastic Block Models

Description

This dataset concerns the aquatic macro-invertebrate community of Broadstone Stream in south-east England. Six seasonal connectance food webs were recorded, one every two months from May 1996 to April 1997. We restricted here to simple presence/absence information on species (nodes) and binary feeding links (edges). This dataset forms a dynamic trophic network with T=6 snapshots (May, August, October, December 1996, February, April 1997). Five species were not sampled each month. Each netowrk is directed.

Usage

data(foodwebWoodward)

Format

An array of size 6x26x26.

Source

Table 2 of Woordward et al

References

Woodward, G., Speirs, D. C., Hildrew, A. G., Quantification and Resolution of a Complex, Size-Structured Food Web. In Food Webs: From Connectivity to Energetics, Vol. 36 of Advances in Ecological Research, pp. 85-135 Academic Press (2005) http://dx.doi.org/10.1016/S0065-2504(05)36002-8

Miele, V and Matias, C, Revealing the hidden structure of dynamic ecological networks, Royal Society Open Science (2017)

Examples

## Not run: 
data(foodwebWoodward)

## mandatory to use many nstart>>1 starting points
## but estimation can be long;
## better to use nb.cores>1 cores
list.dynsbm <- select.dynsbm(Y=foodwebWoodward$Y, 
				present=foodwebWoodward$present, 
				Qmin=1, Qmax=6, edge.type="binary",
				directed=TRUE, self.loop=TRUE, 
				nstart=200, nb.cores=4) 
				

## selection of Q=4 with the ICL method
dynsbm <- list.dynsbm[[4]]

## plotting intra/inter connectivity patterns
connectivity.plot(dynsbm, foodwebWoodward$Y)

## plotting switches between groups
alluvial.plot(dynsbm, timestep.abbrev="D", only.present=F)

## End(Not run)

dynsbm documentation built on March 26, 2020, 7:33 p.m.