dynsbm (version 0.7)

foodwebWoodward: Broadstone Stream seasonal food webs

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.

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)
# }