R/nestedness.R

In bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices

nestedness <-function(m, null.models=TRUE,
                      n.nulls=100, popsize=30, n.ind=7,n.gen=2000,
                      binmatnestout=FALSE
                       )
{

# old version retired in April 2022; all arguments but first ignored 
bmn <- vegan::nestedtemp(m)  
  
# calculates matrix temperature using the binmatnest programm from Miguel Rodriguez-Girones
# Rodriguez-Girones & Santamaria (2006). A new algorithm to calculate the nestedness
# temperature of presence-absence matrices. Journal of Biogeography 33:924-935.
#
# make sure matrix is a valid one as error proofing in the C++ function does not fully work
# and R may crash...

# m <- ifelse(m>0,1,0)   # create a binary matrix
# if (popsize<n.ind) n.ind <-popsize- 1 # you cannot pick more individuals then there are in the population...
# bmn <- .C("bmn5",
#           mat=as.integer(m),   #column dominated....
#           n.rows = as.integer(nrow(m)),      # notice swapping of cols
#           n.cols = as.integer(ncol(m)),      # and rows
#           temperature = as.double(-1.0),
#           n.nullmodels = as.integer(n.nulls),
#           population.size = as.integer(popsize),
#           n.individuals = as.integer(n.ind),
#           binmatnestout = as.integer(binmatnestout),
#           n.generations = as.integer(n.gen),
#           nullmodels = as.integer(null.models),
#           p.null1 = as.double(-1.0),
#           mean.temp.null1 = as.double(-1.0) ,
#           var.temp.null1 = as.double(-1.0),
#           p.null2 = as.double(-1.0),
#           mean.temp.null2 = as.double(-1.0) ,
#           var.temp.null2 = as.double(-1.0),
#           p.null3 = as.double(-1.0),
#           mean.temp.null3 = as.double(-1.0) ,
#           var.temp.null3 = as.double(-1.0),
#           pack.order.col = as.integer(rep(-1,ncol(m))),
#           pack.order.row = as.integer(rep(-1,nrow(m))),
#           PACKAGE="bipartite")
# if (min(bmn$pack.order.col,bmn$pack.order.row)>-1) bmn$packed.matrix <- m[bmn$pack.order.row,bmn$pack.order.col]

bmn
}