Nothing
##==============================================================================
##
## Trophic analysis function
##
##==============================================================================
TrophInd <- function (Flow = NULL, # from-to
Tij = t(Flow), # to-from
Import =NULL, # flow from external (colNr Tij)
Export =NULL, # flow to external (colNr Tij)
Dead=NULL) # flow to dead matter
{
if (is.character(Dead))
dead <- which(rownames(Tij)%in%Dead) else
dead <- Dead
if (length(dead) != length(Dead)) stop("Dead not recognized")
## Check input and calculate internal network
N <- InternalNetwork (Tij,Import,Export)
p <- Diet(N$Tint,dead,N$iN)
ncomp <- ncol(N$Tint) # the number of compartments (without externals)
##
## Trophic level TL TL(i) = 1 + sumj(pij*TL(j))
## TL(i)-sumj(pij*TL(j))= 1
##
A <- -p
# diag(A) <- diag(A)+ 1 # was this
# Karline: changed Januari 2012: organisms that "feed on themselves" are problematic!
diag(A) <- 1
B <- rep(1,ncomp)
TL <- ginv(A) %*% B
##
## Omnivory index: variance of trophic levels of preys
##
OI <- vector (length = ncomp)
for (i in 1:ncomp)
OI[i] <-sum((TL-(TL[i]-1))^2*p[i,])
return(data.frame(TL, OI,row.names=rownames(N$Tint)))
} ## END Trophic
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