#FUNCTION TO PERFORM THRESHOLDED FAUNAL NETWORK ANALYSES IN R
#PARAMETERS REQUIRED - MATRIX, NAME
#DEPENDENT ON IGRAPH PACKAGE


##### THIS IS JOHN ALROY'S FUNCTION FOR CALCULATING FORBES SIMILARITY INDICES ######

forbes<-function(x,y,corrected)	{
	if (missing(corrected))	{
		corrected <- T
	}
	if (is.numeric(x) && is.numeric(y) && min(x) == 0 && min(y) == 0 && length(x) == length(y))	{
		a <- length(which((x * y) > 0))
		b <- length(which(x > 0)) - a
		c <- length(which(y > 0)) - a
	} else	{
		a <- length(na.omit(match(x,y)))
		b <- length(x) - a
		c <- length(y) - a
	}
	n <- a + b + c
	if (corrected == T)	{
		return(a * (n + sqrt(n))/((a + b) * (a + c) + a * sqrt(n) + (b * c)/2))
	} else	{
		return(a * n/((a + b) * (a + c)))
	}
}

forbesMatrix<-function(x,corrected)	{
	x[is.na(x)] <- 0
	m = matrix(nrow=ncol(x),ncol=ncol(x))
	for (i in 1:ncol(x))	{
		for (j in 1:ncol(x))	{
			m[i,j] = forbes(x[,i],x[,j],corrected)
		}
	}
	return(m)
}

############################################
###########    END ALROY CODE    ###########
############################################


faunal_network<-function(mat, n) {

#READ IN OCCURRENCE MATRIX

m<-read.table(mat, header=T, row.names=1)

#REMOVE COLUMNS (IE SITES) WITH FEWER THAN THREE TAXA

# COMMENT OUT IF YOUR MATRIX IS IN FORMAT COLUMNS=LOCALITIES, ROWS=TAXA
m<-t(m)

m<-m[,colSums(m>0)>=3]

#CONVERT OCCURRENCE MATRIX INTO ADJACENCY MATRIX

fm<-forbesMatrix(m)
row.names(fm)<-colnames(m)
colnames(fm)<-colnames(m)

#ESTABLISH THRESHOLD VALUES

t<-c(0.05,0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,0.55,0.6,0.65,0.7,0.75,0.8,0.85,0.9,0.95)

#FOR EACH THRESHOLD VALUE

for(i in 1:length(t)) {

#DUMMY MATRIX

fm1<-fm

#THOSE LOWER THAN THE THRESHOLD TO ZERO

fm1[fm1<t[i]]<-0

#CALCULATE GRAPH FROM ADJACENCY MATRIX

fmg<-graph_from_adjacency_matrix(fm1, mode="undirected", weight=T, diag=F)

#WRITE GRAPH TO FILE

write_graph(fmg, file=paste(n, i,".ncol"),format="ncol")

}

}