#continental US demo, permutation of pariwse interaction network, igraph usage
require(RCurl)
URL = "https://docs.google.com/spreadsheet/pub?key=0ArLJZixvTlU7dDI5c3dnTzdRX1dndzBORUk1UC0wYlE&single=true&gid=0&output=csv"
states = read.csv(textConnection(getURL(URL)), colClass = c("character", "character"))
g = graph.data.frame(states, directed=F)
g.degree = degree(g)
g.degree [g.degree == max(g.degree)] #TN and MO have 8 bordering states
g.shortestpath.m = shortest.paths(g)
str(g.shortestpath.m)
sorted.names = sort( rownames(g.shortestpath.m) )
gsm = g.shortestpath.m[, sorted.names]
gsm = gsm[sorted.names, ]
URL2 = "https://docs.google.com/spreadsheet/pub?key=0ArLJZixvTlU7dC1rTlRhTkw5UlY0eWZGT1JOVUVCWGc&single=true&gid=0&output=csv"
state.year.tb = read.csv(textConnection(getURL(URL2)), colClass = c("character", NA))
permute.pairs.wo.selfpairs = function( inpairs, ncycles=10, debug=1 ) {
if (ncycles >= 1 ) {
if(debug) {
print(paste('ncycles=', ncycles))
}
longids = c(as.character(inpairs[,1]), as.character(inpairs[,2]) )
longids = sample(longids)
len = length(inpairs[,1])
newpairs = data.frame( cbind( longids[1:len], longids[(len+1): (2*len)]) )
names(newpairs) = c('id1', 'id2')
newpairs$id1 = as.character( newpairs$id1)
newpairs$id2 = as.character( newpairs$id2)
newpairs$selfpairs = ifelse( newpairs$id1 == newpairs$id2, 1, 0 )
self.tb = newpairs[ newpairs$selfpairs==1, ]
nonself.tb = newpairs[newpairs$selfpairs==0, ]
if(debug) {
print(self.tb)
}
if( length(self.tb[,1])>0 ) {
if ( ncycles == 0) { return (c(NA,NA, NA) )
} else {
ncycles = ncycles - 1
selectedpairs = rbind(self.tb, nonself.tb[1: (length(self.tb[,1])*2), ] )
restpairs = nonself.tb[ (length(self.tb[,1])*2+1): length(nonself.tb[,1]), ]
return( rbind(restpairs, permute.pairs.wo.selfpairs(selectedpairs, ncycles)))
}
} else {
return (newpairs)
}
} else {
return( c(NA,NA,NA ))
}
}
#test
x = permute.pairs.wo.selfpairs(states)
x2 = permute.pairs.wo.selfpairs(states)
No comments:
Post a Comment