Bulk read network data.

readnet.R

#################################################################
# Network analyses.
# Pedro. 7 Dec 2007
#################################################################
# NOTE: These matrices have rows are animals, columns are plants. 
# NOTE: JORDI's datasets for NESTEDNESS have Rows are plants, 
# columns are animals.
library(bipartite)
library(networksis)
library(igraph)
library(sna)
library(network)
library(netZ)
library(brainwaver)
library(Rgraphviz)
library(DAAG)
#----------------------------------------------------------------
getwd()
[1] "/Users/pedro/Documents/Working/MS_Networks/Fitting"
#----------------------------------------------------------------
# Read 0/1 matrices - No headers
# IMPORTANT NOTE: rows are animals; columns are plants.

### Datasets-Pollination -----------------------------------------
abis<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/abis.txt",header=F,sep="\t",dec=",",na.strings="NA")
acor<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/acor.txt",header=F,sep="\t",dec=",",na.strings="NA")
cep1<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/cep1.txt",header=F,sep="\t",dec=",",na.strings="NA")
cep2<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/cep2.txt",header=F,sep="\t",dec=",",na.strings="NA")
cep3<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/cep2.txt",header=F,sep="\t",dec=",",na.strings="NA")
dona<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/dona.txt",header=F,sep="\t",dec=",",na.strings="NA")
gala<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/gala.txt",header=F,sep="\t",dec=",",na.strings="NA")
gara<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/gara.txt",header=F,sep="\t",dec=",",na.strings="NA")
hes1<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/hes1.txt",header=F,sep="\t",dec=",",na.strings="NA")
hes2<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/hes2.txt",header=F,sep="\t",dec=",",na.strings="NA")
hes3<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/hes3.txt",header=F,sep="\t",dec=",",na.strings="NA")
hock<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/hock.txt",header=F,sep="\t",dec=",",na.strings="NA")
ino1<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/ino1.txt",header=F,sep="\t",dec=",",na.strings="NA")
ino2<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/ino2.txt",header=F,sep="\t",dec=",",na.strings="NA")
kaku<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/kaku.txt",header=F,sep="\t",dec=",",na.strings="NA")
kat1<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/kat1.txt",header=F,sep="\t",dec=",",na.strings="NA")
kat2<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/kat2.txt",header=F,sep="\t",dec=",",na.strings="NA")
kato<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/kato.txt",header=F,sep="\t",dec=",",na.strings="NA")
keva<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/keva.txt",header=F,sep="\t",dec=",",na.strings="NA")
maur<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/maur.txt",header=F,sep="\t",dec=",",na.strings="NA")
mosq<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/mosq.txt",header=F,sep="\t",dec=",",na.strings="NA")
perc<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/perc.txt",header=F,sep="\t",dec=",",na.strings="NA")
peta<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/peta.txt",header=F,sep="\t",dec=",",na.strings="NA")
pri1<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/pri1.txt",header=F,sep="\t",dec=",",na.strings="NA")
pri2<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/pri2.txt",header=F,sep="\t",dec=",",na.strings="NA")
pri3<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/pri3.txt",header=F,sep="\t",dec=",",na.strings="NA")
rami<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/rami.txt",header=F,sep="\t",dec=",",na.strings="NA")
sche<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/sche.txt",header=F,sep="\t",dec=",",na.strings="NA")
zack<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/poll/zack.txt",header=F,sep="\t",dec=",",na.strings="NA")

### Datasets-Frugivory -----------------------------------------
nch<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/nch.txt",header=F,sep="\t",dec=",",na.strings="NA")
nch_lab<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/nch_lab.txt",header=T,sep="\t",dec=",",na.strings="NA")
mont<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/mont.txt",header=F,sep="\t",dec=",",na.strings="NA")
sgen2<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/sgen2.txt",header=F,sep="\t",dec=",",na.strings="NA")
hr<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/hr.txt",header=F,sep="\t",dec=",",na.strings="NA")
hrqt<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/hr_qt.txt",header=T,sep="\t",dec=".",na.strings="NA")
hr_lab<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/hr_lab.txt",header=T,sep="\t",dec=",",na.strings="NA")
wyth<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/wyth.txt",header=F,sep="\t",dec=",",na.strings="NA")
beeh<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/beeh.txt",header=F,sep="\t",dec=",",na.strings="NA")
vis<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/vis.txt",header=F,sep="\t",dec=",",na.strings="NA")
frost<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/frost.txt",header=F,sep="\t",dec=",",na.strings="NA")
guit<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/guit.txt",header=F,sep="\t",dec=",",na.strings="NA")
nnog<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/nnog.txt",header=F,sep="\t",dec=",",na.strings="NA")
nnog_lab<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/nnog_lab.txt",header=T,sep="\t",dec=",",na.strings="NA")
interv<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/interv.txt",header=F,sep="\t",dec=",",na.strings="NA")
interv_new<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/interv_new.txt",header=F,sep="\t",dec=",",na.strings="NA")
crome<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/crome.txt",header=F,sep="\t",dec=",",na.strings="NA")
lamb<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/lamb.txt",header=F,sep="\t",dec=",",na.strings="NA")
snow<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/snow.txt",header=F,sep="\t",dec=",",na.strings="NA")
snow_wyth<-read.table("/Users/pedroj/Documents/Working/MS_Networks/Fitting/matrices/frug/snow_wyth.txt",header=F,sep="\t",dec=",",na.strings="NA")

### Pooled datasets:
pollmat<-list(kat1=kat1,
				cep1=cep1,
				acor=acor,
				cep1=cep1,
				cep2=cep2,
				cep3=cep3,
				dona=dona,
				gala=gala,
				gara=gara,
				hes1=hes1,
				hes1=hes1,
				hes2=hes2,
				hes3=hes3,
				hock=hock,
				ino1=ino1,
				ino2=ino2,
				kaku=kaku,
				kat1=kat1,
				kat2=kat2,
				kato=kato,
				keva=keva,
				maur=maur,
				abis=abis)   # check
frugmat<-list(nch=nch,
				mont=mont,
                snow=snow,   # check
                crome=crome,
				wyth=wyth,
				sgen2=sgen2,
				beeh=beeh,
				vis=vis,
				frost=frost,
				guit=guit,
				nnog=nnog,   # check
				nnog_lab=nnog_lab,   # check
				interv=interv,
                lamb=lamb,
                snow_wyth= snow_wyth,
                interv_new= interv_new,
                hr=hr,
                hrqt=hrqt,
                hr_lab=hr_lab)
#-----------------------------------------------------------------------------