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## networkfamily.R
## Author : Claus Dethlefsen
## Created On : Tue Oct 30 16:43:05 2001
## Last Modified By: Claus Dethlefsen
## Last Modified On: Wed Jul 28 09:39:43 2004
## Update Count : 429
## Status : Unknown, Use with caution!
###############################################################################
##
## Copyright (C) 2002 Susanne Gammelgaard Bottcher, Claus Dethlefsen
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2 of the License, or
## (at your option) any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program; if not, write to the Free Software
## Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
######################################################################
networkfamily <- function(data,nw=network(data),prior=jointprior(nw),
trylist=vector("list",size(nw)),timetrace=TRUE) {
## Creator class for networkfamily
##
## Generates all possible networks with the restriction that
## discrete nodes cannot have continuous parents. (see insert)
## Uses: numbermixed, addarrows, learn.network, cycletest
## and attributes of nw: nd,nc
## Value:
## networklist: A list of network-objects
## trylist: an updated trylist
if (timetrace) {t1 <- proc.time();cat("[networkfamily ")}
nw <- learn(nw,data,prior,trylist=trylist)
trylist <- nw$trylist
nw <- nw$nw
ndiscrete <- nw$nd
ncontinuous<- nw$nc
cat("Creating all (",
numbermixed(ndiscrete,ncontinuous),
" minus restrictions) networks with ",ndiscrete," discrete and ",
ncontinuous," continuous nodes\n",sep="")
nwl <- list() # network list
n <- ndiscrete + ncontinuous
nwl <- list(nw) # current network list
for (node in 2:n) {
for (idx in 1:length(nwl)) {
nws <- addarrows(nwl[[idx]],node,data,prior,trylist=trylist)
trylist <- nws$trylist
nwl <- c(nwl,nws$nw)
}
}
cat("Created",length(nwl),"networks, ")
if (ndiscrete>2|ncontinuous>2) {
cat("removing cycles...\n")
nwlres <- nwl[!unlist(lapply(nwl,cycletest))]
cat(length(nwl)-length(nwlres),"cycles removed, ending up with",length(nwlres),"networks\n")
}
else nwlres <- nwl
class(nwlres) <- "networkfamily"
if (timetrace) {
t2 <- proc.time()
cat((t2-t1)[1],"]\n")
}
list(nw=nwlres,trylist=trylist)
}
plot.networkfamily <- function(x,
layout=rep(min(1+floor(sqrt(length(x))),5),2),
cexscale=5,arrowlength=0.1,
sscale=7,...) {
nwf <- x
par(mfrow=layout)
for (i in 1:length(nwf)) {
par(mar=c(0,0,0,0))
plot(nwf[[i]],cexscale=cexscale,arrowlength=arrowlength,sscale=sscale,showban=FALSE,...)
}
par(mfrow=c(1,1))
}
nwfsort <- function(nwf) {
## sort according to network score, and add relative scores
n <- length(nwf)
## first, create a vector with the indices and scores
tab <- rep(NA,n)
for (i in 1:n)
tab[i] <- nwf[[i]]$score
## then find the sort list of indices
sl <- sort.list(-tab)
relscore <- exp(tab - tab[sl[1]])
## create the sorted family
nwf <- nwf[sl]
for (i in 1:n)
nwf[[i]]$relscore <- relscore[sl[i]]
class(nwf) <- "networkfamily"
nwf
}
print.networkfamily <- function(x,...) {
nwf <- nwfsort(x) ## ensure they are sorted
g <- function(x) x$name
nw <- nwf[[1]]
cat("Discrete: ")
if (nw$nd>0) {
nn <- nw$discrete[1]
cat(nw$nodes[[nn]]$name,"(",nw$nodes[[nn]]$levels,")",sep="")
if (nw$nd>1) {
for (i in nw$discrete[-1])
cat(",",nw$nodes[[i]]$name,"(",nw$nodes[[i]]$levels,")",sep="")
}
cat("\n")
}
else cat("\n")
cat("Continuous:")
if (nw$nc>0) {
nn <- nw$continuous[1]
cat(nw$nodes[[nn]]$name,sep="")
if (nw$nc>1) {
for (i in nw$continuous[-1])
cat(",",nw$nodes[[i]]$name,sep="")
}
cat("\n")
}
else cat("\n")
cat(" log(Score)\t|Relscore\t|Network\n")
printline()
for (i in 1:length(nwf)) {
nw <- nwf[[i]]
cat(i,". ",nw$score,"\t",nw$relscore,sep="")
if (i==1) cat("\t")
cat("\t",sep="")
for (j in 1:nw$n) {
nd <- nw$nodes[[j]]
cat("[",nd$name,sep="")
if (length(nd$parents)>0) {
cat("|",
unlist(lapply(nw$nodes[nd$parents],g)),
sep="")
}
cat("]")
}
cat("\n")
} ## for
invisible(nwf)
}
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