R: Bayesian network data structure

network {deal}

R Documentation

Bayesian network data structure

Description

A Bayesian network is represented as an object of class network. Methods for printing and plotting are defined.

Usage

network(df,specifygraph=FALSE,inspectprob=FALSE,
        doprob=TRUE,yr=c(0,350),xr=yr) 
## S3 method for class 'network'
print(x,filename=NA,condposterior=FALSE,
                          condprior=FALSE,...) 
## S3 method for class 'network'
 plot(x,arrowlength=.25,
                        notext=FALSE,
                        sscale=7,showban=TRUE,yr=c(0,350),xr=yr,
                        unitscale=20,cexscale=8,...)

Arguments

`df`	a data frame, where the columns define the variables. A continuous variable should have type `numeric` and discrete varibles should have type `factor`.
`specifygraph`	a logical. If `TRUE`, provides a call to `drawnetwork` to interactively specify a directed acyclic graph and possibly a ban list (see below).
`inspectprob`	a logical. If `TRUE`, provides a plot of the graph and possibility to inspect the calculated probability distribution by clicking on the nodes.
`doprob`	a logical. If `TRUE`, do not calculate a probability distribution. Used for example in `rnetwork`.
`x`	an object of class `network`.
`filename`	a string or `NA`. If not `NA`, output is printed to a file.
`condprior`	a logical. If `TRUE`, the conditional prior is printed, see `conditional`.
`condposterior`	a logical. If `TRUE`, the conditional posterior is printed, see `learn`.
`sscale`	a numeric. The nodes are initially placed on a circle with radius `sscale`.
`unitscale`	a numeric. Scale parameter for chopping off arrow heads.
`cexscale`	a numeric. Scale parameter to set the size of the nodes.
`arrowlength`	a numeric containing the length of the arrow heads.
`xr`	a numeric vector with two components containing the range on x-axis.
`yr`	a numeric vector with two components containing the range on y-axis.
`notext`	a logical. If `TRUE`, no text is displayed in the nodes on the plot.
`showban`	a logical. If `TRUE`, banned arrows are shown in red.
`...`	additional plot arguments, passed to `plot.node`.

Value

The netork creator function returns an object of class network, which is a list with the following elements (properties),

`nodes`	a list of objects of class `node`. If `doprob` is `TRUE`, the nodes are given the property `prob` which is the initial probability distribution used by `jointprior`.
`n`	an integer containing the number of nodes in the network.
`discrete`	a numeric vector of indices of discrete nodes.
`continuous`	a numeric vector of indices of continuous nodes.
`banlist`	a numeric matrix with two columns. Each row contains the indices `i -> j` of arrows that may not be allowed in the directed acyclic graph.
`score`	a numeric added by `learn` and is the log network score.
`relscore`	a numeric added by `nwfsort` and is the relative network score – compared with the best network in a network family.

Author(s)

Susanne Gammelgaard Bottcher,
Claus Dethlefsen rpackage.deal@gmail.com.

Examples

A <- factor(rep(c("A1","A2"),50))
B <- factor(rep(rep(c("B1","B2"),25),2))
thisnet <- network( data.frame(A,B) )

set.seed(109)
sex     <- gl(2,4,label=c("male","female"))
age     <- gl(2,2,8)
yield   <- rnorm(length(sex))
weight  <- rnorm(length(sex))
mydata  <- data.frame(sex,age,yield,weight)
mynw    <- network(mydata)

# adjust prior probability distribution
localprob(mynw,"sex")   <- c(0.4,0.6)
localprob(mynw,"age")   <- c(0.6,0.4)
localprob(mynw,"yield") <- c(2,0)
localprob(mynw,"weight")<- c(1,0)

print(mynw)
plot(mynw)

prior <- jointprior(mynw)
mynw  <- getnetwork(learn(mynw,mydata,prior))
thebest <- getnetwork(autosearch(mynw,mydata,prior))

print(mynw,condposterior=TRUE)

## Not run: savenet(mynw,file("yield.net"))

[Package deal version 1.2-42 Index]