gRapHD (version 0.2.5)

stepw: Stepwise forward selection

Description

Stepwise forward selection.

Usage

stepw(model,dataset,stat="BIC",saveCH=NULL,forbEdges=NULL,
      exact=FALSE,initial=NULL,threshold=0,join=FALSE)

Arguments

model

gRapHD object.

dataset

matrix (nrow(dataset) observations and ncol(dataset) variables).

stat

measure to be minimized: LR, AIC, or BIC. Default is BIC. It can also be a user defined function with format: FUN(model,dataset,previous, forbEdges); where the parameters are defined as in chStat. The function must return a structure as in chStat.

saveCH

pattern of a file name to save each iteration results. NULL not to save (default).

forbEdges

list with edges that should not be considered. Matrix with 2 columns, each row representing one edge, and each column a vertex. Default is NULL.

exact

logical indicting whether the exact algorithm for finding add-eligible edges is to be used. Default is FALSE.

initial

continue the algorithm from a previous point. The parameter must have the same structure as the result of chStat.

threshold

values greater than the threshold are not included in the model. Default is 0.

join

logical indicating whether disjoint components can be joined. Default is FALSE.

Value

The same structure as model, but adding the new edges, and updating other relevant information. See minForest for the description of the structure.

Details

Performs a stepwise forward selection of edges to be added to a triangulated graph. Only edges preserving the triangularity are considered (findEd). At each step the edge giving the greatest improvement in the chosen statistic is added. The process ends when no further improvement is possible. If exact is FALSE, the list of edges returned may contain a few edges that do not preserve triangularity, requiring further tests (for example mcs) before adding an edge. Otherwise, the list will only contain edges that preserve triangularity. That is, each edge that may be added to the graph such that the resulting graph is triangulated. For graphs with both discrete and continuous vertices, the graph should be triangulated and contain no forbidden paths, and the edges that may be added must preserve both properties. See Lauritzen (1996), p. 11-13.

Examples

# NOT RUN {
set.seed(7,kind="Mersenne-Twister")
dataset <- matrix(rnorm(1000),nrow=100,ncol=10)
m <- minForest(dataset,stat="BIC")

M <- stepw(m,dataset,stat="LR",NULL,NULL)

#######################################################################
# Example with continuous variables
data(dsCont)
# m1 <- minForest(dataset,homog=TRUE,forbEdges=NULL,stat="LR")
#          1. in this case, there is no use for homog
#          2. no forbidden edges
#          3. the measure used is the LR (the result is a tree)
m1 <- minForest(dsCont,homog=TRUE,forbEdges=NULL,stat="LR")
plot(m1,numIter=1000)

# m2 <- stepw(m1,dataset,stat="BIC",saveCH=NULL,forbEdges=NULL)
#          1. m1 is the result of minForest
#          2. the same dataset (this is not checked)
#          3. the default is BIC
#          4. if saveCH="XXX", a file "XXX_00000i.RData" 
#             is saved for each iter
#          5. no forbidden edges
m2 <- stepw(m1,dsCont,stat="BIC",saveCH=NULL,forbEdges=NULL)
plot(m2,numIter=1000)

#######################################################################
# Example with discrete variables
data(dsDiscr)
# m1 <- minForest(dataset,homog=TRUE,forbEdges=NULL,stat="LR")
#          1. in this case, there is no use for homog
#          2. no forbidden edges
#          3. the measure used is the LR (the result is a tree)
m1 <- minForest(dsDiscr,homog=TRUE,forbEdges=NULL,stat="LR")
plot(m1,numIter=1000)

# m2 <- stepw(m1,dataset,stat="BIC",saveCH=NULL,forbEdges=NULL)
#          1. m1 is the result of minForest
#          2. the same dataset (this is not checked)
#          3. the default is BIC
#          4. if saveCH="XXX", a file "XXX_00000i.RData" 
#             is saved for each iter
#          5. no forbidden edges
m2 <- stepw(m1,dsDiscr,stat="BIC",saveCH=NULL,forbEdges=NULL)
plot(m2,numIter=1000)

#######################################################################
# Example with mixed variables
data(dsMixed)
# m1 <- minForest(dataset,homog=TRUE,forbEdges=NULL,stat="LR")
#          1. it is to be considered homogeneous
#          2. no forbidden edges
#          3. the measure used is the LR (the result is a tree)
m1 <- minForest(dsMixed,homog=TRUE,forbEdges=NULL,stat="LR")
plot(m1,numIter=1000)

# m2 <- stepw(m1,dataset,stat="BIC",saveCH=NULL,forbEdges=NULL)
#          1. m1 is the result of minForest
#          2. the same dataset (this is not checked)
#          3. the default is BIC
#          4. if saveCH="XXX", a file "XXX_00000i.RData" 
#             is saved for each iter
#          5. no forbidden edges
m2 <- stepw(m1,dsMixed,stat="BIC",saveCH=NULL,forbEdges=NULL)
plot(m2,numIter=1000)

#######################################################################
# Example using a user defined function
#   The function userFun calculates the same edges weigths as the 
# option stat="BIC". It means that the final result, using either 
# option, is the same.
userFun <- function(model,dataset,previous=NULL,forbEdges=NULL)
{
  p <- ncol(dataset) # number of variables (vertices)
  n <- nrow(dataset) # number of observations
  edges.to.test <- previous$edges.to.test
  SS <- previous$S # minimal separators
  rm(previous)

  num <- nrow(edges.to.test)

  if (num > 0)
    for (i in 1:num)
    {
      x <- edges.to.test[i,1]
      y <- edges.to.test[i,2]
      if ((edges.to.test[i,4]==0) &
          (!is.element((x-1)*p-(x-1)*x/2+y-x,forbEdges)))
      {
        S <- SS[[edges.to.test[i,3]]]
        clique <- c(edges.to.test[i,1:2],S)
        CM <- cov(dataset[,clique],use="pairwise.complete.obs")*
              (nrow(dataset)-1)
        a <- match(edges.to.test[i,1:2],clique)
        d <- log(det(CM)) + 
             log(det(matrix(CM[-a,-a],length(clique)-2)))
        d <- d - (log(det(matrix(CM[-a[1],-a[1]],length(clique)-1))) +
                  log(det(matrix(CM[-a[2],-a[2]],length(clique)-1))))
        edges.to.test[i,4] <- nrow(dataset)*d + log(n)
        edges.to.test[i,5] <- 1
      }
    }
  return(list(edges.to.test=edges.to.test,S=SS))
}

data(dsCont)
m <- minForest(dsCont,stat="BIC")
m1 <- stepw(m,dsCont,stat="BIC")
m2 <- stepw(m,dsCont,stat=userFun)
identical(m1@edges,m2@edges)

#######################################################################
# Example of joining disjoint components
data(dsCont)
m <- minForest(dsCont,stat="BIC")
m1 <- stepw(m,dsCont)
m2 <- m
m2@edges <- matrix(integer(0),,2)
m3 <- stepw(m2,dsCont,join=TRUE)
identical(sortMat(m1@edges),sortMat(m3@edges))
# TRUE
# }