as.dendrogram.vlmc: Dendrogram Construction from VLMCs

In VLMC: Variable Length Markov Chains ('VLMC') Models

Description

This is a method for the as.dendrogram generic function

Usage

## S3 method for class 'vlmc'
as.dendrogram(object, ...)

Arguments

object	a vlmc object.
...	further arguments passed to and from methods.

Value

An object of class dendrogram, i.e. a nested list described on that page.

See Also

as.dendrogram, plot.dendrogram.

Examples

data(presidents)
dpr <- factor(cut(presidents, c(0,45,70,100)), exclude=NULL)# NA = 4th level
(vlmc.pres <- vlmc(dpr))
draw(vlmc.pres)
(dv.dpr <- as.dendrogram(vlmc.pres))
str(dv.dpr)
str(unclass(dv.dpr))


plot(dv.dpr, type ="tr", nodePar = list(pch=c(1,16), cex = 1.5))

## Artificial example
f1 <- c(1,0,0,0) ; f2 <- rep(1:0, 2)
(dt1 <- c(f1,f1,f2,f1,f2,f2,f1))
(vlmc.dt1c01 <- vlmc(dts = dt1, cutoff.prune = 0.1))
(dvlmc <- as.dendrogram(vlmc.dt1c01))

str(dvlmc)

## not so useful:
plot(dvlmc, nodePar= list(pch=c(1,16)))
## complete disaster:
plot(dvlmc, type ="tr", nodePar= list(pch=c(1,16)))

## but this is not (yet) so much better (want the same angles to left
## and right!!
plot(dvlmc, type ="tr", nodePar = list(pch=c(1,16)), center=TRUE,
     main = format(vlmc.dt1c01$call))
mtext(paste("dt1 =", gsub(" ","",deparse(dt1,width=100))))

Example output

'vlmc' a Variable Length Markov Chain;
	 alphabet '0123', |alphabet| = 4, n = 120.
Call: vlmc(dts = dpr);  default cutoff =3.907
 -> extensions (= $size ) :
   ord.MC   context nr.leaves     total 
        2         5         3        42 
AIC =  227.6 
Warning message:
In vlmc(dpr) : alphabet with >1-letter strings; trying to abbreviate
[x]-( 28 60 26 5| 119)
 +--[0]-( 18 7 0 2| 27) <15.22>-T
 +--[1]-( 9 39 11 1| 60) <3.00>
 |   '--[2]-( 0 6 6 0| 12) <4.45>-T
 '--[2]-( 0 12 14 0| 26) <11.57>-T
'dendrogram' with 3 branches and 3 members total, at height 2 
--[dendrogram w/ 3 branches and 3 members at h = 2]
  |--leaf 27 (h= 1 count = c("18", " 7", " 0", " 2"), edgetext = 0 )
  |--[dendrogram w/ 1 branches and 1 members at h = 1]
  |  `--leaf 12 ( count = c("0", "6", "6", "0"), edgetext = 2 )
  `--leaf 26 (h= 1 count = c(" 0", "12", "14", " 0"), edgetext = 2 )
List of 3
 $ 0: atomic [1:1] 27
  ..- attr(*, "members")= int 1
  ..- attr(*, "leaf")= logi TRUE
  ..- attr(*, "height")= int 1
  ..- attr(*, "count")= int [1:4] 18 7 0 2
  ..- attr(*, "edgetext")= chr "0"
 $ 1:List of 1
  ..$ 2: atomic [1:1] 12
  .. ..- attr(*, "members")= int 1
  .. ..- attr(*, "leaf")= logi TRUE
  .. ..- attr(*, "height")= int 0
  .. ..- attr(*, "count")= int [1:4] 0 6 6 0
  .. ..- attr(*, "edgetext")= chr "2"
  ..- attr(*, "0-kids")= int [1:3] 0 1 3
  ..- attr(*, "members")= int 1
  ..- attr(*, "height")= int 1
  ..- attr(*, "count")= int [1:4] 9 33 5 1
  ..- attr(*, "edgetext")= chr "1"
 $ 2: atomic [1:1] 26
  ..- attr(*, "members")= int 1
  ..- attr(*, "leaf")= logi TRUE
  ..- attr(*, "height")= int 1
  ..- attr(*, "count")= int [1:4] 0 12 14 0
  ..- attr(*, "edgetext")= chr "2"
 - attr(*, "0-kids")= int 3
 - attr(*, "members")= int 3
 - attr(*, "height")= int 2
 - attr(*, "count")= int [1:4] 1 2 1 2
 [1] 1 0 0 0 1 0 0 0 1 0 1 0 1 0 0 0 1 0 1 0 1 0 1 0 1 0 0 0

'vlmc' a Variable Length Markov Chain;
	 alphabet '01', |alphabet| = 2, n = 28.
Call: vlmc(dts = dt1, cutoff.prune = 0.1);  cutoff =0.1
 -> extensions (= $size ) :
   ord.MC   context nr.leaves     total 
        7        11         6        66 
AIC =  27.55 
'dendrogram' with 2 branches and 6 members total, at height 7 
--[dendrogram w/ 2 branches and 6 members at h = 7]
  |--[dendrogram w/ 2 branches and 5 members at h = 6]
  |  |--[dendrogram w/ 2 branches and 2 members at h = 5]
  |  |  |--leaf 3 (h= 4 count = c("0", "3"), edgetext = 0 )
  |  |  `--leaf 4 (h= 4 count = c("4", "0"), edgetext = 1 )
  |  `--[dendrogram w/ 1 branches and 3 members at h = 5]
  |     `--[dendrogram w/ 2 branches and 3 members at h = 4]
  |        |--[dendrogram w/ 1 branches and 1 members at h = 3]
  |        |  `--[dendrogram w/ 1 branches and 1 members at h = 2]
  |        |     `--[dendrogram w/ 1 branches and 1 members at h = 1]
  |        |        `--leaf 2 ( count = c("0", "2"), edgetext = 0 )
  |        `--[dendrogram w/ 1 branches and 2 members at h = 3]
  |           `--[dendrogram w/ 2 branches and 2 members at h = 2]
  |              |--leaf 2 (h= 1 count = c("0", "2"), edgetext = 0 )
  |              `--leaf 4 (h= 1 count = c("2", "2"), edgetext = 1 )
  `--leaf 10 (h= 6 count = c("10", " 0"), edgetext = 1 )

VLMC documentation built on May 1, 2019, 11:32 p.m.