Functions for creating and working with horizon (sequence) transition probability matrices.

See the following tutorials for some ideas:

hzTransitionProbabilities(
x,
name = GHL(x, required = TRUE),
loopTerminalStates = FALSE
)

mostLikelyHzSequence(mc, t0, maxIterations = 10)

## Arguments

x

a SoilProfileCollection object.

name

A horizon level attribute in x that names horizons.

loopTerminalStates

should terminal states loop back to themselves?

This is useful when the transition probability matrix will be used to initialize a markovchain object. See examples below.

mc

Passed to markovchain conditionalDistribution()

t0

Passed to markovchain conditionalDistribution()

maxIterations

Maximum number of iterations. Default: 10

## Value

A square matrix of transition probabilities. See examples.

The function genhzTableToAdjMat() returns a square adjacency matrix. See examples.

The function mostLikelyHzSequence() returns the most likely sequence of horizons, given a markovchain object initialized from horizon transition probabilities and an initial state, t0. See examples.

## Note

These functions are still experimental and subject to change.

generalize.hz()

D.E. Beaudette

## Examples


data(sp4)
depths(sp4) <- id ~ top + bottom

# horizon transition probabilities: row -> col transitions
(tp <- hzTransitionProbabilities(sp4, 'name'))
#> Warning: ties in transition probability matrix
#>     A A1 A2 AB       ABt        Bt       Bt1 Bt2 Bt3
#> A   0  0  0  0 0.1111111 0.4444444 0.4444444   0   0
#> A1  0  0  1  0 0.0000000 0.0000000 0.0000000   0   0
#> A2  0  0  0  1 0.0000000 0.0000000 0.0000000   0   0
#> AB  0  0  0  0 0.0000000 0.0000000 1.0000000   0   0
#> ABt 0  0  0  0 0.0000000 0.0000000 1.0000000   0   0
#> Bt  0  0  0  0 0.0000000 0.0000000 0.0000000   0   0
#> Bt1 0  0  0  0 0.0000000 0.0000000 0.0000000   1   0
#> Bt2 0  0  0  0 0.0000000 0.0000000 0.0000000   0   1
#> Bt3 0  0  0  0 0.0000000 0.0000000 0.0000000   0   0
#> attr(,"ties")
#> [1] TRUE

if (FALSE) { # \dontrun{
## plot TP matrix with functions from sharpshootR package
library(sharpshootR)
par(mar=c(0,0,0,0), mfcol=c(1,2))
plotSPC(sp4, name = 'name', name.style = 'center-center')
plotSoilRelationGraph(tp, graph.mode = 'directed', edge.arrow.size=0.5)

data(loafercreek, package='soilDB')

# convert contingency table -> adj matrix / TP matrix
tab <- table(loafercreek$hzname, loafercreek$genhz)

# plot
par(mar=c(0,0,0,0), mfcol=c(1,1))
plotSoilRelationGraph(m, graph.mode = 'directed', edge.arrow.size=0.5)

## demonstrate markovchain integration
library(markovchain)
tp.loops <- hzTransitionProbabilities(sp4, 'name', loopTerminalStates = TRUE)

# init new markovchain from TP matrix
mc <- new("markovchain", states=dimnames(tp.loops)[[1]], transitionMatrix = tp.loops)

# simple plot
plot(mc, edge.arrow.size=0.5)

# check absorbing states
absorbingStates(mc)