Extract a Transition Table for a New Sequence Given an EMM

Finds the state sequence of a new sequence in an EMM and returns a table with the transition probabilities or counts.

Usage

# S4 method for class 'EMM,matrix'
transition_table(
  x,
  newdata,
  type = c("probability", "counts", "log_odds"),
  match_cluster = "exact",
  prior = TRUE,
  initial_transition = FALSE
)

Arguments

x

an EMM object.

newdata

new sequence,

type

the measure to return.

match_cluster

do the new observations have to fall within the threshold of the cluster ("exact") or is nearest neighbor used ("nn")?

prior

add one to each transition count. This is equal to starting with a uniform prior for the transition count distribution, i.e. initially all transitions are equally likely. It also prevents the product of probabilities to be zero if a transition was never observed.

initial_transition

include the initial transition in the table?

Value

A data.frame with three columns (from state, to state and the transition probability/count.)

See also

transition to access transition probabilities and find_clusters for assigning observations to states/clusters.

Examples

data("EMMsim")

emm <- EMM(threshold=.5)
emm <- build(emm, EMMsim_train)

head(transition_table(emm, EMMsim_test))
#>   from to probability
#> 1    5  2  0.44444444
#> 2    2  1  0.88888889
#> 3    1  3  0.49382716
#> 4    3  4  0.91111111
#> 5    4  5  0.09090909
#> 6    5  2  0.44444444
head(transition_table(emm, EMMsim_test, type ="prob", initial_transition=TRUE))
#>   from to probability
#> 1 <NA>  5  0.16666667
#> 2    5  2  0.44444444
#> 3    2  1  0.88888889
#> 4    1  3  0.49382716
#> 5    3  4  0.91111111
#> 6    4  5  0.09090909