rEMM (version 1.0-5)

transition_table: Extract a Transition Table for a New Sequence Given an EMM

Description

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

Usage

## S3 method for class 'EMM,matrix':
transition_table(x, newdata, method = c("prob", "counts", "log_odds"), match_cluster = "nn", plus_one=FALSE, initial_transition = FALSE)

Arguments

x

an EMM object.

newdata

new sequence,

method

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")?

plus_one

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 w

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)

transition_table(emm, EMMsim_test)
transition_table(emm, EMMsim_test, method ="prob", initial_transition=TRUE)