% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/frequencies.R
\name{frequencies}
\alias{frequencies}
\title{Sequence Data Conversion Functions}
\usage{
frequencies(
  data,
  action = "Action",
  id = NULL,
  time = "Time",
  cols = NULL,
  format = c("auto", "long", "wide")
)
}
\arguments{
\item{data}{Data frame containing sequence data in long or wide format.}

\item{action}{Character. Name of the column containing actions/states
(for long format). Default: "Action".}

\item{id}{Character vector. Name(s) of the column(s) identifying sequences.
For long format, each unique combination of ID values defines a sequence.
For wide format, used to exclude non-state columns. Default: NULL.}

\item{time}{Character. Name of the time column used to order actions within
sequences (for long format). Default: "Time".}

\item{cols}{Character vector. Names of columns containing states (for wide
format). If NULL, all non-ID columns are used. Default: NULL.}

\item{format}{Character. Format of input data: "auto" (detect automatically),
"long", or "wide". Default: "auto".}
}
\value{
A square integer matrix of transition frequencies where
\code{mat[i, j]} is the number of times state i was followed by state j.
Row and column names are the sorted unique states. Can be passed directly
to \code{tna::tna()}.
}
\description{
Functions for converting sequence data (long or wide format) into
transition frequency matrices and other useful representations.

Convert long or wide format sequence data into a transition frequency matrix.
Counts how many times each transition from state_i to state_j occurs across
all sequences.
}
\details{
For \strong{long format} data, each row is a single action/event. Sequences
are defined by the \code{id} column(s), and actions are ordered by the
\code{time} column within each sequence. Consecutive actions within a
sequence form transition pairs.

For \strong{wide format} data, each row is a sequence and columns represent
consecutive time points. Transitions are counted across consecutive columns,
skipping any \code{NA} values.
}
\examples{
# Wide format
seqs <- data.frame(V1 = c("A","B","A"), V2 = c("B","A","C"), V3 = c("A","C","B"))
freq <- frequencies(seqs, format = "wide")

# Long format
long <- data.frame(
  Actor = rep(1:2, each = 3), Time = rep(1:3, 2),
  Action = c("A","B","C","B","A","C")
)
freq <- frequencies(long, action = "Action", id = "Actor")

}
\seealso{
\code{\link{convert_sequence_format}} for converting to other
representations (frequency counts, one-hot, edge lists).
}
