build_model: Build a Transition Network Analysis Model
In tna: Transition Network Analysis (TNA)

build_model

R Documentation

Build a Transition Network Analysis Model

Description

Construct a transition network analysis (TNA) model from sequence data. The function takes a data set of sequence of events or states as input and builds a TNA model. It extracts the edge weights and initial probabilities from the data along with the state labels. THe function also accepts weight matrices and initial state probabilities directly.

Usage

build_model(x, type = "relative", scaling = character(0L), ...)

## Default S3 method:
build_model(
  x,
  type = "relative",
  scaling = character(0L),
  inits,
  params = list(),
  ...
)

## S3 method for class 'matrix'
build_model(x, type = "relative", scaling = character(0L), inits, ...)

## S3 method for class 'stslist'
build_model(
  x,
  type = "relative",
  scaling = character(0L),
  cols = seq(1, ncol(x)),
  params = list(),
  ...
)

## S3 method for class 'data.frame'
build_model(
  x,
  type = "relative",
  scaling = character(0L),
  cols = seq(1, ncol(x)),
  params = list(),
  ...
)

## S3 method for class 'tna_data'
build_model(x, type = "relative", scaling = character(0), params = list(), ...)

tna(x, ...)

ftna(x, ...)

ctna(x, ...)

atna(x, ...)

Arguments

`x`	A `stslist` (from `TraMineR`), `data.frame`, a `matrix`, or a `tna_data` object (see `prepare_data()`). For `stslist` and `data.frame` objects `x` should describe a sequence of events or states to be used for building the Markov model. If `x` is a matrix, it is assumed that the element on row `i` and column `j` is the weight of the edge representing the transition from state `i` to state `j`. If `x` is a `data.frame`, then it must be in wide format (see `cols` on how to define columns for the time points).
`type`	A `character` string describing the weight matrix type. Currently supports the following types: `"relative"` for relative frequencies (probabilities, the default) `"frequency"` for frequencies. `"co-occurrence"` for co-occurrences. `"n-gram"` for n-gram transitions. Captures higher-order transitions by considering sequences of n states, useful for identifying longer patterns. `"gap"` allows transitions between non-adjacent states, with transitions weighted by the gap size. `"window"` creates transitions between all states within a sliding window, capturing local relationships (several sequences together). `"reverse"` considers the sequences in reverse order (resulting in what is called a reply network in some contexts). The resulting weight matrix is the transpose of the `"frequency"` option. `"attention"` aggregates all downstream pairs of states with an exponential decay for the gap between states. The parameter `lambda` can be used to control the decay rate (the default is 1)-
`scaling`	A `character` vector describing how to scale the weights defined by `type`. When a vector is provided, the scaling options are applied in the respective order. For example, `c("rank", "minmax")` would first compute the ranks, then scale them to the unit interval using min-max normalization. An empty vector corresponds to no scaling. Currently supports the following options: `"minmax"` performs min-max normalization to scale the weights to the unit interval. Note that if the smallest weight is positive, it will be zero after scaling. `"max"` Multiplies the weights by the reciprocal of the largest weight to scale the weights to the unit interval. This options preserves positive ranks, unlike `"minmax"` when all weights are positive. `"rank"` Computes the ranks of the weights using `base::rank()` with `ties.method = "average"`.
`...`	Ignored. For the `build_model` aliases (e.g., `tna`), this argument matches the actual arguments to `build_model` beside `x`.
`inits`	An optional `numeric` vector of initial state probabilities for each state. Can be provided only if `x` is a `matrix`. The vector will be scaled to unity.
`params`	A `list` of additional arguments for models of specific `type`. The potential elements of this list are: `n_gram`: An `integer` for n-gram transitions specifying the number of adjacent events. The default value is 2. `max_gap`: An `integer` for the gap-allowed transitions specifying the largest allowed gap size. The default is 1. `window_size`: An `integer` for the sliding window transitions specifying the window size. The default is 2. `weighted`: A `logical` value. If `TRUE`, the transitions are weighted by the inverse of the sequence length. Can be used for frequency, co-occurrence and reverse model types. The default is `FALSE`. `lambda`: A `numeric` value for the decay rate. The default is 1.
`cols`	An `integer`/`character` vector giving the indices/names of the columns that should be considered as sequence data. Defaults to all columns, i.e., `seq(1, ncol(x))`.

Value

An object of class tna which is a list containing the following elements:

weights: An adjacency matrix of the model (weight matrix).
inits: A numeric vector of initial values for each state. For matrix type x, this element will be NULL if inits is not directly provided
labels: A character vector of the state labels, or NULL if there are no labels.
data: The original sequence data that has been converted to an internal format used by the package when x is a stslist or a data.frame object. Otherwise NULL.

Examples

model <- build_model(group_regulation)
print(model)

model <- tna(group_regulation)

model <- ftna(group_regulation)

model <- ctna(group_regulation)

model <- atna(group_regulation)

tna documentation built on June 8, 2025, 10:33 a.m.