list_to_matrix: topolow Data Preprocessing Functions

In topolow: Force-Directed Euclidean Embedding of Dissimilarity Data

topolow Data Preprocessing Functions

Description

Converts data from long/list format (one measurement per row) to a symmetric dissimilarity matrix. The function handles both similarity and dissimilarity data, with optional conversion from similarity to dissimilarity.

Usage

list_to_matrix(
  data,
  object_col,
  reference_col,
  value_col,
  is_similarity = FALSE
)

Arguments

data	Data frame in long format with columns for objects, references, and values.
object_col	Character. Name of the column containing object identifiers.
reference_col	Character. Name of the column containing reference identifiers.
value_col	Character. Name of the column containing measurement values.
is_similarity	Logical. Whether values are similarities (TRUE) or dissimilarities (FALSE). If TRUE, similarities will be converted to dissimilarities by subtracting from the maximum value per reference. Default: FALSE.

Details

Convert List Format Data to Dissimilarity Matrix

The function expects data in long format with at least three columns:

• A column for object names

• A column for reference names

• A column containing the (dis)similarity values

When is_similarity = TRUE, the function converts similarities to dissimilarities by subtracting each similarity value from the maximum similarity value within each reference group. Threshold indicators (< or >) are handled appropriately and inverted during similarity-to-dissimilarity conversion.

Value

A symmetric matrix of dissimilarities with row and column names corresponding to the union of unique objects and references in the data. NA values represent unmeasured pairs, and the diagonal is set to 0.

Examples

# Example with dissimilarity data
data_dissim <- data.frame(
  object = c("A", "B", "A", "C"),
  reference = c("X", "X", "Y", "Y"),
  dissimilarity = c(2.5, 1.8, 3.0, 4.2)
)

mat_dissim <- list_to_matrix(
  data = data_dissim,
  object_col = "object",
  reference_col = "reference",
  value_col = "dissimilarity",
  is_similarity = FALSE
)

# Example with similarity data (will be converted to dissimilarity)
data_sim <- data.frame(
  object = c("A", "B", "A", "C"),
  reference = c("X", "X", "Y", "Y"),
  similarity = c(7.5, 8.2, 7.0, 5.8)
)

mat_from_sim <- list_to_matrix(
  data = data_sim,
  object_col = "object",
  reference_col = "reference",
  value_col = "similarity",
  is_similarity = TRUE
)

topolow documentation built on Aug. 31, 2025, 1:07 a.m.