distance_matrix function

Distance matrix calculation

distance_matrix(
  data,
  method = "euclidean",
  upper = FALSE,
  diagonal = FALSE,
  minkowski_p = 1,
  threads = 1
)

Arguments

• data: matrix or data frame
• method: a string specifying the distance method. One of, euclidean, manhattan, chebyshev, canberra, braycurtis, pearson_correlation, simple_matching_coefficient, minkowski, hamming, jaccard_coefficient, Rao_coefficient, mahalanobis, cosine
• upper: either TRUE or FALSE specifying if the upper triangle of the distance matrix should be returned. If FALSE then the upper triangle will be filled with NA's
• diagonal: either TRUE or FALSE specifying if the diagonal of the distance matrix should be returned. If FALSE then the diagonal will be filled with NA's
• minkowski_p: a numeric value specifying the minkowski parameter in case that method = "minkowski"
• threads: the number of cores to run in parallel (if OpenMP is available)

Returns

a matrix

Examples

data(dietary_survey_IBS)

dat = dietary_survey_IBS[, -ncol(dietary_survey_IBS)]

dat = distance_matrix(dat, method = 'euclidean', upper = TRUE, diagonal = TRUE)