Nearest Metric Space Representation of a Dissimilarity Object
Calculates the nearest metric space representation of a dissimilarity object by iterating the transitive closure of the triangle inequality rule
metrify(dis,upper=FALSE,diag=FALSE) as.metric(dis,upper=FALSE,diag=FALSE) is.metric(dis)
dis |
a distance or dissimilarity object returned from |
upper |
a logical switch to control whether to return the lower triangle (upper=FALSE) or upper triangle (upper=TRUE) of the distance matrix |
diag |
a logical switch to control whether to return the diagonal of the distance matrix |
Implements a constrained iteration of the transitive closure of the triangle inequality, such that the distance between any two objects is less than or equal to the sum of the distances from the two objects to a third.
For metrify and as.metric, an object of class ‘dist’. For is.metric returns TRUE or FALSE.
Many multivariate statistical methods are designed for metric spaces, and yet the direct calculation of distance is often inappropriate due to problems with joint absences. metrify takes any dissimilarity matrix and converts it to the closest metric space representation, generally to avoid negative eigenvalues in an eigenanalysis of the matrix.
data(bryceveg) # returns a vegetation data.frame
dis.bc <- dsvdis(bryceveg,'bray/curtis') # calculate a Bray/Curtis
# dissimilarity matrix
dis.met <- metrify(dis.bc) # calculate the nearest euclidean
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