spdep: prunecost – R documentation

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prunecost

Compute cost of prune each edge

Description

If any edge are dropped, the MST are pruned. This generate a two subgraphs. So, it makes a tree graphs and tree dissimilarity values are computed, one for each graph. The dissimilarity is the sum over sqared differences between the observactions in the nodes and mean vector of observations in the graph. The dissimilarity of original graph and the sum of dissimilarity of subgraphs are returned.

Usage

prunecost(edges, data, method = c("euclidean", "maximum", "manhattan", 
    "canberra", "binary", "minkowski", "mahalanobis"), 
    p = 2, cov, inverted = FALSE)

Arguments

`edges`	A matrix with 2 colums with each row is one edge
`data`	A data.frame with observations in the nodes.
`method`	Character or function to declare distance method. If `method` is character, method must be "mahalanobis" or "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowisk". If `method` is one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowisk", see `dist` for details, because this function as used to compute the distance. If `method="mahalanobis"`, the mahalanobis distance is computed between neighbour areas. If `method` is a `function`, this function is used to compute the distance.
`p`	The power of the Minkowski distance.
`cov`	The covariance matrix used to compute the mahalanobis distance.
`inverted`	logical. If 'TRUE', 'cov' is supposed to contain the inverse of the covariance matrix.

Value

A vector with the differences between the dissimilarity of all nodes and the dissimilarity sum of all subgraphs obtained by pruning one edge each time.

Author(s)

Elias T. Krainski and Renato M. Assuncao

Examples

d <- data.frame(a=-2:2, b=runif(5))
e <- matrix(c(1,2, 2,3, 3,4, 4,5), ncol=2, byrow=TRUE)

sum(sweep(d, 2, colMeans(d))^2)

prunecost(e, d)

spdep

Spatial Dependence: Weighting Schemes, Statistics

v1.1-11

GPL (>= 2)

Authors

Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>), Micah Altman [ctb], Luc Anselin [ctb], Renato Assunção [ctb], Olaf Berke [ctb], Andrew Bernat [ctb], Guillaume Blanchet [ctb], Eric Blankmeyer [ctb], Marilia Carvalho [ctb], Bjarke Christensen [ctb], Yongwan Chun [ctb], Carsten Dormann [ctb], Stéphane Dray [ctb], Virgilio Gómez-Rubio [ctb], Martin Gubri [ctb], Rein Halbersma [ctb], Elias Krainski [ctb], Pierre Legendre [ctb], Nicholas Lewin-Koh [ctb], Angela Li [ctb], Hongfei Li [ctb], Jielai Ma [ctb], Abhirup Mallik [ctb, trl], Giovanni Millo [ctb], Werner Mueller [ctb], Hisaji Ono [ctb], Pedro Peres-Neto [ctb], Gianfranco Piras [ctb], Markus Reder [ctb], Jeff Sauer [ctb], Michael Tiefelsdorf [ctb], René Westerholt [ctb], Levi Wolf [ctb], Danlin Yu [ctb]

Initial release

2021-09-07