component.adj.matrix: Create an adjacency matrix from a data.frame of component...

In sharpshootR: A Soil Survey Toolkit

Create an adjacency matrix from a data.frame of component data

Description

Create an adjacency matrix from SSURGO component data

Usage

component.adj.matrix(
  d,
  mu = "mukey",
  co = "compname",
  wt = "comppct_r",
  method = c("community.matrix", "occurrence"),
  standardization = "max",
  metric = "jaccard",
  rm.orphans = TRUE,
  similarity = TRUE,
  return.comm.matrix = FALSE
)

Arguments

d	data.frame, typically of SSURGO data
mu	name of the column containing the map unit ID (typically 'mukey')
co	name of the column containing the component ID (typically 'compname')
wt	name of the column containing the component weight percent (typically 'comppct_r')
method	one of either: community.matrix, or occurrence; see details
standardization	community matrix standardization method, passed to vegan::decostand
metric	community matrix dissimilarity metric, passed to vegan::vegdist
rm.orphans	logical, should map units with a single component be omitted? (typically yes)
similarity	logical, return a similarity matrix? (if FALSE, a distance matrix is returned)
return.comm.matrix	logical, return pseudo-community matrix? (if TRUE no adjacency matrix is created)

Value

a similarity matrix / adjacency matrix suitable for use with igraph functions or anything else that can accommodate a similarity matrix.

Author(s)

D.E. Beaudette

Examples

if (requireNamespace("igraph") && requireNamespace("vegan")) {
  # load sample data set
  data(amador)

  # convert into adjacency matrix
  m <- component.adj.matrix(amador)

  # plot network diagram, with Amador soil highlighted
  plotSoilRelationGraph(m, s = 'amador')
}

sharpshootR documentation built on Oct. 23, 2024, 1:06 a.m.