`R/component.adj.matrix.R`

`component.adj.matrix.Rd`

Create an adjacency matrix from SSURGO component data

```
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
)
```

- 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)

a similarity matrix / adjacency matrix suitable for use with `igraph`

functions or anything else that can accommodate a *similarity* matrix.

```
if (requireNamespace("igraph")) {
# 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')
}
#> Loading required namespace: igraph
```