Data-driven evaluation of generalized horizon labels using nMDS and silhouette width.

evalGenHZ(obj, genhz, vars, non.matching.code = "not-used",
stand = TRUE, trace = FALSE, metric = "euclidean")

Arguments

obj

a SoilProfileCollection object

genhz

name of horizon-level attribute containing generalized horizon labels

vars

character vector of horizon-level attributes to include in the evaluation

non.matching.code

code used to represent horizons not assigned a generalized horizon label

stand

standardize variables before computing distance matrix (default = TRUE), passed to daisy

trace

verbose output from passed to isoMDS, (default = FALSE)

metric

distance metric, passed to daisy

Details

Non-metric multidimensional scaling is performed via isoMDS. The input distance matrix is generated by daisy using (complete cases of) horizon-level attributes from obj as named in vars.

Silhouette widths are computed via silhouette. The input distance matrix is generated by daisy using (complete cases of) horizon-level attributes from obj as named in vars. Note that observations with genhz labels specified in non.matching.code are removed filtered before calculation of the distance matrix.

Value

a list is returned containing:

horizons

c('mds.1', 'mds.2', 'sil.width', 'neighbor')

stats

mean and standard deviation of vars, computed by generalized horizon label

dist

the distance matrix as passed to isoMDS

See also

get.ml.hz