aqp (version 1.32)

evalGenHZ: Evaluate Generalized Horizon Labels

Description

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

Usage

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

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

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.

See Also

get.ml.hz