aqp: evalGenHZ – R documentation

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aqp

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`

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

Author(s)

D.E. Beaudette