R: Evaluate Generalized Horizon Labels

evalGenHZ {aqp}

R Documentation

Evaluate Generalized Horizon Labels

Description

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

Usage

evalGenHZ(
  obj,
  genhz = GHL(obj, required = TRUE),
  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, passed to `cluster::daisy()`
`trace`	verbose output from passed to `MASS::isoMDS()`
`metric`	distance metric, passed to `cluster::daisy()`

Details

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

Silhouette widths are computed via cluster::silhouette(). The input distance matrix is generated by cluster::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 vars, computed by generalized horizon label
dist: the distance matrix as passed to MASS::isoMDS()

Author(s)

D.E. Beaudette