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
- 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.