evalGenHZ: Evaluate Generalized Horizon Labels
In aqp: Algorithms for Quantitative Pedology

Description Usage Arguments Details Value Author(s) See Also

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

1 2	evalGenHZ(obj, genhz, vars, non.matching.code = "not-used", stand = TRUE, trace = FALSE, metric = "euclidean")

`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`

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.

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

D.E. Beaudette

get.ml.hz

aqp documentation built on May 2, 2019, 4:51 p.m.