Replacement for `profile_compare()`

.

Performs a numerical comparison of soil profiles using named properties, based on a weighted, summed, depth-segment-aligned dissimilarity calculation.

Variability in soil depth can interfere significantly with the calculation of between-profile dissimilarity-- what is the numerical ``distance'' (or dissimilarity) between a slice of soil from profile A and the corresponding, but missing, slice from a shallower profile B? Gower's distance metric would yield a NULL distance, despite the fact that intuition suggests otherwise: shallower soils should be more dissimilar from deeper soils. For example, when a 25 cm deep profile is compared with a 50 cm deep profile, numerical distances are only accumulated for the first 25 cm of soil (distances from 26 - 50 cm are NULL). When summed, the total distance between these profiles will generally be less than the distance between two profiles of equal depth. Our algorithm has an option (setting replace_na=TRUE) to replace NULL distances with the maximum distance between any pair of profiles for the current depth slice. In this way, the numerical distance between a slice of soil and a corresponding slice of non-soil reflects the fact that these two materials should be treated very differently (i.e. maximum dissimilarity).

This alternative calculation of dissimilarities between soil and non-soil slices solves the problem of comparing shallow profiles with deeper profiles. However, it can result in a new problem: distances calculated between two shallow profiles will be erroneously inflated beyond the extent of either profile's depth. Our algorithm has an additional option (setting add_soil_flag=TRUE) that will preserve NULL distances between slices when both slices represent non-soil material. With this option enabled, shallow profiles will only accumulate mutual dissimilarity to the depth of the deeper profile.

Slices are classified as 'soil' down to the maximum depth to which at least one of variables used in the dissimilarity calculation is not NA. This will cause problems when profiles within a collection contain all NAs within the columns used to determine dissimilarity. An approach for identifying and removing these kind of profiles is presented in the examples section below.

A notice is issued if there are any NA values within the matrix used for distance calculations, as these values are optionally replaced by the max dissimilarity.

Our approach builds on the work of (Moore, 1972) and the previously mentioned depth-slicing algorithm.

- x
`SoilProfileColection`

object, should be pre-filtered to remove profiles with horizon depth logic, see`HzDepthLogicSubset`

- vars
character vector, names of horizon attributes to use in the classification

- fm
formula, formula as specified to

`dice()`

, not yet implemented- weights
numeric vector, same length as

`vars`

: variable importance weights, need not sum to 1- maxDepth
numeric, maximum depth of analysis

- k
numeric, weighting coefficient, see examples

- isColor,
logical: variables represent color, should be CIELAB coordinates (D65 illuminant), weights are ignored. Variables should be named

`L`

,`A`

,`B`

in specified in that order.- rescaleResult
logical, distance matrix is rescaled based on max(D)

- progress
logical, report progress

- verbose
logical, extra output messages

- returnDepthDistances
logical, return a list of distances by depth slice

`NCSP()`

will overwrite the `removed.profiles`

metadata from `x`

.

J.J Maynard, S.W. Salley, D.E. Beaudette, J.E Herrick. Numerical soil classification supports soil identification by citizen scientists using limited, simple soil observations. Soil Sci. Soc. Am. J. 2020; 84: 1675-1692. doi:10.1002/saj2.20119 .

D.E. Beaudette, P. Roudier, A.T. O'Geen, Algorithms for quantitative pedology: A toolkit for soil scientists, Computers & Geosciences, Volume 52, 2013, Pages 258-268, ISSN 0098-3004, doi:10.1016/j.cageo.2012.10.020 .

Moore, A.; Russell, J. & Ward, W. Numerical analysis of soils: A comparison of three soil profile models with field classification. Journal of Soil Science, 1972, 23, 194-209.