NCSP  R Documentation 
Replacement for profile_compare()
.
Performs a numerical comparison of soil profiles using named properties, based on a weighted, summed, depthsegmentaligned dissimilarity calculation.
Variability in soil depth can interfere significantly with the calculation of betweenprofile 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 nonsoil reflects the fact that these two materials should be treated very differently (i.e. maximum dissimilarity).
This alternative calculation of dissimilarities between soil and nonsoil 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 nonsoil 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 depthslicing algorithm.
NCSP(
x,
vars,
fm = NULL,
weights = rep(1, times = length(vars)),
maxDepth = max(x),
k = 0,
isColor = FALSE,
rescaleResult = FALSE,
progress = TRUE,
verbose = TRUE,
returnDepthDistances = FALSE
)
x 

vars 
character vector, names of horizon attributes to use in the classification 
fm 
formula, formula as specified to 
weights 
numeric vector, same length as 
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 
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
.
Dylan E. Beaudette and Jon Maynard
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: 16751692. \Sexpr[results=rd]{tools:::Rd_expr_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 258268, ISSN 00983004, \Sexpr[results=rd]{tools:::Rd_expr_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, 194209.
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