PeerJ (Oct 2018)
In search of an optimum sampling algorithm for prediction of soil properties from infrared spectra
Abstract
Background The use of visible-near infrared (vis-NIR) spectroscopy for rapid soil characterisation has gained a lot of interest in recent times. Soil spectra absorbance from the visible-infrared range can be calibrated using regression models to predict a set of soil properties. The accuracy of these regression models relies heavily on the calibration set. The optimum sample size and the overall sample representativeness of the dataset could further improve the model performance. However, there is no guideline on which sampling method should be used under different size of datasets. Methods Here, we show different sampling algorithms performed differently under different data size and different regression models (Cubist regression tree and Partial Least Square Regression (PLSR)). We analysed the effect of three sampling algorithms: Kennard-Stone (KS), conditioned Latin Hypercube Sampling (cLHS) and k-means clustering (KM) against random sampling on the prediction of up to five different soil properties (sand, clay, carbon content, cation exchange capacity and pH) on three datasets. These datasets have different coverages: a European continental dataset (LUCAS, n = 5,639), a regional dataset from Australia (Geeves, n = 379), and a local dataset from New South Wales, Australia (Hillston, n = 384). Calibration sample sizes ranging from 50 to 3,000 were derived and tested for the continental dataset; and from 50 to 200 samples for the regional and local datasets. Results Overall, the PLSR gives a better prediction in comparison to the Cubist model for the prediction of various soil properties. It is also less prone to the choice of sampling algorithm. The KM algorithm is more representative in the larger dataset up to a certain calibration sample size. The KS algorithm appears to be more efficient (as compared to random sampling) in small datasets; however, the prediction performance varied a lot between soil properties. The cLHS sampling algorithm is the most robust sampling method for multiple soil properties regardless of the sample size. Discussion Our results suggested that the optimum calibration sample size relied on how much generalization the model had to create. The use of the sampling algorithm is beneficial for larger datasets than smaller datasets where only small improvements can be made. KM is suitable for large datasets, KS is efficient in small datasets but results can be variable, while cLHS is less affected by sample size.
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