Soil & Tillage Research 124 (2012) 111118

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Soil & Tillage Research

journal homepage: www.elsevier.com/locate/still

Mapping soil compaction in 3D with depth functions

Fabio Veronesi *, Ron Corstanje, Thomas Mayr
National Soil Resources Institute, Craneld University, Craneld, Bedfordshire, MK43 0AL, United Kingdom

A R T I C L E I N F O

A B S T R A C T

Article history:
Received 20 May 2011
Received in revised form 19 March 2012
Accepted 14 May 2012

Soil compaction is a form of physical degradation that causes soil densication and distortion that can
lead to changes in three-dimensional soil structure variability. For this reason we proposed a method for
mapping compaction in three-dimensional space (3D), based on simple soil-specic depth functions.
This method, denoted the top down method, is based on a multi-step approach that starts with a
framework for selecting the best depth function, considers which shape best describes the soil-specic
variation by depth and ends with an interpolation of the coefcients of the function across the eld.
Subsequently, for each interpolated point this function is solved in order to estimate compaction in 3D
space. The top down method was evaluated using a cone resistance dataset, collected at the CULS (Czech
University of Life Sciences) farm in Lany. The accuracy of this method in predicting cone-index variation
in the 3D space was compared with the generally accepted 3D ordinary kriging interpolation, using
descriptive statistics of the predicted values and cross validation. We found that the top down method
better represented observed information and generally performs better than 3D kriging with a far
smaller sample size. The cross validation results suggest that ordinary kriging can predict cone-index
obtaining a value of root mean squared deviation (RMSD) of 0.54 at 10% soil proles excluded, and 0.57 at
50% exclusion; on the contrary the top down mapping method obtains an RMSD value of just 0.47, at 10%
exclusion, and 0.53, with 50% exclusion. We also found that the depth function method was more
representative of the observed variability in the predicted dataset, avoiding the smoothing ltering
effect typical of kriging interpolation. We then created a cone-index map of the CULS Lany eld with a
vertical resolution of 10 cm using the top down method. The map can be seen as a series of three videos
where it is possible to observe the cone-index pattern in three-dimensions.
2012 Elsevier B.V. All rights reserved.

Keywords:
Soil cone-index
Three dimensional digital soil mapping
Soil compaction
Kriging

1. Introduction
Soil compaction is a form of physical degradation that causes
soil densication and distortion decreasing soil porosity and
permeability. This obstructs the movement of air, water and
nutrients and restricts root penetration. In arable soils compaction
is often caused by repeated ploughing or heavy harvesting
machinery and it can occur at the surface or in subsurface
horizons. Ploughing can rectify topsoil compaction but once
subsoil compaction occurs it is extremely difcult and expensive to
alleviate. Compaction may also accumulate over time, creating
compacted soil layers that are almost impermeable and highly
resistant to root penetration (Jones and Montanarella, 2001), i.e. a
plough pan. This changes the three-dimensional soil structure
variability, and these modications can be high even in relatively
homogeneous soil (Carrara et al., 2007). Therefore we require a
rapid and accurate method for mapping soil compaction and the
changes in three-dimensional soil structure that it causes.

* Corresponding author.
E-mail address: f.veronesi@gmail.com (F. Veronesi).
0167-1987/$ see front matter 2012 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.still.2012.05.009

Measuring cone penetration resistance is an inexpensive way

to monitor and assess soil compaction and the resistance
measured by a penetrometer can be assumed as roughly
equivalent to the pressure encounter by roots (Carrara et al.,
2007). However, penetrometer measures have two main disadvantages: the rst is that the accuracy of the penetrometer
measure is dependent on the operator being able to push the rod at
a constant speed, and this is almost impossible. Therefore when
dealing with cone-index data we need to consider the difcult to
assess uncertainty related to each measured point. The second
disadvantage of the cone penetrometer measurements is related
to the fact that compaction occurs at any point throughout the
prole, and this can be highly variable both by depth and across
a eld. It is not feasible to make penetrometer measurements
at every location in a eld and usually not cost effective to do so
at sufcient locations to capture the vertical and horizontal
variability in soil compaction.
For this reason, penetrometer measures are interpolated using
geostatistics in order to produce high resolution 3D maps of soil
strength (Castrignano` et al., 2002). However, a 3D model can be
very difcult to present, having to rely on volumetric rendering or
slicing, and this can limit the effectiveness of the 3D soil map.

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The method described in this paper overcomes these two

limitations (i.e. point uncertainties and difcult interpretation of
3D models) and affords easier access to the important information
embedded in the 3D model. It is based on a framework for selecting
the most accurate soil specic depth function; the one that can
parsimoniously and effectively describe the average pattern of the
soil property variation with depth, decreasing the impact of the
measured point uncertainties. By tting this general function to
the soil proles and looking at its goodness of t, it is possible to
determine if a particular soil prole deviates signicantly from the
general behaviour of the soil. If a particular goodness of t value is
low, this means there are localized changes in soil proles that
need to be assessed more carefully. This way we obtain a
preliminary assessment of soil compaction before the creation
of the 3D model. After this step we use geostatistics to interpolate
the coefcients of the function in order to create a more detailed
map. We denote this method topdown mapping.
In this paper, we also compare the topdown mapping method
with the more generally accepted 3D geostatistical interpolation in
order to illustrate the advantages of introducing a depth function
prior to interpolation.
2. Materials and methods
2.1. Study site and sampling methods
The study site was the CULS (Czech University of Life Sciences)
Farm at Lany (21 ha) located in the Czech Republic, in central
Bohemia, near the city of Ruda (50.14 N, 13.86 E), 40 km W of
Prague (Fig. 1). The eld was in arable use and managed by
conventional ploughing techniques.
The soil type, according to the WRB classication, is a Haplic
Cambisol and according to the geological map at scale of 1:50,000,
the Lany Farm is located on an alluvial terrace with a rocky to
gravelly calcareous texture, which lies directly over a formation
composed primarily of basaltic breccias, conglomerates and
sandstones (Czech Geological Survey, 2004).
The Lany dataset consisted of cone-index data measured at 57
locations with a static penetrometer PM 10, designed and
constructed in the Czech University of Life Sciences (using a cone
with a vertex angle of 308 and a base area of 3.23 cm). The
instrument measured cone-index in intervals of 0.04 m to a depth
of 0.52 m; the value obtained is the average along the soil thickness

Table 1
Brief statistical description of the cone-index dataset used in the study.
Cone-index data (MPa)
Mean
Standard deviation
Median
Minimum value
Maximum value
Skewness
Kurtosis
Octile skew
Variance

1.95
0.73
1.88
0.82
4.2
0.49
0.65
0.55
0.54

sampled. Every sample was located at an average distance of 55 m

on a regular grid. The cone-index values measure the soil
resistance in terms of amount of pressure necessary to push a
metal rod with a terminal cone into the soil. The soil resistance is
related to soil density which characterizes the soil compaction. The
data were collected in spring 2005, at eld capacity, in two days
with homogeneous weather condition.
Two correction factors were applied to the dataset. We
disregarded the rst measure, from 0 to 0.04 m, because the
instrument is known to generate unreliable surface readings.
We also identied an observation at depth 0.44 m as an outlier.
Table 1 presents the basic summary statistics of the dataset. In
order to underline the major characteristics of the dataset, in
addition to normal summary statistics, we present the octile skew
(Brys et al., 2004) which takes into account the symmetry of the
rst and the seventh octile on the median (Lark and Bishop, 2007).
In Fig. 2a we present a box-plot of the distribution and the median
cone-index value of each measured layer from which can be
observed that, on average, this dataset presents a simple pattern
with depth, characterized by two distinct layers. The rst layer
begins at 0.08 m and ends at 0.28 m, with cone-index values
varying from 0.7 to a maximum of 17 MPa. The second layer has
values varying from 15 to 35 MPa, starting at 0.28 m to the
maximum sampling depth. This average pattern is not applicable
to every sample, as shown in Fig. 2b where we compare two very
different cone index soil proles (samples 25 and 54). Sample 25
has a pattern very similar to the average cone-index prole; while
sample 54 presents a very different shape, with a constant
increase in the cone-index value throughout the whole investigated depth.

Fig. 1. Location of the study area. The CULS Lany farm is in the Stredocesky Region, near the city of Ruda, about 40 km W of Prague.

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113

Fig. 2. (a) Plot cone-index/depth for the entire Lany dataset. In this graph is possible to appreciate the general pattern of the dataset. (b) This pattern is not recognizable in
every soil prole but the Eq. (1) is perfectly able to describe both proles.

2.2. Depth function

In order to nd the most accurate depth function with which to
describe the changes in soil property with depth, we developed a
specic framework, in which different groups of common
functions are evaluated for their general ability to describe
cone-index variation by depth. These generic groups contained
for instance, exponential functions and sets of polynomials.
At rst, we tted generic functions to the soil proles in order to
nd the category that best described the average soil specic
pattern. For example Hiederer (2009) suggested that a general
category of exponential equations can be considered in 3D soil
organic carbon mapping.
In this case, a 2nd order polynomial best described the observed
variation in the depth proles, with values of R2, coefcient of
multiple correlation, of 0.79 and root mean squared deviation
(RMSD, Schunn and Wallach, 2005) of 0.26. We then screened these
particular groups of polynomials to obtain the best and most
parsimonious function based on the same set of t statistics. In this
stage, the tting becomes more detailed and the exponents of each
variable are changed repeatedly in order to nd the polynomial that
best describes the observed pattern in the data. We then selected the
most parsimonious equation based on the assumption that a simple
curve can best describe the average soil pattern disregarding the
local uncertainties related to the penetrometer point measures.
The following polynomial was chosen as the soil specic depth
function:
yi; j b1  x6i; j b2  x3i; j b3

(1)

For every point of depth x(i,j), the value of the soil compaction,
y(i,j), can be calculated with a polynomial in which b1, b2 and b3 are
the coefcients of the equation, tted with a least squares
estimation.
In order to examine in detail the behaviour of the soil
property and the error associated with the regression,
we present a spatial study of the goodness of t measures
(e.g. RMSD) and of the residuals from the polynomial
regression.
2.3. Geostatistical interpolation
The top-down method relies on the tting of a polynomial
depth function to the cone-index data plus an interpolation of the
coefcients of the polynomial. We used an ordinary kriging
interpolation, with the variogram model tted using a residual
maximum likelihood (REML) estimator. We choose the REML
estimator because it was demonstrated by Kerry and Oliver
(2007) that prediction based on variogram models tted with the
REML estimator are generally more accurate and a sample size of
around 50 sites is adequate for kriging under these circumstances.
In order to demonstrate the accuracy of our method, we
compare it with the generally accepted 3D ordinary kriging, which
has already been used by Castrignano` et al. (2002) for mapping
cone-index data.
We refer to Deutsch and Journel (1998), Lark et al. (2006), Kerry
and Oliver (2007) and Webster and Oliver (2007) for a detailed
description of the two methods.

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2.4. Validation
The validation process involved a random subsampling of a
percentage of soil proles (10, 20, 30, 40 and 50% of the population).
We validate the mapping method by re-predicting the cone-index
values of the subsampled population, and by comparing the
observed value with the predicted one using common statistical
indexes, e.g. R2 and RMSD, repeating the process 500 times.
2.5. Software
The geostatistical analyses were undertaken with the statistical
programming language R (R Development Core Team, 2009) and
the package gstat (Pebesma, 2004). The three dimensional
visualization of the soil map was created using Golden Software
Voxler (Golden Software, 2008).
3. Results and discussion
3.1. Polynomial depth function
We developed the topdown mapping for describing the
horizontal and vertical variation of cone resistance, based on 3D
mapping with a simple soil-specic depth function. This method is
based on the assumption that penetrometer data are characterized
by uncertainties at each measured point due in part to the use of a
manually inserted instrument that is unlikely to be inserted into
the soil at a constant speed each time. For this reason our
hypothesis is that a simple depth function can optimally describe
the general cone resistance prole without being constrained by
these point uncertainties that would cause errors with more
complex functions. The topdown mapping is based on a
framework developed for determining the best site specic depth
function, from which we selected the polynomial in Eq. (1) as best
predictor. This function can describe the average pattern (Fig. 2a)
very accurately, because its shape effectively reproduces a pattern

Fig. 3. Scatterplot of observed/predicted values. On the X axis the observed values

excluded during the cross validation are represented; on the Y axis are represented
the values predicted by the proposed mapping method. The selected depth function
is able to predict the cone-index data with a high level of accuracy.

generated by two distinct soil layers; a relatively loose topsoil over

a more compacted subsoil. This is demonstrated by the goodness of
t analysis, presented in Fig. 3 in the form of an observed versus
predicted scatterplot, which shows high accuracy in predicting
cone-index along the prole (a mean R2 value of 0.84 and RMSD of
0.22). However, the average pattern described in Fig. 2a is the
combination between areas where the cone resistance increases
uniformly along the proles (Fig. 2b, sample 54) and areas in which
there is a rapid increase in cone resistance between 0.24 m and
0.32 m (Fig. 2b, sample 25), which may be explained by the
presence of a plough pan.
A polynomial depth function can effectively be used as a
diagnostic tool, as it can only describe a very limited set of
geometries and therefore, in proles where its predictive accuracy is
low, this would indicate a fundamental change in the pattern of soil
resistance. In this instance, this would suggest the presence of a
plough pan. In order to explore this concept, we created two spline
interpolated maps of Lany eld, showing the distribution of R2 and
RMSD values throughout the eld (Fig. 4a and b). In these maps the
largest proportion (>70%) of the area sampled is represented by
good t statistics (mean R2 of 0.88 and RMSD of 0.20). In these areas,
the function effectively describes the distribution of soil resistance
by depth. However, there are areas of the eld in which the
polynomial is not as accurate, coloured in darker shades of grey in
Fig. 4a and b, meaning that the soil resistance depth proles present
a different shape compared to the average pattern described by the
depth function. There are two reasons for this: the rst occurs where
the plough pan causes a peak in the cone-index value far greater than
that observed in the average soil pattern, and this causes the
polynomial to under-predict soil resistance. The second reason is
related to an increase in the data scattering in the lower layer. If this
scattering is too severe the polynomial fails in describing the local
soil compaction pattern.
We further explored the ability of the polynomial in describing
the cone-index spatial pattern by computing and interpolating the
values of the residuals for three depth layers (0.12, 0.32 and
0.44 m; Fig. 4c). From the residual values it is evident that the top
layer is the most homogeneous, with low values indicating a
general good performance of the polynomial in describing the
topsoil cone-index values. On the contrary, the subsoil presents
locally high absolute residuals which signify areas with cone-index
values that are different from the depth average. In the 0.32 m
layer the residuals values are mostly positive, meaning an above
average compaction consistent with the presence of a plough pan.
On the contrary, in the deeper layer the residuals are mostly
negative indicating a below average compaction that can be due to
a general decrease in soil compaction probably caused by a
restoration of natural compaction conditions. Using this uncertainty analysis it is possible to determine the amount and the
spatial distribution of areas affected by subsoil compaction, before
undertaking the full geostatistical analysis.
In order to compare the topdown mapping with 3D kriging we
created two 3D maps of the eld using both methods and then
compared using descriptive statistics and the goodness of t
statistics from cross validation. The observed variance of the
measured cone-index data is 0.54. The variances of the two
predicted datasets are 0.40 for the polynomial mapping method
(a reduction of 26%) and 0.33 for the 3D kriging prediction
(a reduction of 39%). This suggests the main advantage of the top
down mapping method lies in its ability to reproduce the variance
of the predicted population to a level comparable with the original
dataset, avoiding the smoothing typical of kriging (Deutsch and
Journel, 1998). The subsequent cross validation was based on
randomly excluding soil proles from the original dataset, and
then re-predicting their cone-index 500 times. The results are
presented in Fig. 5 and Table 2 and indicate that the top down

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115

Fig. 4. (a) and (b) Interpolated maps, with a spline algorithm, of the two goodness of t indexes: R squared and RMSD. The two colour scales are created in a way that light grey
reects areas of good performances and darker colours indicate areas of worst performance. (c) Map of the residuals for the Eq. (1). The colour scale is centre based, therefore
also in this case a darker colour reect a worse performance.

Table 2
Results of the cross validation.
3d Ordinary kriging

Polynomial mapping method

Exclusion percentage

10

20

30

40

50

10

20

30

40

50

Mean
Median
Standard deviation
Minimum
Maximum

0.54
0.53
0.10
0.32
0.81

0.54
0.54
0.07
0.36
0.77

0.55
0.56
0.05
0.41
0.70

0.56
0.56
0.05
0.44
0.70

0.57
0.57
0.04
0.47
0.68

0.47
0.46
0.10
0.28
0.99

0.48
0.47
0.09
0.32
0.84

0.49
0.48
0.07
0.34
0.84

0.52
0.48
0.32
0.36
6.18

0.53
0.49
0.45
0.38
9.14

Fig. 5. Results of the independent validation. The accuracy of the proposed mapping
method is higher than 3D kriging even when the percentage of exclusion reaches
50%, meaning that it can theoretically be used for mapping with a fraction of the
original dataset.

method has a higher accuracy than 3D ordinary kriging even when

the exclusion percentage is 50%. We nd that the topdown
mapping can achieve a higher mapping accuracy because it can
effectively reduce the smoothing associated with 3D geostatistics
interpolation, and it can be used where sample size is small. It is
also generally less complex to apply because it relies on
bidimensional interpolation which is more commonly used that
its 3D counterpart.
We then used three different visualization techniques with
which to present the results from the 3D mapping. We did so as
visualization of 3D information is complex and none of the
techniques available were satisfactory. First, horizontal slices
(Fig. 6) were considered, which are commonly used for presenting
soil maps. The advantage of this technique is that it is widely used
and very common and maps of sequential depth slices can be easily
compared. The disadvantages are that the depth slice selection is
subjective, and it is difcult from these maps to determine the
lateral or vertical relations between soil depth proles.
The second technique, based on 3D visualization (Fig. 7), uses
vertical slices and contours for the horizontal plane. The advantage
of this technique is that it effectively shows areas of higher

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Fig. 6. Results of the comparison. Three depth layers are presented: 0.1 m (surface), 0.3 m (approximate depth of the plough layer) and 0.5 m (maximum investigation
depth). On the left are depicted the results of the 3D kriging and on the right the results of the proposed mapping method.

compaction, which are highlighted by darker colours and by a

denser set of contours. The main disadvantage is that it is very
difcult to interpret because the user needs to keep track of the
orientation of the 3D image, which is difcult even for people
experienced in viewing 3D models.
The third visualization technique we considered subdivides the
3D map in slices along the three geometrical axes. This way we can
group the slices for each axis into a video animation that produces
a y-through experience that gives the user a more readable way
to visualize the 3D model. The disadvantage of this visualization
technique is that it requires a considerable effort in both the
production of slices (in this case we had to create 48 images for
each axis) and creating the animations.
The advantage of applying the topdown mapping method is
that it is possible the visualization of soil compaction pattern in the
3D domain, from the preliminary analysis. Therefore we can
identify areas of higher compaction and visualize them using a
limited number of slices, in order to assess their horizontal and
lateral extent, avoiding the necessity for complex visualization
techniques.
3.2. Soil interpretation
The risk of soil compaction depends on several factors: water
content, soil texture, soil organic matter content and land use
(Medvedev and Cybulko, 1995; Soane and van Ouwerkerk, 1995;

Busscher et al., 1997; Hamza and Anderson, 2005). At the CULS Lany
farm, the variation in the cone-index values, especially in the topsoil,
is predominantly caused by land use. The eld is covered by arable
crops and is managed by conventional ploughing technology. The
predominance of the land use over other factors is illustrated by the
relative homogeneity of the topsoil. There is a transition zone, at
around 30 cm, between the managed topsoil and the natural subsoil,
and this is observed as an increase in the cone resistance values.
However, this increase of the soil compaction is not always related to
the presence of a plough pan, in certain areas the increase is
smoother. This pattern could suggest the presence of an external
phenomenon that has modied the original soil pattern at that
depth, possibly a paleobed which would be compatible with the
alluvial deposits below the study eld.
Below 35 cm the soil pattern becomes more complex with areas
of high cone-index data and areas with low cone-index values
distributed without any recognizable pattern. In general, directly
below the plough layer, there is a decreasing tendency in the coneindex values but there are areas in which high values of cone-index
are maintained throughout the survey depth. Although the
homogeneity of the topsoil is certainly due to the Lany land
management, the factors that may cause the observed patterns in
the subsurface to be less easily identiable and compaction may be
derived from several factors. There are not enough textural and
moisture data to fully clarify which one is the cause of the depth
distribution of the cone-index data below the plough layer.

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117

Fig. 7. 3D maps of Lany eld. These maps are the results of the mapping procedure proposed in the text. They are created by mixing two kinds of 3D visualization, 2D slices and
contours. Each image is composed by ve slices on the XZ plane, spaced by 100 m, ve slices on the YZ plane, spaced by 100 m, and one contour slice, on the XY plane, at the
three depth layers indicated (0.07, 0.30 and 0.50 m).

4. Conclusions
We present a novel method, based on site specic depth
functions, to improve the accuracy of predicting cone resistance
variation by depth. With this technique we can decrease the
impact of the unknown uncertainties related to penetrometer
measurements. We also demonstrate with descriptive statistics
and cross validation that the proposed method is more accurate
than 3D kriging, and we suggest that its results are easier to
interpret.
This study presents an example of soil mapping with a limited
dataset and its successful application to 3D mapping. Although this
study was limited to a eld with particular soil properties, in

theory this approach could be applied in a larger landscape if a

general soil pattern is recognizable. If it is possible to identify a
general pattern and determine a simple depth function, then it is
also possible to map the eld with less analytical data.
Acknowledgements
This studentship was funded by the iSOIL project. iSOILInteractions between soil related sciences Linking geophysics,
soil science and digital soil mapping is a Collaborative Project
(grant agreement number 211386) co-funded by the Research DG
of the European Commission within the RTD activities of the FP7
Thematic Priority Environment.

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F. Veronesi et al. / Soil & Tillage Research 124 (2012) 111118

The authors are grateful to the Czech University of Life Sciences

team in Prague for the penetrometer sampling of Lany eld.
Appendix A. 3D animation
To visualize the soil compaction pattern in the Lany eld, we
created a 3D animation. Eq. (1) was solved for a regular grid of 6700
points starting from the coefcients predicted with the kriging. The
vertical resolution of the 3D grid is 1 cm, the horizontal is 1 m. We
performed a volumetric rendering with a natural neighbour
interpolator, on the 3D grid and the resultant volume was sliced
along X, Y, and Z. The result is a collection of slices every metre for
X, and Y directions and a slice every centimetre along Z.
All these images are presented in three animations, one for each
direction, in which the viewer could navigate through the ground
and appreciate the compaction pattern. In these animations the
blue and light blue colours characterize low compaction values.
The rapid change due to the plough layer is highlighted by the
green colour. The presence of the plough layer is particularly
evident in section along X and Y; the top soil layer presents a
general blue colour and a constant width. Below 35 cm, depth of
the plough layer, the complexity become easily appreciable
because of the presence of high compaction lenses, with colour
from orange to red.
Appendix B. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.still.2012.05.009.
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