The spcosa-package implements algorithms for
These algorithms are based on the k-means algorithm (de Gruijter et al., 2006, Walvoort et al., 2010).
Spatial coverage sampling is known to be an efficient sampling method for model-based mapping (kriging). Random sampling from compact geographical strata is recommended for design-based estimation of spatial means, proportions, etc.
In this vignette, the usage of the package will be demonstrated by means of several examples.
The spocsa-package can be attached by means of
Loading required package: rJava
In addition, we will also attach the ggplot2-package for modifying plots:
Although the implemented optimisation algorithms are deterministic in
nature, they use a user-specified number (
examples below) of random initial configurations to reduce the risk of
ending up in an unfavourable local optimum. In order to be able to
reproduce the sampling patterns at a later stage, the pseudo random
number generator of R has to be initialised first:
The spcosa-package depends on the sp-package (Pebesma & Bivand, 2005) for storing spatial information, and the ggplot2-package (Wickham, 2009) for visualisation. A basic knowledge of the sp-package is highly recommended. Knowledge of the ggplot2-package is only needed for fine-tuning spcosa graphics. Consult the superb ggplot2-website for details and illustrative examples.
The basic idea is to distribute sampling points evenly over the study area by selecting these points in compact spatial strata (a.k.a. geostrata). Compact strata can be constructed by k-means clustering of the points making up a fine grid representing the study area of interest. Two k-means algorithms have been implemented in the spcosa-package: a transfer algorithm and a swopping algorithm (Walvoort et al, 2010). The transfer algorithm obtains compact clusters (strata) by transferring cells from one cluster to the other, whereas the swopping algorithm achieves this by swopping cells between clusters. The first algorithm results in compact clusters, whereas the second algorithm results in compact clusters of equal size. For reasons of efficiency, both algorithms have been implemented in the Java language and communicate with R (R Core Team, 2015) by means of the rJava-package (Urbanek, 2013).
In this section, the spcosa-package will be demonstrated by means of several examples.
First, a vector or raster representation of the study area has to be created that uses one of the spatial classes of the sp-package (Pebesma & Bivand, 2005). In this section, we simply create a grid programmatically.
To obtain a uniform distribution of sampling points over the study
area, the sampling points will be selected at the centroids of compact
spatial strata. Compact strata can be constructed by invoking the
In this example, the study area has been partitioned into 75 compact strata. The resulting stratification can be plotted by means of:
Each plot can be modified by adding
ggplot2-functions to the
spsample-method, an overloaded method from the
sp-package, can be used for selecting the centroid of
plot-method can be used to visualise the resulting
The sampling pattern can also be plotted on top of the stratification:
The resulting sampling locations can be extracted by means of a
simple type cast to class
s1 s2 1 79.971831 45.74648 2 13.703704 13.19753 3 11.338710 40.56452 4 26.808824 24.67647 5 4.090909 26.96104 6 25.298246 33.70175
Sometimes, samples from previous sampling campaigns are available. In
these situations, spatial infill sampling may be performed. This type of
spatial coverage sampling aims to distribute new sampling points evenly
over the study area, while taking the locations of existing sampling
points into account. Suppose a
data.frame is available
containing the coordinates of 50 existing sampling points:
s1 s2 1 45.27948 42.4586466 2 40.11544 7.1302025 3 10.18353 0.8628835 4 85.06315 25.0265617 5 86.31620 49.7829571 6 68.99990 36.4598513
Twenty-five new points can be assigned to sparsely sampled regions by means of:
Note that the total number of strata, and therefore the total number
of points, equals 50+25=75. In addition, also note that the
nTry argument has been set to 100. The algorithm will now
use 100 random starting configurations and keeps the best solution to
reduce the risk of ending up in an unfavourable local optimum.
Note that prior points and new points are represented by different symbols.
In this section, the global mean clay and organic matter contents of
the study area will be estimated by means of stratified simple random
sampling. We will use grid
grd (created in a previous
section) as a representation of the study area. The study area will be
partitioned into 25 compact strata:
spsample-method can be used to randomly sample two
sampling units per stratum:
Sampling points can be extracted by means of a type cast to class
s1 s2 2234 33.88272 22.85582 2236 35.53852 23.26313 4841 40.56035 49.25627 4732 32.31102 47.60208 999 98.98614 10.30268 986 85.60128 10.48244
Next, some field and laboratory work has to be done. Suppose the
resulting clay and SOM contents are stored in
my_data (note that in this example we use simulated
clay SOM 1 0.11155230 0.027001630 2 0.10683151 0.028900583 3 0.01279166 0.003675933 4 0.07658828 0.017279823 5 0.06358627 0.009849191 6 0.14557616 0.012373539
The spatial mean clay and soil organic matter contents can be estimated by (de Gruijter et al., 2006):
clay SOM 0.07339864 0.01884442
In estimating the spatial mean, differences in surface area of the
strata are taken into account. Note, that the spatial mean is estimated
for all columns in
my_data. The standard error can be
estimated in a similar way:
clay SOM 0.006511187 0.003650515
The spatial cumulative distribution function (SCDF) (see de Gruijter et al., 2006) can be estimated by means of
The SCDFs are returned as a list of matrices, i.e. one matrix for each property:
value cumFreq [1,] 0.01279166 0.0000 [2,] 0.01835631 0.0192 [3,] 0.01839286 0.0349 [4,] 0.02048009 0.0585 [5,] 0.02064662 0.0769 [6,] 0.02177574 0.0960
value cumFreq [1,] 0.0003909092 0.0000 [2,] 0.0004350313 0.0195 [3,] 0.0010540480 0.0386 [4,] 0.0015136903 0.0579 [5,] 0.0023285072 0.0772 [6,] 0.0024394096 0.1028
The SCDFs for clay and SOM are visualised below.
In this example, the aim is to estimate the global mean clay and
organic matter contents of a field. To reduce laboratory costs, the soil
aliquots collected at the sampling locations will be bulked into
composite samples. The study area is a field near the village of
Farmsum, in the North-East of the Netherlands. An ESRI shape file of
this field is available in the
maps directory of the
spcosa-package. It can be loaded by means the
st_read-function in the sf package
(Pebesma, 2018; Pebesma & Bivand, 2023):
Linking to GEOS 3.11.1, GDAL 3.6.3, PROJ 9.2.0; sf_use_s2() is TRUE
Reading layer `farmsum' from data source `/tmp/RtmpIg8k9r/Rinst59902673bfbe/spcosa/maps' using driver `ESRI Shapefile' Simple feature collection with 1 feature and 4 fields Geometry type: POLYGON Dimension: XY Bounding box: xmin: 259229.1 ymin: 587145.2 xmax: 259440 ymax: 587397.8 CRS: NA
First, the field will be stratified into, say, 20 compact strata of equal size. Strata of equal size are desirable to simplify fieldwork, i.e. equal supports of soil can be collected at the sampling locations (Brus et al., 1999, de Gruijter et al., 2006).
Next, two sampling units will be selected at random in each stratum. At least two sampling units per stratum are required to estimate the sampling variance of the estimated mean.
Sampling points can be extracted means of:
composite x1 x2 1 1 259387.4 587268.7 2 2 259404.4 587248.0 3 1 259262.0 587302.4 4 2 259250.6 587269.0 5 1 259414.7 587215.7 6 2 259411.2 587220.8
Note that an extra column has been added specifying the sampling
units to be bulked into each composite. A composite sample is formed by
bulking one aliquot (sampling unit) per stratum. Field work now results
in a composite sample of size two. These data will be stored in a
The spatial mean and its standard error can be estimated by means of:
clay SOM 10.05 5.05
clay SOM 0.1225 0.0225
If we do not want to bulk soil aliquots, the same stratification can be used to select a sample of 20 \(\times\) 2 sampling locations:
x1 x2 1 259368.8 587267.6 2 259389.6 587262.2 3 259261.1 587269.5 4 259249.3 587277.6 5 259403.0 587211.9 6 259377.9 587232.4
When the projection attribute of a map is set to EPSG:4326 (lon/lat), great circle distances will be used for stratification. Otherwise, Euclidean distances will be used. At field scale, the differences between these distance measures is rather small. However, at continental and global scales, the projection attribute should be set to EPSG:4326.
To illustrate the effect of stratification on smaller spatial scales, consider two (relatively coarse) regular grids covering the surface of the earth:
grd is identical to
except for projection attribute .
Both grids will be partitioned into 50 compact geographical strata:
grd seems to have more compact strata near the
geographic poles than
grd_crs. However, the contrary is
true. This becomes evident when both stratifications are projected on a
The left figure is based on
grd, and the right figure on
grd_crs. The strata of
grd_crs are clearly
more compact than those of
grd. In addition,
grd suffers from pronounced edge effects near the poles and
at 180 degrees longitude. The strata are discontinuous at this meridian,
i.e., two points on opposite sides of the meridian are treated
as very distant when squared Euclidean distances are used. The strata of
grd_crs, on the other hand, have been optimised on a sphere
by using squared great circle distances, and don’t suffer from edge
effects, i.e., the great circle distance between two nearby
points on opposite sides of this meridian is small.
Although the spcosa-package is about sampling from
compact strata, it can also be used for simple random sampling, by
nStrata = 1:
Reading layer `mijdrecht' from data source `/tmp/RtmpIg8k9r/Rinst59902673bfbe/spcosa/maps' using driver `ESRI Shapefile' Simple feature collection with 1 feature and 2 fields Geometry type: POLYGON Dimension: XY Bounding box: xmin: 115796.2 ymin: 463380.5 xmax: 121670.8 ymax: 471524.6 CRS: NA
In case of spatial coverage sampling, sampling the centroid of each cluster may become problematic in case of non-convex areas. A centroid may be situated well outside the area of interest. If this happens, the sampling point will be relocated to the nearest grid cell that is part of the target universe. This pragmatic solution usually gives reasonable results. However, in some extreme situations the solution may be less desirable. As an example, consider the ‘doughnut’-shaped field below.
Note that this problem does not arise in random sampling from compact geographical strata.
R version 4.2.3 (2023-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Arch Linux Matrix products: default BLAS: /usr/lib/libblas.so.3.11.0 LAPACK: /usr/lib/liblapack.so.3.11.0 locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=C  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8  LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  sf_1.0-12 sp_1.6-0 ggplot2_3.4.2 spcosa_0.4-2 rJava_1.0-6 loaded via a namespace (and not attached):  Rcpp_1.0.10 highr_0.10 bslib_0.4.2 compiler_4.2.3  pillar_1.9.0 jquerylib_0.1.4 class_7.3-21 tools_4.2.3  digest_0.6.31 jsonlite_1.8.4 evaluate_0.20 lifecycle_1.0.3  tibble_3.2.1 gtable_0.3.3 lattice_0.20-45 pkgconfig_2.0.3  rlang_1.1.0 DBI_1.1.3 cli_3.6.1 rgdal_1.6-5  yaml_2.3.7 xfun_0.38 fastmap_1.1.1 e1071_1.7-13  withr_2.5.0 dplyr_1.1.1 knitr_1.42 generics_0.1.3  vctrs_0.6.1 sass_0.4.5 classInt_0.4-9 grid_4.2.3  tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.4  rmarkdown_2.21 farver_2.1.1 magrittr_2.0.3 units_0.8-1  scales_1.2.1 htmltools_0.5.5 colorspace_2.1-0 labeling_0.4.2  KernSmooth_2.23-20 utf8_1.2.3 proxy_0.4-27 munsell_0.5.0  cachem_1.0.7
Brus, D.J., L. E. E. M. Spätjens, J.J. de Gruijter (1999).A sampling scheme for estimating the mean extractable phosphorus concentration of fields for environmental regulation. Geoderma 89: 129-148
de Gruijter, J., D. Brus, M. Bierkens & M. Knotters (2006). Sampling for Natural Resource Monitoring. Springer Berlin
Diggle, P.J. & Ribeiro Jr, P.J. Model Based Geostatistics Springer, New York, 2007
Pebesma, E.J. & R.S. Bivand, 2005. Classes and methods for spatial data in R. R News 5 (2), https://cran.r-project.org/doc/Rnews/Rnews_2005-2.pdf
Pebesma, E., 2018. Simple Features for R: Standardized Support for Spatial Vector Data. The R Journal 10 (1), 439-446, https://doi.org/10.32614/RJ-2018-009
Pebesma, E., & Bivand, R. (2023). Spatial Data Science: With Applications in R (1st ed.). Chapman and Hall/CRC. https://doi.org/10.1201/9780429459016
R Core Team (2015). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.r-project.org/.
Urbanek, S. (2013). rJava: Low-level R to Java interface. R package version 0.9-6. https://cran.r-project.org/package=rJava
Venables, W. N. & Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth Edition. Springer, New York. ISBN 0-387-95457-0
Walvoort, D. J. J., Brus, D. J., and de Gruijter, J. J. (2010) An R package for spatial coverage sampling and random sampling from compact geographical strata by k-means Computers & Geosciences 36: 1261-1267 Available online at https://dx.doi.org/10.1016/j.cageo.2010.04.005
Wickham, H (2009). ggplot2: elegant graphics for data analysis. Springer New York