Computers and Electronics in Agriculture xxx (xxxx) xxx–xxx

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Computers and Electronics in Agriculture

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

Original papers

AgroDSS: A decision support system for agriculture and farming

⁎
Rok Rupnik, Matjaž Kukar, Petar Vračar, Domen Košir, Darko Pevec, Zoran Bosnić
University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, Slovenia

A R T I C LE I N FO A B S T R A C T

Keywords: Decision support systems, data analysis and data mining have become significant tools for improving business in
Decision support system professional world. The emerging technologies are making the precision agriculture omnipresent and allow
Agriculture potential for enriching it with computer-assisted decision support systems for farm management. In this paper
Farming we describe a novel system AgroDSS that bridges the gap between agricultural systems and state-of-the-art
2000 MSC: decision support methodology. The described system is intended for integration into the existing farm man-
68U35 agement information systems and provides a cloud-based decision support toolbox, allowing farmers to upload
68T05 their own data, utilize several data analysis methods and retrieve their outputs. The implemented tools include
predictive modeling with explanation, accuracy evaluation, time series clustering and decomposition, and
structural change detection. They can help users make predictions for simulated scenarios and better understand
the dependencies (interactions) within their domain. We apply the AgroDSS system on a case study of pest
population dynamics, illustrating the potential for its use.

1. Introduction
In mid 1990s, Heuvel (1996) wrote about precision agriculture – the
big information upgrade in agriculture that was yet to arise. In his work
he emphasized that the emerging technologies are driving the devel-
opment of agriculture, which will be able to evolve to a more efficient
level in terms of agricultural production and land stewardship. It seems
that today we are in the era of making precision agriculture omnipre-
sent, whilst trying to enrich it with computer-assisted Decision Support
Systems (DSS) for entire farm management (with the goal of optimizing
returns on inputs while preserving resources).
The majority of marketed state-of-the-art software products for
agriculture utilize various sensors to collect data, in contrast to history
that involved manual data input (Kaloxylos et al., 2012; Sørensen et al.,
2010). Although this results in large amounts of stored data, data is
most frequently analyzed only with basic statistical or visualization
methods. The latter neglects the potential for application of advanced
data analysis tools that stem from the fields of data mining. The reason
for this mostly lies in the fact that the development and deployment of
advanced data mining methods demand cutting-edge knowledge and
skills in understanding these methods.
In this paper we describe a novel system AgroDSS that bridges the
gap between agricultural systems and state-of-the-art decision support
methodology. The described system is intended to provide computer
decision support to farmers in an approachable manner. The system is
designed as a decision support toolbox, where farmers can upload their
own data of interest, utilize several offered artificial intelligence (data
mining and statistical) tools and retrieve their outputs. The output re-
sults are intended to provide users with automated decision support,
predictions for simulated scenarios, better understanding of the sub-
mitted data and explanation of the dependencies (interactions) within
the data.
As motivated by related work (Fountas et al., 2015a; Kaloxylos
et al., 2014; Sørensen et al., 2011), AgroDSS is implemented as a cloud-
based service, which enables various software products for agriculture
to facilitate decision support to users. As many other existing decision
support systems, we aim AgroDSS to be a tool that can improve business
value through savings, avoiding risks, better planning and taking better
advantage of resources. As AgroDSS can be used with different problem
domains, business benefits depend on each individual business case; we
conclude the paper by summarizing such a case study.
The paper is structured as follows. In Section 2 we provide a his-
torical overview of how the computers and decision support systems
have been used in agriculture and farming. In Section 3 we describe the
design, functionalities and the implementation of the novel AgroDSS
system. We proceed in Section 4 by providing a brief case study of pest
analysis in orchards and fields, which serves as a demonstrative proof of
concept. We conclude the paper in Section 5.

⁎
Corresponding author.
E-mail addresses: rok.rupnik@fri.uni-lj.si (R. Rupnik), matjaz.kukar@fri.uni-lj.si (M. Kukar), petar.vracar@fri.uni-lj.si (P. Vračar), domen.kosir@fri.uni-lj.si (D. Košir),
darko.pevec@fri.uni-lj.si (D. Pevec), zoran.bosnic@fri.uni-lj.si (Z. Bosnić).

https://doi.org/10.1016/j.compag.2018.04.001
Received 14 November 2017; Received in revised form 20 February 2018; Accepted 1 April 2018
0168-1699/ © 2018 Elsevier B.V. All rights reserved.

Please cite this article as: Rupnik, R., Computers and Electronics in Agriculture (2018), https://doi.org/10.1016/j.compag.2018.04.001
R. Rupnik et al.
2. Related work
Before the advent of precision agriculture, only a few works about
use of information technologies in farming or agriculture were pub-
lished. Through the time, use of decision support systems, data analysis,
and data mining have become more significant tools for improving
business in professional world. One of the earliest systems that provided
computer-assisted decision support was CropSyst (Stöckle et al., 2003).
Its development started in early 1990s and evolved into a suite of
programs that include a cropping simulator, a weather generator, GIS
(Geographic Information System) cooperator program, a watershed
model, and several miscellaneous utility programs. According to the
website1, the developed model simulates the soil water budget, soil-
plant nitrogen budget, crop canopy and root growth, dry matter pro-
duction, yield, residue production and decomposition, and erosion,
using several parameters, such as cultivar selection, crop rotation, ir-
rigation, nitrogen fertilization, tillage operations, and residue man-
agement. An important advantage of the contemporary systems is
availability in a cloud (Ampatzidis et al., 2016; Kaloxylos et al., 2014),
which can ensure greater availability of the systems to users and ap-
plications.
Crop simulations and predictions. Many such systems for simu-
lating crops through a myriad of tweakable variables were developed
and evaluated with different crops and climate conditions. In more
recent publications, Abedinpour et al. (2012) performed an evaluation
of AquaCrop model for maize crop in a semi-arid environment. This
model attempts to balance accuracy, simplicity and robustness by using
a relatively small number of explicit and mostly intuitive parameters
and input variables. These simulators can be successfully combined
with other models; for example, García-Vila and Fereres (2012) com-
bined AquaCrop with an economic model for the optimization of irri-
gation management at farm level. Irrigation management had become
very important so dedicated models have spurred. Bazzani (2005) de-
veloped a Decision Support System for Irrigation for short and long
term analyses of water, labor and machinery, considering different
types of soils, irrigation systems, water-yield functions and seasonality
trough multicriterial mathematical programming techniques; Paredes
et al. (2014) examined partitioning evapotranspiration, yield prediction
and economic returns of maize under various irrigation management
strategies. Today, soil moisture is analyzed with inferential frameworks
that combine data to infer moisture, precipitation, temperature and
canopy coverage variation (Ghosh et al., 2014). Giusti and Marsili-
Libelli (2015) proposed a fuzzy decision support system, intended to
improve the irrigation based on given crop and site characteristics. It
comprises an inference system that outputs the best irrigation action to
keep the soil moisture in the suitable bounds, resulting in significant
water savings.
In theory, the proposed models could be used with arbitrary crops,
though in practice, many specific simulators for specific crops have
been developed. For example, Mohanty et al. (2012) parameterized the
APSIM model (Keating et al., 2003) for soybean and wheat crop of
subtropical central India; Sepaskhah et al. (2013) developed a dynamic
yield and growth model for saffron under different irrigation regimes;
Dreassi et al. (2014) dealt with semicontinuous skewed spatial data of
grape wine production; Sun and Ren (2014) assessed crop yield and
optimize water scheduling for winter wheat and summer maize using
soil and water assessment tool. In order to cope with the vast variability
of nature and the uncertainties of agricultural production, the concept
of crop biometrics was defined as the scientific analysis of agricultural
observations confined to spaces of reduced dimensions and known
position with the purpose of building prediction models (Rovira-Más
and Sáiz-Rubio, 2013).
Dairy farms. Allore et al. (1995) made a data-driven decision
1
http://www.bsyse.wsu.edu/CS_Suite/CropSyst.
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Computers and Electronics in Agriculture xxx (xxxx) xxx–xxx
support system MAST to systematically summarize the data related to
mastitis; Kerr et al. (1999) developed a knowledge-based decision
support system for strategic planning on sub-tropical dairy farms. More
recently, Bryant et al. (2010) evaluated Farmax Dairy Pro that can
predict annual yields (per cow and per hectare) for milk, fat, protein
and milk solids. Baudracco et al. (2012) proposed e-Cow that predicts
herbage intake, milk yield and live weight change in dairy cows grazing
temperate pastures with and without supplementary feeding.
Other examples of DSS for farming. Perini and Susi (2004) fo-
cused on design issues faced during the development of a DSS to be used
by technicians of the advisory service performing pest management
according to an integrated production approach. Abdullah and Hussain
(2006) put decades worth of pest scouting recordings, agriculture and
metrological data into a novel Pilot Agriculture Extension Data Ware-
house and present some interesting findings through data mining using
an indigenous technique based on the crossing minimization paradigm.
Xu et al. (2008) proposed a systematic approach based on integrated
information systems for agricultural ecosystem management that ex-
tracts and integrates data about terrain, land use and planting. Sus-
tainable agriculture was discussed by Kurlavičius (2009), where they
proposed a DSS that predicts what kind of crops should be grown in
particular areas, what/how many animals should be kept and what/
how much of resources are required under the environmental and other
conditions. Antonopoulou et al. (2010) proposed a Web-based Decision
Support System to help farmers select the alternative crops and provide
the information about the cultivation period.
Cloud-based decision support services. Kaloxylos et al. (2012)
surveyed the key functionalities of Farm Management Information
Systems (FMIS) and possibilities for their future improvement. They
emphasized that farmers need the global market of services in the
cloud, which can collect joint intelligence that can be used to extend
their FMIS. Furthermore, the authors predict that the solutions/tools for
intelligence might in the future be located solely in the cloud, which
requires the intelligence to be distributed between the cloud and farms
to compensate for lack of a stable Internet link in fields and rural areas.
In their further work, Kaloxylos et al. (2014) presented a conceptual
implementation of a cloud-based FMIS for managing a greenhouse.
Farmers who evaluated the FMIS characterized the use of services in the
cloud as valuable due to possibility of selecting and changing a service
provider, availability of decision support services, and open and stan-
dardized interfaces of the cloud FMIS that can enable cooperation
among stakeholders.
Fountas et al. (2015a) have explored future perspectives of FMIS
and advocate that cloud computing will be one of the key drivers in
their future development. Nikkilä et al. (2010) and Tayyebi et al.
(2016) argue that FMIS for precision agriculture needs access to various
systems and propose a concept of multi-tier architecture where any
application can access FMIS data through web services exposed by
FMIS. Sørensen et al. (2011) explore the concept of external assisting
services, such as ones that can be implemented in a cloud, to facilitate
standardized data exchange formats, data semantics, and transforma-
tion of data into useful knowledge for decision making. Tan (2016)
brought to attention that the further development of precision agri-
culture requires advanced tools to process data and transform them to
practical decision actions. He developed a cloud-based decision support
system, which allows easier extensibility, integration of data from
various sources (in different formats and semantics) and centralized
control of field devices.
2.1. Decision support systems methods and approaches
In the related work, several different decision support models and
approaches, which are based on data mining, have been used. In the
following we summarize their most common occurrences in the litera-
ture:
R. Rupnik et al.
• Probabilistic and optimization models: For sow herding, Pla et al.
(2004) developed a decision support system based on an embedded
Markov model, while Pomar and Pomar (2005) developed a system
in Milord II for efficient early identification of sows having low
prolificacy performance in commercial pig farms. Scott et al. (2015)
proposed a method for selecting appropriate suppliers that considers
stakeholder requirements. They integrated their basic method,
called Analytic Hierarchy Process–Quality Function Deployment
(AHP–QFD), with constrained programming and validated it within
the bioenergy industry. Thomopoulos et al. (2015) proposed an
argumentation-based decision support system for agri-food chains
that aims to optimize the nutritional, sensorial, practical and hy-
gienic value of the food quality. Their system incorporates backward
logical reasoning, starting from the goal, utilizing knowledge elici-
tation from domain experts or scientific papers. Although the au-
thors conclude that the task of knowledge modeling cannot be au-
tomated, they emphasize the importance of argumentation and
modeling in decision support systems.
• Supervised learning models: It is worth mentioning that the well-
known data mining software WEKA (Witten et al., 2016) started as a
project, funded from 1993 by the New Zealand government, aimed
to create a data mining workbench for contributing also to the
agricultural industries (Hall et al., 2009). WEKA today features an
abundance of supervised learning algorithms, used by a wide re-
search community. For example, Ramesh and Ramar (2011) used
WEKA to be the first to evaluate data mining techniques for Tamil
Nadu (state of India) soil data sets. They compared the performance
of the decision trees, naive Bayes classifier and random forests and
achieved 100% classification accuracy with the latter two.
Today, many other implementation of classification and regression
algorithms have been applied in various application areas; we pro-
vide some typical examples below. Cortez et al. (2009) used the
support vector machines (SVM) to outperform neural networks and
multiple regression for predicting the human wine preferences
(quality of wine) from objective physicochemical analytical tests.
Their model revealed, which variables can be controlled during the
production, providing a direct insight into ways for improving wine
quality. Rumpf et al. (2010) tackled the problem for an early de-
tection of sugar beet diseases using the SVM. They achieved the
classification accuracy of up to 97% for differentiation of healthy vs.
diseased leaves and classification accuracy between 65% and 90%
(depending on the type and stage of the disease) for early detection
of diseases. Pradhan (2013) compared the prediction performance of
decision trees (DT), support vector machine and adaptive neuro-
fuzzy inference system (ANFIS) for landslide susceptibility problem
in Malaysia using aerial photographs. They built several models
from different input attribute sets and achieved good predictive
performance, especially with DT and ANFIS.
Irmak et al. (2006) applied the back-propagation neural network to
predict the spatial distribution of soybean yields and to understand
the causes of yield variability. The goal of Panda et al. (2010) was to
investigate the strength of key spectral vegetation indices for corn
crop yield prediction using neural network techniques. They showed
that the corn yield was best predicted (with accuracy of
83.50–96.04%) using models that used the means and standard
deviations of perpendicular vegetation index grid images. Karimi
et al. (2006) compared the performance of support vector machine
with artificial neural networks (ANN) for classification of hyper-
spectral images of corn fields in order to predict nitrogen application
and weed infestation rates. They achieved favorable results,
showing lower misclassification rates of SVM for that task than those
of ANN.
In the last decade, the advantages of the random forest classifier
have been emphasized, including its non-parametric nature, high
predictive ability, internal evaluation of attributes, robustness to
noise, and lack of proneness to overfitting. Several researches have
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shown its high predictive value: Oliveira et al. (2012) compared it
with the multiple regression on a fire occurrence in Mediterranean
Europe domain; Rodriguez-Galiano et al. (2012) evaluated its use
for land cover classification; Tatsumi et al. (2015) used it for crop
classification of homogeneous landscapes.
• Bayesian models: Wang et al. (2012) developed a Bayesian hier-
archical model that naturally combines information from multiple
monthly surveys measured on different temporal supports, including
field measurement surveys and two farmer interview surveys. Their
results indicate that the hierarchical model produces superior fore-
casts to both the panel of experts and the composite estimator of the
mean of a normal distribution, while providing an accurate measure
of uncertainty.
• Other classification models: The paper of Waheed et al. (2006)
investigates the potential of hyperspectral remote sensing data for
providing better crop management information for use in precision
farming. In the study, the ability of the classification and regression
trees (CART) decision tree algorithm were examined to classify
hyperspectral data of experimental corn plots into categories of
water stress, presence of weeds and nitrogen application rates. Li
et al. (2012) were modeling maize irrigation with WOFOST simu-
lator, they performed an additional analysis of uncertainty that re-
vealed new insight into the risks associated with individual deci-
sions. Du et al. (2013) presented a new algorithm for forecasting
demand for perishable farm products, based on the support vector
machine. To fit a Gamma model, to get small area estimates and to
evaluate their precision, Dreassi et al. (2014) used a hierarchical
Bayesian approach in their Small area estimation for semicontin-
uous skewed spatial data (an application to the grape wine pro-
duction in Tuscany).
• Time series analysis: Michel and Makowski (2013) compared the
performance of seven basic statistical models and the dynamic linear
model, for analyzing yield time series and prediction of yield trends.
They visualized yield increase rates obtained with a dynamic linear
model for wheat from 1960 to 2010.
• Genetic programming: Alhadidi et al. (2012) proposed and eval-
uated a mathematical model that describes the reported data on
crop pests to get an accurate prediction of production costs, food
safety, and the protection of the environment. Their proposed ap-
proach is based on genetic programming and is explicitly directed at
solving the symbolic regression of crop pest forecasting. Forecasting
agricultural output with an improved grey forecasting model based
on the genetic algorithm was performed by Ou (2012).
Rose et al. (2016) surveyed the available decision support tools in
the UK and discovered that 49% of farmers used some kind of decision
support tool to inform decisions. They determined that effectiveness of
decision support is influenced by fifteen following characteristics: per-
formance, ease of use, peer recommendation (encouragement of
knowledge exchange), trust, cost, matching to farmers’ existing habits,
relevance, targeting of advisers, user age compatibility, scale of busi-
ness, farming type, IT education, infrastructure (internet, devices,
workflows), compliance with market and legislation, and level of
marketing.
Based on the surveyed work we conclude that decision support
systems have been extensively studied for various aspects of agriculture
and farming. The related work shows an increasing demand for (1)
predictive modeling, (2) data understanding and (3) statistical data
analysis, which motivates us to propose a system that can provide a
simplified utilization of such algorithms. In regard to positive char-
acteristics of random forests (Oliveira et al., 2012; Rodriguez-Galiano
et al., 2012; Tatsumi et al., 2015), which include the model’s non-
parametric nature, high predictive ability, internal evaluation of attri-
butes, robustness to noise, and avoidance of overfitting, we decide to
implement it as a predictive model within AgroDSS. We intend to ad-
dress at least six factors of effectiveness, given by (Rose et al., 2016)
R. Rupnik et al.
(performance, ease of use, matching to farmers’ existing habits, re-
levance, farming type) that can be easily addressed technologically and
by offering non-domain-specific data mining algorithms. We present the
chosen data mining algorithms and the proposed system in the fol-
lowing sections.
3. Decision support system AgroDSS
In the recent years, farm management information systems (FMIS)
have evolved from simple farm recordkeeping into sophisticated and
complex systems to support all aspects of production management
(Fountas et al., 2015b). The purpose of modern FMIS is to manage
demands to reduce production costs, comply with agricultural stan-
dards, and maintain high product quality and safety by ensuring access
to timely information, elaborate estimation, simulation and decision
making tools. Decision support system that integrates all of the above is
therefore a crucial step in both day-to-day and strategic decision
making.
In this paper we describe a novel decision support system for agri-
culture and farming, called AgroDSS. The decision support aspect of the
proposed system is based on data mining approaches, which can extract
useful information from large volumes of data. Data mining uses ad-
vanced algorithms to analyze the data and identify trends, distributions
and find patterns that can be hard to see with the naked eye. The newly
acquired knowledge can help better understand the data, see how data
changes in time and help predict the future impact of different actions.
The modular architecture of AgroDSS allows easy (generic) integration
of API services into existing FMIS, and also exposes a simplified Web
user interface (UI) to the end-user (farmer). While the integration with
web services is intended as a primary use of AgroDSS, the Web UI only
represents an additional demonstration/evaluation tool. The main
production use of the AgroDSS will therefore originate from within
FMIS, where data is to be prepared and submitted for evaluation, and
results presented without unnecessary user interaction. The inter-
mediate purpose of the AgroDSS will be to model the data and evaluate
the produced models.
Although AgroDSS utilizes data mining algorithms, it is designed in
a way that is approachable also to non-experts in the field. While in-
tegration of API services into existing FMIS requires a programmer’s
knowledge (only during the integration), the farmers are the primary
users that should provide the domain knowledge prior to the integration,
i.e., define what the problem for the analysis is (e.g., prediction of a
certain phenomenon, what is a target prediction variable, change de-
tection, seasonality analysis etc.). After the integration, the use should
become routine, allowing farmers to run and understand the analyses
with no difficulty.
We approached planning, design and implementation of the
AgroDSS system by considering the well-known Cross-industry standard
process for data mining (CRISP-DM) (Chapman et al., 2000; Shearer,
2000), illustrated in Fig. 1. This standard encompasses good practices
for applying data mining techniques and defines the phases of data
Business Data
understanding understanding
Data
Deployment DATA
preparation
Modeling
Evaluation
Fig. 1. Phases of the cross-industry standard process for data mining (CRISP-
DM) that was the guideline for the development of the AgroDSS system.
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Computers and Electronics in Agriculture xxx (xxxx) xxx–xxx
mining process: business understanding, data understanding, data
preparation, modeling, evaluation and deployment. The CRISP-DM
process model therefore breaks down the life cycle of a data mining
project into the six phases, which all include a variety of tasks. The
relation of CRISP-DM phases to the AgroDSS workflow steps is depicted
in Fig. 2. The workflow steps (step 1 – dataset creation, optional step 2 –
dataset update, step 3 – quick data analysis, step 4 – training a pre-
dictive model, step 5 – model evaluation, and step 6 – predictive ana-
lysis) typically comprise one or more CRISP-DM phases. CRISP-DM
phases are related to AgroDSS workflow steps (Fig. 2) as follows:
1. Business (problem) understanding: focuses on understanding the
project objectives from business (user’s) perspective and trans-
forming it into a data mining problem (domain) definition. At the
end of the phase the project plan is produced. In AgroDSS, this phase
is a precondition for step 1 (users – farmers – should know what
their farming problem is).
2. Data understanding: starts with an initial raw data collection and
proceeds with activities such as getting familiar with data, dis-
covering first insights into the data and identifying possible data
quality problems. In AgroDSS, this phase is a precondition for step 1.
In order to utilize the AgroDSS Web user interface, the user (farmer)
should possess a reasonable amount of domain and technical
knowledge. He should be able to define the decision problem (e.g.,
how to improve cattle feeding in order to increase milk production),
identify relevant collected data (e.g., feed composition, daily milk
production), format and upload the data, and review the results.
However, in a real-life situation the AgroDSS services will be in-
tegrated into a FMIS that will handle the problem definition (if not
pre-defined) and all the data handling process.
3. Data preparation: covers all activities to construct the final data set
from the initial raw data including selection of data, data cleaning,
the construction of data, the integration of data and the data for-
matting. In AgroDSS, this phase corresponds to steps 1, 2 and 3
(creation of a dataset and partial uploads of data, as well as basic
data analysis – descriptive statistics). While the data preparation
step is mandatory and time-consuming for the demonstrational
AgroDSS Web interface users, this will be different in practice – the
data will be collected and preprocessed in FMIS, and after selecting
the required analysis, the data preparation phase will commence
automatically, followed by communication using the AgroDSS API
services.
4. Modeling: covers the creation of various data mining models. The
phase starts with the selection of data mining methods, proceeds
with the creation (training) of data mining models and finishes with
the assessment of the models. Some data mining methods have
specific requirements on the form of data and the step back to data
preparation phase is often necessary. In AgroDSS, this phase corre-
sponds to step 4 (depending of the problem type, users can select
appropriate data mining methods).
5. Evaluation: evaluates the data mining models created in the mod-
eling phase. The aim of the model evaluation is to confirm that the
models are of high enough quality to achieve the business objec-
tives. In AgroDSS, this phase corresponds to step 5 (depending of the
problem type, users can visualize evaluation reports for their data-
sets).
6. Deployment: comprises of activities to organize knowledge gained
through data mining models and present it in a way users can use it
within their decision making workflow. In AgroDSS, this phase
corresponds to step 6. The selected trained model is stored for future
re-use, and can be retrieved and utilized at any time. The storing of
the model is performed by serializing an R model object (R Core
Team, 2014), which is returned after the model’s generation, and
saving it as a string into the database.
We designed the AgroDSS system with the following main goals:
R. Rupnik et al.
CRISP-DM:
CRISP-DM:
1 - business understanding
2 - data understanding
3 - data preparation
2. APPEND data
to existing dataset
1. create a
START: new dataset
datasetready
de¿netKeproElem
FolleFttKedata IorproFessing
3. run data
ANALYSIS
dataanalysis
results
Fig. 2. Workflow within the AgroDSS System. The boldface text denotes the CRISP-DM steps and text in the rounded rectangles denotes the AgroDSS workflow steps.
The latter are: dataset creation (step 1), update (optional step 2), quick data analysis (step 3), training a predictive model (step 4), model evaluation (step 5) and
predictive analysis (step 6). Steps within the workflow relate to corresponding phases of the CRISP-DM model.
• We aimed to implement a flexible and easy-to-use system that can be
also used by non-experts from the data mining field.
• The data mining tools should work with data from various domains;
the system should therefore allow users to upload and process their
own data. Minimal requirements about the data format (tabular
form) should be defined.
• The implemented collection of data mining tools should be general
enough to be used with various problem domains. It should cover
analyses from diverse subfields of data mining, such as supervised
learning (predictive modeling), unsupervised learning (clustering),
and time series analysis.
• Users should receive numeric or visual feedback with the results of
their queries.
• The system should be online and easily accessible to users.
• The system’s tools should be accessible by other information systems
through an application programming interface (API).
The final architecture of the AgroDSS system is illustrated in Fig. 2.
In step 1, the data for the analysis needs to be uploaded (in CSV format,
target/dependent variable in the first column) to be made available for
the data mining algorithms. To do this, the users create and name a new
dataset. At any later time, data can be optionally appended to existing
uploaded datasets (step 2), which is useful if we are dealing with per-
iodic data collections (e.g. daily measurements). Afterwards, users can
either run any of the quick data analyses (step 3; clustering, structural
analysis and sequence decomposition) or train a predictive model (step
4) that is required for making predictions. Users can either evaluate the
accuracy of the predictive model on training or on independent test
data (step 5) or use model to make predictions (step 6) for new, yet
unseen data or for the simulated scenarios.
3.1. Decision support functionalities
Following the goals, described in the previous section, we im-
plemented the following data mining function within the AgroDSS
system:
1. Data upload and preprocessing. The function provides the farmers
to upload their data, which subsequently becomes stored on the
server. The uploaded data is required to be in tabular form, where
the rows represent individual observations (examples) and columns
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Computers and Electronics in Agriculture xxx (xxxx) xxx–xxx
prediFtive
CRISP-DM:
model 5 - evaluation
evaluation
5. EVALUATE a
predictive model
4. TRAIN a
predictive model
prediFtive CRISP-DM:
modelready 4 - modeling
6. compute
PREDICTIONS
prediFtive CRISP-DM:
analysisresults 6 - deployment
represent attributes (different descriptives of the current example).
Since the input data may contain missing values and many data
mining algorithms require a full data table, the preprocessing op-
tions allow automatic imputation of missing values. For imputation,
the k-nearest neighbors algorithm (with k = 10) was used, which
utilizes the most similar examples to deduce and fill-in the missing
values.
2. Predictive modeling with explanation.
(a) Predictive modeling function builds a data mining model from
a given dataset (training dataset) that was uploaded to the
server. The resulting data model can be afterwards used to make
predictions for examples in another dataset from the same
problem domain (testing dataset). To model the data, random
forest prediction model was used. Along with modeling the
training set, the model performance is also estimated using the
out-of-bag (OOB) error that is assessed internally as the random
forest is being constructed. Each tree in the random forest is
namely trained using a different bootstrap sample (leaving out
about one third of the examples) and its performance is un-
biasedly estimated on the left-out examples. The system auto-
matically selects the appropriate performance measure, de-
pending on the type of the target variable – classification
accuracy for classification problems (discrete target variable)
and the mean squared error for regression problems (continuous
target variable). Additionally, the random forest model also
outputs the importance of individual attributes (estimated by
the accuracy decrease given different attribute permutations
and by the Gini index decrease after a node split over all trees)
for predicting the outcome, which can be useful for post hoc
feature selection performed by the user in FMIS.
(b) Prediction computation function for computing predictions
for testing dataset or new examples.
(c) Explanation of the learned knowledge in the model that
computes contributions of examples’ attribute values and returns
its visual representation. The computed contributions represent
the explanation of the learned knowledge within the prediction
model (Štrumbelj et al., 2009; Štrumbelj and Kononenko, 2010).
The absolute size of a contribution value is an indicator of the
attribute’s influence on the final decision, while its sign signifies
whether the particular attribute value influenced the class
probability in a positive way (by raising the predicted
R. Rupnik et al.
probability of the class) or negative way (by lowering the pre-
dicted probability of the class). As such, they explain the im-
portance of different attributes and may reveal new knowledge
about the problem domain.
(d) Predictive accuracy analysis plot that shows the dependency
of the predictive error on the number of trees, returned from the
random forest prediction model.
3. Time series analysis:
(a) Time series clustering that is intended for discovering simila-
rities within a dataset and represent them in separate data
groups. To implement this function we used the Permutation
Distribution Clustering method (Brandmaier, 2015) that is tai-
lored to clustering time series. The clustering method finds si-
milar time series by observing differences between data per-
mutation distributions. The method is robust and suitable for
time series with changing distributions (i.e. containing concept
drift) and with changing lengths.
(b) Time series decomposition function decomposes a time series
into seasonal, trend and irregular components using moving
averages. The function is intended for detection of periodic as
well as extraordinary events in the time stream. The decom-
position was peformed using function decompose within statis-
tical package R (R Core Team, 2014).
(c) Structural change detection that is intended to detect abrupt
changes in dynamics of time series. Such function can be ben-
eficial in case of population or parameter modeling, where
alarms need to be raised in case of big data changes. For im-
plementation of this function we utilized the strucchange library
(Zeileis et al., 2003) in statistical package R (R Core Team,
2014).
3.2. System architecture
We implemented the data mining infrastructure using the WildFly
Application Server2, custom R server and PostgreSQL DB Server as a
data persistence layer. The system architecture (shown in Fig. 3) allows
use of the data mining services via a REST API. The core of data pro-
cessing and computation is implemented in R – a statistical software
package suited for data mining tasks (R Core Team, 2014). For the
purposes of development and service exploration we have also im-
plemented an HTML web interface. We used the following R libraries:
• RCurl: for connecting to external data sources,
• RPostgreSQL: for connecting to the PostgreSQL database,
• jsonlite: support for JSON data format,
• cluster: for data clustering,
• strucchange: for finding structural changes in time series,
• pdc: for clustering time series data,
• randomForest: for classification and regression using random forests.
The database provides storage for users’ data, requested tasks, and
their results. Task execution is performed asynchronously, guided with
task queuing and facilitated using the Wildfly application server (EJB
Message Driven Beans). When user requests a data analysis, only meta-
data (name of the dataset, analysis type and other parameters) are re-
trieved from the database and sent to the R data mining server. The R
server afterwards requests the actual dataset contents and runs the
analysis. The results are saved into the database and are available to be
presented to the user, who can retrieve them using a task’s unique ID.
The database also stores data from autonomous weather stations (in
real time), provided by one of the AgroIT project partners (see Section
4), and sample test benchmark datasets. The weather data can be used
to augment other data, if spatially proximate weather data is available.
2 4
http://wildfly.org/.
6
Computers and Electronics in Agriculture xxx (xxxx) xxx–xxx
The available test datasets include: iris (prediction of the Iris flower
species, Anderson (1935)), beavers (body temperature series of two
beavers, Reynolds (1994)) and chickwts (chicken weights by feed type,
McNeil (1977)).
The REST API includes an option to adjust the randomForest mod-
eling to specific use cases by providing alternative settings for default
values of parameters: ntree (the number of trees to grow), mtry
(number of randomly sampled variables at each split), and maxnodes
(maximum number of terminal nodes).
The services, implemented as Enterprise JavaBeans (EJB), can be
used through REST API3. Its main request/response interface is de-
scribed in Table 1, and the user interface of the developed system is
shown in Fig. 4.
4. Case study: Population dynamics of the pests in orchards and
fields
After the development of the system, a small case study was per-
formed on data that were obtained from one of the partners (EFOS
d.o.o., Slovenia) that collaborated within the EU-funded project AgroIT.
The goals of the AgroIT project were to implement a cloud platform for
integration of existing applications for farming, and to facilitate the
pilot use of those applications. As a part of the AgroIT, four pilot pro-
jects were initiated in four EU countries, including the TrapView4
platform that was implemented by EFOS. TrapView enables pest mon-
itoring in vineyards and orchards through pest traps. Pests are lured
into pest traps, where their photos are taken with a certain frequency
and transmitted to TrapView servers over mobile network for analysis
and pest recognition.
Our case study was performed on pests data, collected by TrapView.
The objective of the case study was to briefly demonstrate AgroDSS
functionalities, illustrate the system’s use, and provide examples of the
obtained results – thus, to serve as a proof-of-concept. The data includes
measurements on various locations in four European countries between
May 2014 and December 2015. Each measurement includes a descrip-
tion of the location (country, spatial coordinates and location type that
can be one of: field, forest, orchard or vineyard), a description of the
measuring device (model and device id), the timestamp of the mea-
surement, the type of measurement (automatic, manually reviewed),
the count of trapped pests, and the type of pest species. A sample of the
collected data is shown in Fig. 5. One of farmers using TrapView was
tackling the problems of predicting the pest population size, its dy-
namics and its potential anomalies (e.g. trap failure, maintenance
problems). To address these goals, we decided to perform time series
clustering for stream similarity detection (functionality 3a from Sec-
tion 3.1), time series decomposition (functionality 3b), and struc-
tural change detection (functionality 3c). We found that the re-
maining functionalities were not relevant for analysis in this problem
domain; some of their use is, however, illustrated in the screenshot of
the system in Fig. 4.
Changes in the population of pests in each single location represent
a time series, which we uploaded to the AgroDSS system and analyzed.
A visualization example of such time series (data stream) is shown in
Fig. 6. The data refer to the Plum fruit moth captured in an orchard in
Poland. Each point represents the maximum value of the measurements
from that day.
Performed time series clustering enabled us to perform stream si-
milarity analysis, as shown in Fig. 7. The clustering dendrogram (tree)
shows separation of all available data streams into several groups ac-
cording to their mutual similarity. By observing similarities one can
quickly deduce that they differ in the pest population dynamics. Two
sequences at the bottom (denoted with black lines) seem smoother than
3
The API is fully documented at http://agroit-dm.fri.uni-lj.si/docs/.
http://www.trapview.com/.
R. Rupnik et al. Computers and Electronics in Agriculture xxx (xxxx) xxx–xxx

PostgreSQL
database
server

HTTP API
Data mining
services

R data
mining server

Fig. 3. Architecture of the implemented AgroDSS system.

Table 1
Interface of the implemented REST API.
Task Request Parameters Response

get the list of existing datasets GET/datasets/ / JSON encoded array of datasets

get the content of an existing GET/datasets/name name – name of dataset JSON encoded response containing the datasets
dataset name, size and CSV data

save a dataset POST/datasets/ name – name of new dataset JSON encoded response with name, size and
create csv – content of new dataset status

append data PUT/datasets/ name – name of new dataset JSON encoded response with name, size and
append/ csv – content of new dataset status

run a data mining task POST/analysis/run/ name – name of new dataset JSON encoded response containing status and
task – type of analysis (one of: build_model, eval_model, clustering, results (key-values or images)
structanalysis, seqdecomposition)
task_params – optional list of task-dependent parameters

the above four sequences (denoted with grey lines). By further ana-
lyzing the results of clustering, it turned out that each group represents
different pest species – the four black sequences represent species Os-
trinia nubilalis and two black sequences represent the Codling moth
species. This example demonstrates how clustering tools can be used to
automatically detect similarities between independent data streams.
Afterwards, users can further utilize this acquired knowledge to de-
termine the factors that affect the detected data similarities, or to au-
tomatically detect the anomalies in the data. An example of the latter
would be a detected sudden difference between expectedly similar data
stream (measuring points), which could indicate a fault in measuring
devices or procedures.
Structural change detection enabled us to detect abrupt changes in
population dynamics. Fig. 8 illustrates points in time (dashed vertical
lines) where the underlying methodology detected such changes, while
the horizontal lines represent the average values of measurements on
individual segments. Such sudden and unexpected changes in the
structure of sequences can represent an argument for automatic raising
of alarms and notifying experts about the event that could alternatively
also indicate a malfunction of the measuring equipment. For the users
of the AgroDSS Web user interface the alarms basically mean just sig-
nificant structural changes in the time series. However, for a particular
problem, and within an appropriately configured FMIS with automatic
data preparation and evaluation, it will be possible to daily check for
significant anomalies and raise alarms in order to notify either the
farmer or the problem expert. In our specific case study of observing
pests population dynamics, the farmer could be notified of anomalies,
indicating an early need to replace the overfull sticky plate or the
pheromone bait. On the other hand, for some anomalies (such as
unseasonably early occurrence of specific pests) the domain expert (e.g.
from the company EFOS) could be informed as well, so that he could
raise the alarm for a wider area or nationwide.
Fig. 9 shows the decomposition of a measurement sequence into the
seasonal, trend and remainder (random) components. The trend com-
ponent shows the overall movement in the measurements and offers the
possibility of further analyzes (e.g. searching for causal relationships
between different factors and the observed trend within the pest po-
pulation). The seasonal component (in this particular case, the basic
cycle represents one week) provides insights into processes that drive
the pests population. Within our case study, the analysis allows detec-
tion of the increasing global trend of caught pest population over time,
as well as detection of the seasonal periodic cycles that correlate with
weekly cycles. The sum of the trend, seasonal and remainder compo-
nents equals the original data series. The bars on the right hand side of
the plot represent the same data range, allowing a relative comparison
of the magnitudes of each component. Relatively low magnitudes of the
seasonal component (denoted by a high vertical bar) suggest that the
weekly variability in the pest population is negligible.
The farmers and analysts from the AgroIT project team reported that
the use of AgroDSS brought a significant added value to TrapView
users. Although TrapView already contained its own decision support
module that is based on monitoring, it was not able to make predictions
for the future. AgroDSS supplemented the basic decision support with
predictive functionalities that enabled farmers to effectively plan
spraying according to the predicted population size of particular pest
species. For example, given the prediction that a particular pest will be
at the stage of deposition of larvae in three days at a particular location
of TrapView, a farmer is able to timely purchase and plan the use of a

7
R. Rupnik et al.
Fig. 4. User interface of the AgroDSS system. The user interaction displays an example of generated data explanation (top), model performance (middle) and test data
output (below).
spray that is dedicated exactly for that particular stage of larvae de-
position.
Additionally, the project analysts also calculated the financial out-
comes due to the use of AgroDSS functionalities. Within the analyses,
the data from the first two years of the AgroDSS use (2015 and 2016)
were compared to the average data of three years preceding the in-
tegration with AgroDSS (2012–2014). Table 2 displays the results for
three farms (denoted with A, B and C) that were able to provide reliable
8
Computers and Electronics in Agriculture xxx (xxxx) xxx–xxx
data from their ERP systems. The data show that the use of the AgroDSS
positively influenced two key factors that contribute to a better fi-
nancial outcome: (1) the increased crop quality, resulting in higher
gained price of crop, and (2) the decreased spraying costs, caused by a
lower number of needed sprayings. Note that although the cost of in-
secticide sprays slightly differed between farms and between years (the
difference was less than 1.5%), the number of yearly sprayings de-
creased from 6 or 7 to 4 or 5.
R. Rupnik et al. Computers and Electronics in Agriculture xxx (xxxx) xxx–xxx

Fig. 5. A sample of the data about orchard pest count that was used for the case study.
120
100
80
Number of Pests
60
40
20
0

201í08í1 201í0í14 201í10í14 201í11í1 201í12í1

Date
Fig. 6. An example of a time series expressing pest population in a single location.

Fig. 7. Time series clustering, which automatically detected groups of different pest species.

5. Conclusion AgroDSS that provides a cloud-based decision support toolbox, allowing

farmers to upload their own data, utilize several data analysis methods
The emerging technologies are making the precision agriculture and retrieve their outputs. The implemented tools include predictive
omnipresent and allow potential for enriching it with computer-assisted modeling with explanation, accuracy evaluation, time series clustering
decision support systems for farm management. We developed a system and decomposition, and structural change detection. Within the short

9
R. Rupnik et al. Computers and Electronics in Agriculture xxx (xxxx) xxx–xxx

20
Number of Pests
15
10
5

2015í06í04 2015í06í2 2015í0í16 2015í08í11 2015í10í04

Date
Fig. 8. Detection of structural changes in population dynamics (indicated by vertical lines).

Fig. 9. Decomposition of the measured data into

components. The decompositions allows better un-
25

derstanding of underlying patterns in a time series:

data

the trend component represents a long-term

15

change in the data, the seasonal component re-

presents a repetitive pattern with a fixed period,
and the remainder represents variations in the
5

data that remain unexplained after the other com-

ponents have been removed.
seasonal

00
í04
0
trend

20
10

0
remainder

í5
í15

5 10 15 20
time

Table 2
Data for three farms (denoted with A, B and C) for three years before using the AgroDSS (2012–2014) and first two years when the AgroDSS was used (2015 and
2016). The data reveals positive changes in two key factors (in boldface): crop price (reflected by crop quality) and spraying costs.
Average for 2012–2014 2015 2016

A B C A B C A B C

Crop per hectar [ton] 65,45 48,51 56,76 67,09 49,43 58,19 69,72 52,21 57,98
Number of hectars 8 15 24 8 15 24 8 15 24
Price earned for one tone of crop [€] 145 150 150 160 155 160 165 160 170
Crop revenue [€] 75.922 109.148 204.336 85.875 114.925 223.450 92.030 125.304 236.558
Cost for insecticide spraying [€] 1.960 3.150 5.040 1.400 2.100 4.200 1.120 2.100 4.020

10
R. Rupnik et al.
case study we outlined potential benefits of the implemented tools that
can enable knowledge extraction from the data and optimization of
business. While the AgroDSS Web user interface demonstrates the sys-
tem’s functionalities, the main use is provided by the REST API that
allows straightforward integration with existing FMIS and enables the
full use of AgroDSS services even for non-technical users.
The CRISP-DM process model, as described in full in the paper, is
not a practical solution for the majority of users, as the first three steps
(problem understanding, data understanding and data preparation)
require domain expert and data expert knowledge. These steps are to
remain firmly within the FMIS – a farmer will need to specify the
problem and data sources, the data will be prepared and submitted to
the AgroDSS service. AgroDSS therefore provides a tool to address the
steps in the second half of the CRISP-DM that can be automated:
modeling, evaluation, and the majority of deployment (by visually
presenting the learned knowledge). Once deployed, a model will easily
be utilized from the FMIS.
Within our further work we shall pursue the implementation of
additional functionalities within the AgroDSS system. The further de-
velopment will include (1) development of additional predictive models
(such as naive Bayes, decision trees and neural networks) and ensemble
learning (bagging), (2) possibility of model evaluation on independent
test sets (including computation of evaluation measures, such as: sen-
sitivity, specificity and F1-measure for classification; (relative) mean
squared error and (relative) mean absolute error for regression), and (3)
inclusion of feature selection methods (ReliefF, information gain, Gini
index). Although currently implemented random forests allows good
accuracy and robustness, we shall implement the additional predictive
models to offer additional tools that can improve either interpretability
(naive Bayes, decision trees) or predictive accuracy. Namely, the de-
veloping field of deep learning using neural networks allows automatic
construction of new features that can improve capabilities of predictive
modeling systems. Evaluation on independent test sets, additional
performance measures and feature selection methods shall allow users
to evaluate data either prior to learning or longitudinally. They shall
enable greater control of the built model’s quality and signal the pos-
sible need to repeat the learning process. Possibilities to implement
other data mining algorithms are also open – however, this demand
shall be driven by specific business requirements of users, who re-
present the crucial part of the AgroDSS development process.
Acknowledgments
The AgroDSS system has been developed within the AgroIT project,
which has been co-financed through the European union programme
CIP-ICT PSP.
The authors thank EFOS d.o.o., Slovenia, for providing their col-
lected data and collaborating within the case study.
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