b i o s y s t e m s e n g i n e e r i n g 1 6 2 ( 2 0 1 7 ) 5 7 e6 6

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Research Paper

Assimilation of canopy cover and biomass

measurements in the crop model AquaCrop

Raphael Linker*, Ilya Ioslovich

Faculty of Civil and Environmental Engineering, Technion, Haifa 32000, Israel

article info
Measurements indicative of crop development, such as leaf area index, canopy cover or
Article history: biomass are typically performed only a few times throughout the season at irregular time
Received 23 February 2017 intervals. Furthermore, due to the inherent spatial variability that exists in the field,
Received in revised form combining measurements taken at different locations in the field usually leads to large
21 July 2017 uncertainty around the mean value. These factors, together with the fact that crop-soil
Accepted 2 August 2017 models are strongly non-linear, render assimilation of measurements in crop-soil
models non-trivial. This work presents procedures for performing such data assimila-
tion, using the crop model AquaCrop as specific example. The procedures are based on
Keywords: Extended Kalman Filter, with some heuristic adjustments, and enable re-initialisation of
Crop modelling state variables and/or adjustments of selected parameters of the model. The uncertainties
Data assimilation of the measurements are taken into account explicitly in the proposed assimilation
Extended Kalman Filter scheme. The procedures were tested with data obtained from experiments conducted with
Potato potato in Denmark and cotton in Greece. In both cases the data available consisted of
Cotton canopy cover and biomass (average and standard deviation on 5e10 days), and a locally-
FIGARO calibrated AquaCrop model was used as starting point for the assimilation process. The
results demonstrate the soundness of the approach but also emphasise the inherent
limitations associated with data assimilation. In particular, assimilation of easy-to-obtain
canopy cover measurements did not always improve the predictions of biomass.
© 2017 IAgrE. Published by Elsevier Ltd. All rights reserved.

1. Introduction
There is an urgent need to increase agricultural production
while preserving water resources, especially in semi-arid and
arid regions. Mathematical models that describe the crop-soil-
atmosphere interactions are central to the investigation of
irrigation scenarios and the development of improved irriga-
tion strategies. A large number of such scientific models have
been developed and used to develop irrigation decision
support systems (DSS) (e.g. Amir & Fisher, 2000; Behera &
Panda, 2016; Epperson, Hook, & Mustafa, 1993; Ioslovich,
Borshchevsky, & Gutman, 2012; Jiang et al., 2016; Linker &
Ioslovich, 2014; Shani, Tsur, & Zemel, 2004). In particular,
the Food and Agriculture Organization (FAO) has developed
the crop water productivity simulation model AquaCrop (FAO,
2009; Steduto, Hsiao, Raes, & Ferengeset, 2009) as a farm-level
tool for simulating various irrigation scenarios. The main
characteristics of AquaCrop are its simplicity and robustness,

* Corresponding author.
E-mail address: linkerr@tx.technion.ac.il (R. Linker).
http://dx.doi.org/10.1016/j.biosystemseng.2017.08.003
1537-5110/© 2017 IAgrE. Published by Elsevier Ltd. All rights reserved.
58 b i o s y s t e m s e n g i n e e r i n g 1 6 2 ( 2 0 1 7 ) 5 7 e6 6
together with a reasonable accuracy which has been estab-
lished by a number of studies with various crops and at
various locations (see https://www.zotero.org/groups/
aquacrop_publications for a complete list of publications
involving the AquaCrop model). An executable version of this
model can be downloaded freely from the FAO website (http://
www.fao.org/nr/water/aquacrop.html). Although AquaCrop
has been successfully calibrated for a large number of crops
and locations, the question remains as how to improve model
predictions by using measurements performed during the
season.
Numerous studies on data assimilation have been con-
ducted with various crop/soil models, most of them focussing
on assimilation of measurements obtained via remote sensing
(e.g. Aubert, Loumagne, & Oudin, 2003; Dente, Satalino,
Mattia, & Rinaldi, 2008; de Wit and van Diepen, 2007; Gue
rif
& Duke, 2000; Ines, Das, Hansen, & Njoku, 2013; Launay &
Guerif, 2005; Olioso et al., 2005; Prevot et al., 2003;
Vazifedoust, van Dam, Bastiaanssen & Feddes, 2009). Some
of these studies considered only “static” data assimilation, i.e.
re-calibration of some model parameters (or initial conditions)
using all the data available. For instance, Gue
rif and Duke
(2000) and later Launay and Guerif (2005) developed proced-
ures for assimilating remote sensing data into the SUCROS
model coupled with the radiative transfer model SAIL. Four
parameters chosen a priori were re-calibrated using least
square optimisation. A similar approach was considered by
Prevot et al. (2003) who used remote sensing data for cali-
brating five parameters of the STICS wheat model. More
recently, Dente et al. (2008) reported assimilation of leaf area
index (LAI) derived from remote sensing into the CERES wheat
model. Three of the model's parameters were adjusted in
order to minimise a functional that combined deviations be-
tween observed and estimated LAIs and the estimated and
nominal values of the parameters, taking into account the
uncertainties associated with the measured LAIs. More com-
plex data assimilation methods based on Kalman filter, and its
extensions Extended Kalman Filter and Ensemble Kalman
Filter, have also been developed. Vazifedoust et al. (2009)
presented assimilation of satellite data into agro-
hydrological models. After converting the satellite data into
leaf area index and relative evapotranspiration using a land
surface energy algorithm, assimilation into the distributed
agro-hydrological model was done with a constant-gain Kal-
man filter. Ines et al. (2013) used an Ensemble Kalman Filter to
assimilate remote sensing data in the modified DSSAT-CSM-
Maize model. Overall, regardless of the data assimilation
technique implemented, the majority of these studies
concluded that remote sensing provides useful measure-
ments which can be used to improve yield predictions.
Despite their increasing popularity, remote sensing mea-
surements have some limitations in terms of temporal and
spatial resolution. On the other hand, leaf area index, or
canopy cover, can easily be estimated from downward-
looking digital colour images which can be acquired by
farmers with minimal training (e.g Weiss, Baret, Smith,
Jonckheere, & Coppin, 2004 (software available at https://
www6.paca.inra.fr/can-eye/Download), Liu & Pattey, 2010,
Liu, Pattey, & Admiral, 2013 (software available at http://
www.flintbox.com/public/project/5470/)).
This work presents a general framework and procedures
for performing data assimilation in crop-soil models, using
the crop model AquaCrop as specific example. The procedures
are based on Extended Kalman Filter, with some heuristic
adjustments, and enable re-initialisation of state variables
and/or adjustments of selected parameters of the model. The
uncertainties of the measurements are taken into account
explicitly in the proposed assimilation scheme. The proced-
ures were tested using canopy cover and biomass data ob-
tained from experiments conducted with potato in Denmark
and cotton in Greece. In both cases a locally-calibrated
AquaCrop model was used as starting point for the assimila-
tion process.
2. Materials and methods
2.1. Experimental data
Two datasets were used to evaluate the performance of the
proposed procedures. In both cases the measurements con-
sisted of canopy cover and biomass at various time
throughout the season. Individual measurements were not
available but only averages and standard deviations (of an
unknown number of measurements) were available, so that it
was not possible to calculate the cross-variance matrices even
when the canopy cover and biomass measurements were
performed on the same day. At both locations an AquaCrop
model calibrated using data from similar experiments con-
ducted in previous years was used as starting point for the
data assimilation reported below. Details about the calibration
of the AquaCrop models can be found in Battilani et al. (2016,
pages 22e24 and 45e57).
2.1.1. Dataset 1: Potato in Denmark
The experimental data consisted of measurements performed
in parallel on four irrigation treatments conducted at Aarhus
University-Jyndevad research station in 2014. Details about
the soil, planting pattern and drip irrigation system have been
given by Linker, Ioslovich, Sylaios, Plauborg, and Battilani
(2016) and Zhou, Andersen, and Plauborg (2016). The irriga-
tion treatments consisted of “full irrigation” in which irriga-
tion was applied every two days to replenish soil water to 90%
of field capacity (treatment If in Zhou et al. (2016)); “deficit
irrigation” in which crop received 80% of the amount of water
given to If in the tuber initiation stage and 60% of If during the
tuber bulking stage (treatment Id in Zhou et al. (2016)); “custom
irrigation” (treatment IFigaroN3 in Battilani et al. (2016), pages
22e24); “no irrigation” (treatment I0 in Zhou et al. (2016)). The
irrigation schedules are given in Table 1. Canopy cover (CC)
and dry matter biomass were measured every nine and five
days, respectively, simultaneously for all treatments. Canopy
cover was estimated from digital images taken 1.5 m above
the canopy. The CC estimates were obtained by calculating
the excess greenness index image (Chen, Zhang, Su, & Guo,
2010) and applying thresholding to create a binary image in
which white pixels corresponded to canopy. The threshold
value (25) was determined by trial-and-error and visual in-
spection of several images. Biomass was determined using
eight plants, which were dried for 24 h at 80
C in a forced
 b i o s y s t e m s e n g i n e e r i n g 1 6 2 ( 2 0 1 7 ) 5 7 e6 6 59

days. Additional information about the experiment and the

Table 1 e Irrigation schedules of irrigated potato.
measurement procedures have been given by Tsakmakis et al.
Day after Amount (mm) (2017) and Battilani et al. (2016, pages 41e51).
sowing
Full irrigation Custom irrigation
treatment (If) treatment (IFigaroN3) 2.2. Assimilation procedure
48 3 3
51 5 1 The assimilation procedure was designed according to the
53 3 3 Extended Kalman Filter (EKF) methodology with some heu-
55 6 e ristic simplifications. The EKF procedure is as follows (e.g.,
57 3 3
Aubert et al., 2003). The observation vector zk and state vector
62 12 5
xk at time k are connected by the equation
64 3 3
68 11 e
zk ¼ hðxk Þ (1)
69 e 11
71 9 which can be linearised using the matrix H. The errors of the
73 e 4 measurements are represented by the measurement error
74 4 e
covariance matrix Rk. The covariance matrix of the errors in
99 2 5
state variables is denoted as Pk. If Pk is known, then the gain
101 8 8
103 4 10 matrix Kk can be calculated according to
105 6 12
1
Kk ¼ Pk HTk Hk Pk HTk þ Rk (2)
convection oven. Potato tubers were harvested mechanically The a posteriori state vector x~k is then equal to a priori state
and yield was determined after drying the samples at 80
C. vector xk plus the difference between the observation and
state vectors multiplied by the gain matrix Kk:
2.1.2. Dataset 2: Cotton in Greece
The experimental data consisted of canopy cover and biomass x~k ¼ xk þ Kk ðzk  hðxk ÞÞ (3)
measurements performed in two plots during the 2015 sea- Note that for canopy cover and biomass the matrix H is a
son. The experimental site, located in Xanthi coastal plain in unity matrix of size 2  2. The matrix Pk (which in the present
Northern Greece, has been described by Tsakmakis et al. case is diagonal) is not known, and we estimate its elements
(2017). The plots used in the present study were labelled as the “unexplained dispersion”, which is the difference be-
Subplot 1 and 2 by Tsakmakis et al. (2017). The irrigation tween the square of the model residuals and the dispersion of
treatment was the same in the two plots and is given in the measurements. The model residual is defined as the dif-
Table 2. Canopy cover and dry matter biomass were measured ference between the measured and predicted values, denoted
every 10 days, simultaneously in both plots. Canopy cover was as Ok and Mk, respectively. The dispersion of the measure-
determined using pictures taken with a mobile phone at a ments is determined as the square of standard deviation of
height of 2 m. In each plot, the pictures were taken at fixed the measurements, sk. In order to calculate Pk we take into
locations chosen at the beginning of the season. Three pic- account only the residuals (Mk  Ok) that exceeds the standard
tures were taken at each location and GIMP software was used error of measurements, sk. Accordingly, the matrix Pk is
to estimate CC. Biomass was determined by collecting two calculated as
plants close to the location of the CC measurements. Dry
  2 
weight was determined after drying the plants at 65
C for two
Pk ¼ max 0; ðMk  Ok Þ2  sk (4)

This is similar to how Gutman and Velger (1990) [eq. 12]

Table 2 e Irrigation schedule of cotton plots. suggest updating the values of P when their piece-wise linear
Day Amount (mm) process changed its character. However, presently we do not
2 32 use propagation of the matrix P along the process because of
11 26 its highly nonlinear character, but rather recalculate the value
55 27 of Pat each new time of measurement. In our opinion the
68 48 propagation process without assimilation of the new mea-
75 17
surements would only increase the uncertainty related to the
81 30
linearisation of the model dynamics and to the unknown
86 7
88 12 initial data of the model errors.
92 18
95 12 2.3. Model recalibration procedure
97 8
100 6 The procedure described in Section 2.2 can also be applied to
102 5
adjust model parameters rather than state variables. In this
109 13
case the model parameters are considered as state variables
111 12
115 5 that do not change dynamically but which can be adjusted
117 25 using the Kalman gain whenever measurements are available.
60 b i o s y s t e m s e n g i n e e r i n g 1 6 2 ( 2 0 1 7 ) 5 7 e6 6
Such an approach has been used for instance by Speetjens,
Stigter, and van Straten (2009) in a work related to green-
house climate modelling. Three parameters of AquaCrop
related to canopy development were selected for testing this
approach: CGC, CCX and CDC. CGC is the canopy growth co-
efficient (relevant to early growth stage), CCX is the maximum
canopy cover fraction, and CDC is the daily decrement of
canopy cover toward the end of the season (for more detailed
information about these parameters, see AquaCrop docu-
mentation available at http://www.fao.org/nr/water/
aquacrop.html). Since all three parameters are related to
canopy cover and not biomass, only the canopy cover mea-
surements were used when testing this procedure. The com-
ponents of the partial derivatives matrix Hk were calculated
numerically at each instance of canopy cover measurement.
The (unknown) diagonal components of the matrix Pk were
calculated from the assumption that the corresponding
standard deviation of each of the chosen parameters is equal
to 20% of the current value of corresponding parameter. To
prevent extreme variations of the parameter values, the in-
crease or decrease of the value of each parameter at each
adjustment was limited to 5%.
2.4. Performance indices
The performance of the assimilation process was quantified
via four indices:
 Normalised Root Mean Square Error
vffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
u
1u XðMk  Ok Þ2
NRMSE ¼ t
M k
N custom procedures for reading and overwriting the entries cor-
where M denotes the mean value of the measurements, and N
is the number of days on which measurements are available.
Good agreement between model and measurements corre-
sponds to low values of this index.
 Weighted Least Squares
XðMk  Ok Þ2
WLS ¼
s2k
k DER ¼ average
In the weighted least squares, the weights of the squared
residuals are inversely proportional to the corresponding
variances: measurements with low variance are given higher
weights and measurements with higher variance are given
lower weights. Good agreement between model and mea-
surements correspond to low values of this index.
 Index of Agreement
P 2
k ðMk  Ok Þ
d1 ¼ 1  P
2
k Mk  M þ Ok  M
This index developed by Willmott (1981) is a standardised
measure of the degree of model prediction error. For good
agreement this index must be close to one. This index is
considered to be overly sensitive to extreme values due to the
squared differences.
 Robust Index of Agreement
P  
0; ðMk  Ok Þ2  s2k
k max
d2 ¼ 1  P
2 (8)
k Mk  M þ Ok  M
This index penalises only modelling errors which exceed
the standard deviation of the corresponding measurements.
We propose this modification of the index of agreement d1 in
order to estimate how far beyond the margins defined by the
standard deviations of the measurements is the model tra-
jectory. This so-called Robust Index of Agreement is always
larger than d1 and should be close to one when the model fits
well to the measurements.
2.5. AquaCrop implementation
Figure 1 shows the flowchart of the implementation of the
procedures detailed in Sections 2.2 and 2.3. This imple-
mentation was performed in Matlab 2016a using custom
functions that read/wrote the appropriate text files and called
the EXE AquaCrop file (plug-in Version 5.0).
2.5.1. Assimilation procedure
One of the features included in AquaCrop Version 5.0 is the
ability to perform “Hot Starts”: When a simulation ends within
the growing cycle, all the results are stored in a temporary file
(<AquaCropRootFolder>ySIMULyHotStartData.SIM). If the
first day of the subsequent run corresponds to the next day of the
growing cycle, AquaCrop recognises this situation as a ‘hot start’
and loads the saved results as initial conditions for the next run.
Although this file is currently undocumented, Prof. Raes kindly
provided us with the format of this file, which enabled us to write
(5)
responding to the state variables “canopy cover” and “biomass”.
2.5.2. Model recalibration procedure
As mentioned in Section 2.3, adjustment of the values of the
parameters required numerical calculation of the partial de-
rivatives matrix Hk. Each partial derivative was approximated
via the average of the change observed for a one-day step after
changing the parameter value by ±10%:
(6)  
CCþ  CC0 CC  CC0
;
D D
where DER denotes the approximation of the derivative, CC0
denotes the canopy cover value with the nominal parameter,
and CCþ and CC denote the canopy cover values after
increasing and decreasing the parameter by D%. The changes in
the parameter values were implemented via a custom procedure
which overwrote the corresponding entries in the CRO file con-
taining the crop parameter values. Note that since the runs
performed for these calculations affected the Hot Start file Hot-
StartData.SIM, an unaltered version of this file was saved before
(7) starting the calculations and restored after their completion.
3. Results and discussion
Two types of analyses were conducted. In the first, only data
assimilation was performed, i.e. the parameters of the
b i o s y s t e m s e n g i n e e r i n g 1 6 2 ( 2 0 1 7 ) 5 7 e6 6 61

Fig. 1 e Flowchart of the procedure.

62 b i o s y s t e m s e n g i n e e r i n g 1 6 2 ( 2 0 1 7 ) 5 7 e6 6

AquaCrop model were not updated, and the measurements

0.979
0.990
0.982
0.988

0.999
1.000
1.000
0.999
were used only to reset the state variables as described in

d2
Section 2.2. In the second analysis, both data assimilation

Canopy cover and biomass

(state variables reset) and model recalibration (parameter

0.926
0.927
0.916
0.933

0.994
0.997
0.999
0.995
adjustments, Section 2.3) were performed.

d1
Three scenarios were evaluated:

39.389

12.054
15.376
15.376
- Only canopy cover measurements used

WLS

1.792
0.770
9.670
9.110
- Only biomass measurements used (data assimilation only)
- Both canopy cover and biomass measurements used

NRMSE

0.141

0.134

0.070
0.039
0.103
0.149

0.167

0.106
Simulations with the nominal (locally calibrated) AquaCrop
models, without any data assimilation, were used as reference.

3.1. Results for potato

0.979
0.965
0.996
0.998

1.000
1.000
1.000
0.997
d2
3.1.1. Data assimilation
Typical results are shown graphically in Fig. 2. For this specific

0.924
0.860
0.926
0.946

0.995
0.991
0.997
0.993
d1
treatment, assimilation of the canopy cover (CC) measure-

Biomass
ments (red dashed line) led to two major adjustments, on days
43 and 56. It should be noticed that while the first adjustment

12.054
42.118
18.862
18.862
WLS

3.720
8.208
1.271
12.34
led to better prediction of CC on day 49, it led to large over-
estimation on day 56, which was only partially corrected by
the second adjustment. Figure 2b shows that the first adjust-

NRMSE

0.157
0.134

0.099
0.149
0.195

0.131
0.074
0.119
ment led to increased biomass development while the second
adjustment had virtually no influence on biomass.

0.979
0.990
0.982
0.988

1.000
1.000
1.000
1.000
d2

0.926
0.927
0.913
0.933

0.997
0.995
0.999
0.990
d1
Canopy cover

15.327
39.389

18.604
13.217

20.848
WLS

9.110
2.699
0.770
NRMSE

0.147
0.141

0.039
0.170
0.148

0.173
0.083

0.127

The best results according to NRMSE and WLS are indicated in bold.
Table 3 e Results of the assimilation procedure for potato.

0.978
0.965
0.996
0.998

1.000
0.995
1.000
0.991
d2

0.924
0.858
0.926
0.946

0.994
0.981
0.997
0.984
d1
None

12.629
41.986
19.484

12.076

15.173

32.174
WLS

4.856

1.268
NRMSE

0.157
0.134
0.149
0.197

0.101
0.168
0.074
0.162

Fig. 2 e Results for potato (Treatment Id). The “*” symbols

correspond to the measurements and the error bars
Results for canopy cover

correspond to one standard deviation. The blue lines

Performance index

correspond to the nominal model. The red dashed lines

Results for biomass

correspond to assimilation of canopy cover only. The green

dashed-dotted lines correspond to assimilation of biomass
IFigaroN3

IFigaroN3
Data used

Treatment

only. The black dotted lines correspond to assimilation of

canopy cover and biomass. (For interpretation of the
Id

Id
I0

I0

references to colour in this figure legend, the reader is

If

If

referred to the web version of this article.)

 b i o s y s t e m s e n g i n e e r i n g 1 6 2 ( 2 0 1 7 ) 5 7 e6 6 63

Assimilation of biomass measurements (green dash-dotted
line) led to one major adjustment (on day 80), which caused
overestimation of the final biomass. Assimilation of both CC
and biomass measurements (black dotted line) led to “super-
position” of the previous results: Canopy development
adjusted according to CC measurements and biomass devel-
opment adjusted according to biomass measurements.
Similar trends were observed for all four treatments, as can
be inferred from Table 3 which summarises the results. The
following observations can be made from Table 3:
 According to NRMSE and WLS indices, assimilation of CC
measurements alone improved CC predictions only in two
of the four treatments. Biomass predictions were improved
in three of the treatments.
 According to NRMSE and WLS indices, assimilation of
biomass measurements alone improved biomass pre-
dictions in three of the four treatments.
 According to NRMSE and WLS indices, assimilation of both
CC and biomass measurements led to the best results in
terms of CC and biomass.

Table 4 e Results of the assimilation & recalibration procedure for potato.

Data used None Canopy cover Canopy cover and biomass
Performance index NRMSE WLS d1 d2 NRMSE WLS d1 d2 NRMSE WLS d1 d2
Results for canopy cover
Treatment
IFigaroN3 0.149 41.986 0.924 0.978 0.143 118.421 0.930 0.976 0.144 118.514 0.926 0.979
I0 0.197 19.484 0.858 0.965 0.112 13.307 0.954 0.988 0.114 13.353 0.952 0.988
If 0.157 12.629 0.926 0.996 0.145 19.103 0.936 0.977 0.149 19.21 0.933 0.977
Id 0.134 12.076 0.946 0.998 0.134 9.448 0.935 0.984 0.149 10.726 0.932 0.984
Results for biomass
IFigaroN3 0.101 4.856 0.994 1.000 0.089 7.157 1.000 1.000 0.112 9.726 0.993 0.999
I0 0.168 15.173 0.981 0.995 0.090 3.857 0.994 1.000 0.074 2.069 0.997 1.000
If 0.074 1.268 0.997 1.000 0.055 1.072 0.998 1.000 0.055 1.072 0.998 1.000
Id 0.162 32.174 0.984 0.991 0.127 20.848 0.987 0.994 0.112 11.703 0.994 0.998

The best results according to NRMSE and WLS are indicated in bold.

Fig. 3 e Results for cotton (left frames: Plot #1, right frames: Plot #2). Symbols and colours as in Fig. 2. (For interpretation of
the references to colour in this figure legend, the reader is referred to the web version of this article.)
64 b i o s y s t e m s e n g i n e e r i n g 1 6 2 ( 2 0 1 7 ) 5 7 e6 6

 Data assimilation resulted in only very small variations of

0.961
0.997

1.000
1.000
the value of the index d1, which reflected the overall good

d2
agreement between model and measurements.

Canopy cover and biomass

 The very high values obtained for d2 show that the model

0.928
0.958

0.990
0.994
predictions were always very close (or within) the margins

d1
defined by the standard deviation of the measurements,
even when no data assimilation was performed.

104.79

21.326
24.176
WLS

9.945
3.1.2. Data assimilation and model recalibration
Table 4 summarises the results obtained when using the

NRMSE

0.364
0.151
0.105

0.449
measurement for simultaneous adjustments of the model
states and the parameters related to CC development. It
can be observed that, as in Table 3, the indices d1 and d2 are
not informative. According to the NRMSE index, this pro-

0.885
0.999

1.000
1.000
d2
cedure always led to improved predictions of CC and
biomass. However, this was not always reflected in the
WLS index.

0.831
0.968

0.991
0.994
d1
Biomass
3.2. Results for cotton

22.485
281.40

22.264
WLS

7.770
3.2.1. Data assimilation
The results are shown in Fig. 3. First, it should be noticed that,
despite the fact that the same irrigation treatment was

NRMSE

0.092

0.232
0.232

0.365
applied to both plots, the observed crop development differed
significantly between the two plots. The differences observed
in canopy development can be attributed mainly to differ-
ences in soil composition, soil initial water content and soil

0.962
1.000

1.000
1.000
d2
compaction, which all strongly influenced root growth and
overall crop development. As a result of these measurement
differences, data assimilation led to contrasting results in the
0.928
0.958

0.998
0.993
d1
Canopy cover

two plots. In plot #1 (left frames), assimilation of CC mea-

surements led to repeated adjustments, starting on day 72.
104.79

22.565
26.650
These adjustments had only a very small impact on biomass
WLS

9.910

development. Assimilation of biomass measurements did

not result in any significant adjustment. In particular, it
should be noticed that although there were large difference
NRMSE

0.143
0.105

0.276
0.371

between the (average) measured and predicted biomass on

days 116 and 131, virtually no adjustments were made due to
The best results according to NRMSE and WLS are indicated in bold.
Table 5 e Results of the assimilation procedure for cotton.

the large standard deviations associated with the measure-

0.888
1.000

1.000
1.000

ments on those dates. In plot #2 (right frames), assimilation

d2

of CC measurements only led to two minor adjustments on

days 44 and 59. These did not affect biomass. Assimilation of
0.830
0.968

0.998
0.993

biomass measurements led to a minor adjustment on day 72

d1

followed by a much more significant adjustment on day 116.

None

The latter had a dramatic impact on the predictions of final

284.22

24.244
23.902
WLS

7.765

biomass.
The summary of the results presented in Table 5 shows
that assimilation of CC and/or biomass measurements did not
NRMSE

yield consistent improvement of the predictions of CC and

0.092
0.221

0.269
0.376

biomass development.
Results for canopy cover

3.2.2. Data assimilation and model recalibration

Performance index

Table 6 shows that the results are not consistent across

Results for biomass

performance indices and plots: CC predictions were

improved in plot #1 but not in plot #2. Biomass predictions
Data used

were improved in plot #2, but in plot #1 WLS indicated an

improvement of the predictions while, according to NRMSE,
Plot 1
Plot 2

Plot 1
Plot 2

data assimilation and parameter adjustments led to worse

biomass predictions.
 b i o s y s t e m s e n g i n e e r i n g 1 6 2 ( 2 0 1 7 ) 5 7 e6 6 65

Table 6 e Results of the assimilation & recalibration procedure for cotton.

Data used None Canopy cover Canopy cover and biomass
Performance index NRMSE WLS d1 d2 NRMSE WLS d1 d2 NRMSE WLS d1 d2
Results for canopy cover
Plot 1 0.221 284.22 0.830 0.888 0.138 86.927 0.940 0.968 0.138 86.927 0.940 0.968
Plot 2 0.092 7.765 0.968 1.000 0.111 11.068 0.953 0.994 0.111 11.068 0.953 0.994
Results for biomass
Plot 1 0.269 24.244 0.998 1.000 0.442 21.524 0.991 1.000 0.447 20.616 0.990 1.000
Plot 2 0.376 23.902 0.993 1.000 0.368 26.657 0.993 1.000 0.366 23.408 0.994 1.000

The best results according to NRMSE and WLS are indicated in bold.

3.3. Discussion calibrated locally and hence provided reasonable predictions

Overall, the results summarised in Tables 3e6 are not as clear-
cut as one might have expected. Using a specific type of
measurements (e.g. canopy cover) almost always led to some
improvement of the predictions for that variable, at least ac-
cording to some of the performance indices investigated.
However, improved predictions of canopy cover did not al-
ways lead to improved predictions of biomass, and vice-versa.
This result may seem surprising since many studies have
implied that accurate knowledge of light interception, and
hence canopy cover, is critical for predicting biomass accu-
rately. However, the current result may be due to the fact that
AquaCrop is a purely water-driven model in which solar ra-
diation and light interception are not considered explicitly, so
that the overall impact of canopy cover on crop development
may be underestimated. This result clearly emphasises the
limitations of using “easy-to-obtain” measurements (such as
canopy cover) in order to improve the predictions of another
variable, such as biomass.
The results of Fig. 3d, and to a lesser extent Fig. 2b, show
that resetting the values of a state variable periodically is not
always enough to correct deviations due to inherent flaws of
the model. In case of cotton, the measurements in plot #2
indicated that biomass levels-off or even decreases after day
115. AquaCrop is not able to simulate such a behaviour, and
therefore the adjustment made on day 115 led to over-
estimation of biomass at harvest. Similarly, for potato (Fig. 2b),
adjusting biomass on day 80 without introducing in the model
a process which would slow down biomass accumulation
starting from day 98 resulted in overestimated biomass at
harvest. Although this conclusion may seem trivial, this issue
does not seem to have received the attention it warrants in
previous studies. In this respect, adjusting model parameters
has the advantage that this affects the future dynamics of the
model. However, due to the large number of parameters
which typically affect a complex process such as biomass
accumulation, it is very difficult to identify a priori which pa-
rameters should be modified, and due to the limited quantity
and/or quality of the data, the usefulness of sensitivity-based
approaches, such as Ioslovich, Seginer, and Gutman (2004), is
limited.
Finally, it must be noted that the potential benefit of
within-season model adjustments depends directly on how
good (or bad) the initial model is. In the present study, the
nominal models consisted of models which had already been
for all treatments. This is clear from Tables 3e6 which show
that the index d2 of the nominal models was almost always
higher than 0.9, indicating that the predicted nominal trajec-
tories were very close to the margins defined by the standard
deviations of the measurements. Implementing the proposed
procedures starting with poorer nominal models would have
resulted in larger improvements. However, while this may
explain the much more positive results reported in some
previous studies, this would not have altered the general
trends described above.
4. Conclusions
A framework for data assimilation and parameter adjust-
ments has been developed. This framework, which could be
applied to any situation in which the user has (1) few samples
at irregular time intervals and (2) a dynamic model which can
be re-parametrised or re-initialised and “hot-started”, was
illustrated with the crop model AquaCrop. The proposed
procedures followed a simplified (extended) Kalman filter
approach with some heuristic adjustments. These procedures
were applied to two case studies corresponding to very
different crops and climates. Both case studies demonstrated
the soundness of the procedures, but also emphasised the
inherent limitations associated with data assimilation.
Acknowledgments
The authors wish to thank Prof. Georgios Sylaios and Dr. Finn
Plauborg for providing the experiment data, as well as Prof.
Dirk Raes for providing undocumented information about the
AquaCrop files.
The research leading to these results has received funding
from the European Community's Seventh Framework Pro-
gram (FP7/2007e2013) under grant agreement no. 311903 e
FIGARO (Flexible and Precise Irrigation Platform to Improve
Farm-Scale Water Productivity) (http://www.figaro-irrigation.
net/). The contents of this document are the sole re-
sponsibility of the FIGARO Consortium and can under no cir-
cumstances be regarded as reflecting the position of the
European Union. This Research was supported also by
Technion General Research Fund.
66 b i o s y s t e m s e n g i n e e r i n g 1 6 2 ( 2 0 1 7 ) 5 7 e6 6

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Modeling irrigation management for water conservation by