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JNS MD Accepted Version
JNS MD Accepted Version
Mert Dedeoglu
Abstract
The aim of this study was to predict the critical nitrogen (N) content in peach trees using spectrometric measurements. A
nutrient-controlled hydroponics experiment was designed for this purpose. Peach saplings were grown under three N
conditions: deficient, sufficient, and excessive. The reflectance values of a plant leaves were measured using a handheld
field spectroradiometer fitted with a plant probe. The N contents of leaves were determined in the laboratory and Gaussian
mixture discriminant analysis (GMDA) was used to estimate N levels in the leaves from reflectance values. The N levels were
categorized for each of the three different N conditions. The wavelengths at 425 nm, 574 nm, 696 nm, and 700 nm were
found to be diagnostic of the different N levels. The model developed here classified the experimental plants with high
accuracy for NDeficient, 89.28%; NSufficient, 96.30%; and NExcess, 71.42% with 85.71% coefficients. The reliability of the model
was also tested under field conditions using 96 peach trees representing the three different N status. Leaves were analyzed
by reflectance at 425 nm, 574 nm, 696 nm, and 700 nm, which functioned in real N, percentage classes determined based on
the laboratory analyses of the orchard samples, and the data were categorized as NDeficient, NSufficient, and NExcess with a
similarity ratio of 77.78%, 80%, and 67.74%, respectively with the general correct classification rate of 75%. The study
findings showed that the model developed using hyperspectral reflectance data can discriminate different N nutritional
status in plants with an accuracy of 70% and can be applied under field conditions. The results of this research provide a
new perspective for future studies by showing that GMDA with hyperspectral remote sensing may be useful for the
classification of different plant nutrient contents.
Keywords
Hydroponics experiment, mixture discriminant, nitrogen, peach, VNIR spectroscopy
Received 21 February 2020; accepted 10 June 2020
Introductions
The energy that can cause the stretching and bend-
Visible and near infrared (VNIR) spectroscopy is a ing of bonds between the atoms of organic molecules
rapidly developing analytical technique with an appli- within the plants, such as –CH, –OH, –NH, C ¼ O,
cation in agriculture. It has many advantages, such as and –SH, is absorbed in the infrared region.12,13 As a
being rapid and simple to use, and has a low associ- result, significant differences in energy absorbance by
ated cost and good reproducibility and is environ- plants can occur in the visible and near infrared
mentally friendly.1–4 The most common type of region. Using multivariate statistical analysis,14
VNIR spectroscopy in agricultural applications is many researchers have reported studies involving
spectroradiometry, which is used in hyperspectral near infrared spectroscopy and its application to
remote sensing.5,6 Spectroradiometers are used for fruit trees, which show that reflectance characteristics
the quantitative measurement of radiance, irradiance,
are directly related to leaf chlorophyll and mineral
reflectance, and transmission,7 and the key element of
content15–18; therefore, it is possible that nutrient
spectroradiometric methods is to find the unique
reflectance values of objects within the electromagnet-
ic spectrum.8 Different plants have specific reflectance Department of Soil Science and Plant Nutrition, Agricultural Faculty,
values,6,9 due to differences in their chemical compo- Selcuk University, Konya, Turkey
sitions10 and morphological features which contain Corresponding author:
the spatial information about the size and shape of Mert Dedeoglu, Department of Soil Science and Plant Nutrition,
the plants profiles.11 Agricultural Faculty, Selcuk University, Konya, Turkey.
Email: mertdedeoglu@gmail.com
Estimation of Critical Nitrogen Contents in Peach Orchards using VNIR
Abstract
The aim of this study was to predict the critical nitrogen (N) content in peach trees using the
this purpose. Peach saplings were grown under three N conditions: deficient, sufficient, and
excessive. The reflectance values of a plant leaves were measured using a handheld field
spectroradiometer fitted with a plant probe. The N contents of leaves were determined in the
laboratory and Gaussian mixture discriminant analysis (GMDA) was used to estimate N levels
in the leaves from reflectance values. The N levels were categorized for each of the three
different N conditions. The wavelengths at 425, 574, 696, and 700 nm were found to be
diagnostic of the different N levels. The model developed here classified the experimental
plants with high accuracy for N Deficient, 89.28%; N Sufficient, 96.30%; and N Excess, 71.42% with
85.71% coefficients. The reliability of the model was also tested under field conditions using
96 peach trees representing the three different N status. Leaves were analyzed by reflectance
at 425 nm, 574 nm, 696 nm, and 700 nm, which functioned in real N, percentage classes
determined based on the laboratory analyses of the orchard samples, and the data were
categorized as N Deficient, N Sufficient, and N Excess with a similarity ratio of 77.78%, 80%, and
67.74%, respectively with the general correct classification rate of 75%. The study findings
showed that the model developed using hyperspectral reflectance data can discriminate
different N nutritional status in plants with an accuracy of ≥70% and can be applied under field
conditions. The results of this research provide a new perspective for future studies by showing
that GMDA with hyperspectral remote sensing may be useful for the classification of different
1
Keywords: Hydroponics experiment, Mixture discriminant, Nitrogen, Peach, VNIR
spectroscopy
Introductions
with an application in agriculture. It has many advantages, such as being rapid and simple to
use, and has a low associated cost and good reproducibility with being environment - friendly.1-
4
The most common type of VNIR spectroscopy in agricultural applications is
used for the quantitative measurement of radiance, irradiance, reflectance, and transmission,7
and the key element of spectroradiometric methods is to find the unique reflectance values of
objects within the electromagnetic spectrum.8 Different plants have specific reflectance
values,6,9 due to differences in their chemical compositions10 and morphological features which
contain the spatial information about the size and shape of the plants profiles11.
The energy that can cause the stretching and bending of bonds between the atoms of organic
molecules within the plants, such as –CH, –OH, –NH, C=O, and –SH, is absorbed in the IR
region.12,13 As a result, significant differences in energy absorbance by plants can occur in the
visible and near-infrared region. These differences are identified at each wavelength by
spectroradiometers and are presented as graphical data. Using multivariate statistical analysis,14
many researchers have reported studies involving near-infrared technology and its application
to fruit trees, which show that reflectance characteristics are directly related to leaf chlorophyll
and mineral content;15-18 therefore, it is possible that nutrient deficiencies could also be
determined using spectral methods.19,20 Plant nutrient stress has been studied by researchers for
many years as a major abiotic factor in plant health.4,21,22 Leaf chlorosis is a common symptom
of nutrient deficiency or toxicity that can be observed in the field; however, the detection of
2
chlorosis is subjective and dependent of the experience of the horticulturist. Such
unnecessary use of fertilizers results in soil salinization, water contamination, and substance
accumulation in plants, all of which result in economic losses and environmental pollution.23
Because of these negative consequences that affect living beings either directly or indirectly,
early detection of nutrient stress prior to the occurrence of chlorosis in plants has been an
important goal of hyperspectral sensing studies.18,24,25 These studies have been based on
leaves.26,27
The most useful wavelengths used to determine the effects of stress through the spectral
reflectance are the red, red-edge (680–760 nm), and near-infrared (NIR) spectral ranges.28 In
these studies, the most investigated plant nutrient has been nitrogen (N).29-33 N is one of
seventeen essential nutrients required by fruit trees for growth and for the optimal fruit yield
and quality.34 It is also an important element for the production of many compounds, such as
Early diagnosis of N deficiency in fruit trees can assist in the management of N-fertilization to
improve crop yields. However, the determination of N content is time-consuming and labor-
intensive and requires the use of dangerous chemical reagents (e.g., Kjeldahl method) that may
result in environmental contamination.34 For these reasons, numerous researches have sought
to estimate the N status of plant leaves under field conditions by using ground-based VNIR
examining green plant leaves from a certain height (canopy) or by direct contact with the plant
tissue.24 It is known that there is a high positive correlation between the reflectance values
3
obtained from spectrometry techniques and the N content.6,21,39 It has been reported that the
amount of N applied to soil was estimated with high accuracy (PLS, r = 0.945) in orange leaves
(Citrus sinensis L.).40 Similarly, wavelengths of 540–560 nm (visible green) and 990–1010 nm
(near-infrared) were found to be an indicator for active iron levels in apple, cherry, and peach
trees with an accuracy of 76.70%, 75.28%, and 78.69%, respectively.4 In addition, studies
demonstrated that the VNIR both alone or in combination with visible spectroscopy has
capability and accuracy as a predictive tool for the analysis of citrus products. Research were
examples for the analysis of acidity, soluble solids, and firmness in mandarins;41 for the
measurement of soluble solids content in oranges,42 and citrus fruits before harvest;43 and for
the classification and analysis of citrus oils.44 Additionally, the results of another study showed
that ground-based hyperspectral techniques can also produce reliable results in predicting the
N status of the plants;27,45,46 however, it has been suggested that more studies using ground-
based hyperspectral measurement techniques in different plots and study designs are required
concentrations.17,45,47,48
Therefore, it was aimed that a model was developed for estimating critical N content in peach
Gaussian mixture discriminant analysis (GMDA). N was chosen as a nutrient because it is the
most requirement ingredient in fertilizers and plays a critic role in the optimal development of
peaches (Prunus persica L. Batsch). Peach was selected as the test plant because it is a globally
popular fruit and has high nutritional value.49,50 It was also a product that has considerable
4
Materials and Methods
The study has five stages which 1) growing the peach saplings, 2) hyperspectral measurements,
3) leaf sampling and laboratory analysis, 4) data analysis and modeling, 5) testing the reliability
of the method.
Study area
The study was based on the comparison the results of laboratory analyses and reflectance
measurements on peach leaves grown using hydroponics experiment also and cultivated in
Egirdir in the Isparta region of Turkey. Nitrogen deficiency is a common and significant
This area has Mediterranean climate characteristics with an annual rainfall of 524 mm and the
average temperature of 12.5 °C. Based on multi-year averages, the highest temperatures occur
in July, with an average of 23.8 °C. December is the wettest month (79.6 mm), whereas August
One age seedling was planted into perlite, and nutrient solutions were poured into an automated
targeted that nutrient concentration was 6.3 pH and electrical conductivity of 1.2–1.8 dS/m.
More than 50% of the calculated as standard nutrient content was delivered to the hydroponic
5
The plants were divided into three groups based on the applied N content, which were based
on the work of Jones et al.53 and classified as low, optimal and high for one-year-old peach
samplings (Table 2). The experiment was conducted three times, with 21 plants in each
replicate. Samples were taken four times, once each in the months of May, June, July, and
August.
In orchards, samples were collected both from healthy trees and from those exhibiting
symptoms of nutrient deficiency. The young offshoots leaves were used as samples. Samples
were collected from 96 different trees in eight separate orchards, and this was repeated three
times over the month of June. In total, 252 leaf samples obtained from the experiment were
used to make a model. Also, 288 leaves samples obtained from orchards were used for
accuracy assessment. Upon the calculation of replication averages, 84 and 96 chemical analysis
results and spectral reflectance values were used for the experiment field and the orchards,
respectively.
A Plant Probe accessory, combined with the Leaf Clip assembly (Analytical Spectral Devices
Inc., Boulder, CO, USA), coupled in the high-resolution spectroradiometer ASD FieldSpec
Handheld was used to measure the spectral reflectance of peach leaves. The Leaf Clip
assembly is designed for use with the Plant Probe accessory, which has an integrated halogen
bulb that emits radiation over the 400 to 1000 nm spectral range. Its design minimizes
measurement errors associated with the stray light. Leaf Clip includes a gripping system for
holding the target sample in place without inflicting damage to the leaf. It also has a two-sided
6
rotating head (2 cm in diameter) that allows both bidirectional reflectance and transmittance
measurements.54
The process of methodology was presented in Figure 1 as a diagram for generating the model
and N% classification based on spectral measurement by using plant probe which has an active
light source with the accessories of leaf clip holding the lamina.
Reflectance values were obtained from each sample using 3 separate measurements. Spectral
measurement and leaf samples were collected between 12:00 and 14:30 hours local time in
every sampling period. Spectral reflectance was collected from the ends of leaves by placing
the laminas between the leaf veins under the active light source of plant probe. Special attention
was paid that the leaves in the orchard samples had not biological or mechanical damage. In
7
addition, care was taken to ensure that no contaminants such as dust or pesticide residues were
present on the leaves. Barium sulfate-doped (BaSO4) spectralon was used as a white reference
and was measured at the beginning of each survey and every 10–15 minutes thereafter.17
ViewSpec Pro software (Analytical Spectral Devices, Inc., Boulder CO, USA) was used to
process the reflectance values. The nitrogen status of the leaves was determined chemically
using the Kjeldahl method in the laboratory.55 Nutrient contents of the plants were shown in
Table 3. The nitrogen contents of samples obtained from the experiment were ranged between
1.77% and 4.27%. The samples were found to distribute on all N classes, including low,
In order to determine whether the model developed using the training data could be used on
the test data, an independent two-sample t-test was applied among the N contents determined
from the experiment field and orchard samples.56 p values for NDeficient–NSufficient–NExcess groups
were found to be 0.163 (p > 0.05), 0.460 (p > 0.05), and 1.00 (p > 0.05), respectively. Thus, it
was determined that the model produced from the experiment field samples could be used on
the orchard samples. The histogram graphs obtained as a result of the laboratory analysis of the
experiment field and orchard samples using the descriptive statistical methods of Minitab 1657
were presented in Figures 2. Distributions of N levels indicating that it did not adhere to a strict
8
normal distribution; thus, the model fulfilled the conditions required for the implementation of
Histogram (with Normal Curve) of N from Experiment Histogram (with Normal Curve) of N from Orchards
16
18
Mean 3.267 Mean 3.194
14 StDev 0.6365 16 StDev 0.6379
N 84 N 96
12 14
10 12
Frequency
Frequency
10
8
8
6
6
4
4
2 2
0 0
2.0 2.5 3.0 3.5 4.0 4.5 2.0 2.4 2.8 3.2 3.6 4.0 4.4 4.8
N, % N, %
The laboratory analyses for the orchard samples revealed an N distribution between 1.91 and
4.84% as expected, which encompassed the three different classes of N found in trees in the
region. Similarly, histogram graphs of the orchard samples showed these data did not conform
to a strict normal distribution. This showed that the sampling size and the test data set
represented a population containing all the N classes in this study. In order to achieve the
intended objectives of the study with the 96 samples obtained from orchards, the N contents of
Data analysis
The N contents of the experiment samples were categorized with the corresponding reflectance
measurements into three different N classes. Thus, in order to develop a model, a training data
set was created from 84 observations (n), consisting of 601 reflectance variables (p) between
the wavelengths of 400 and 1000 nm for each observation. However, the sample size being
lower than the number of variables (n < p) is an important factor that decreases the power of a
model for multivariate analyses that do not fulfill the normal distribution requirement.58 In fact,
9
multivariate modeling studies are used for making inferences to provide the maximum benefit
with the minimum number of variables.59 Therefore, feature selection was performed with the
absolute correlation to determine which of the 601 reflectance values in the training data set
were most appropriate for N classification, and the most effective wavelengths were
determined. In this way, the n > p requirement was fulfilled by dimension reduction. The scaled
of one or more Gaussian distributions.61,62 Suppose we have 𝐾 classes in our population and
the mixture discriminant model based on multivariate Gaussian mixture model has been
𝑓(𝐱, 𝛙) = ∑ 𝜋𝑘 𝑓𝑘 (𝐱, 𝛉𝑘 )
𝑘=1
where 𝐱 is 1 × 𝑝 dimensional observation vector and 𝜋𝑘 is prior probability of 𝑘th class (𝜋𝑘 ∈
(0,1) and ∑𝐾
𝑘=1 𝜋𝑘 = 1). 𝛙 = (𝜋1 , … , 𝜋𝐾 , 𝛉1 , … , 𝛉𝐾 ) is the vector containing all unknown
parameters of the mixture discriminant model based on multivariate Gaussian mixture model.
𝑓𝑘 (𝐱, 𝛉𝑘 ) is probability density function of multivariate Gaussian mixture model for 𝑘th class
and 𝑓𝑘 (𝐱, 𝛉𝑘 ) is defined and presented below.
𝐺𝑘
1 1 −1 𝑇
𝑓𝑘 (𝐱, 𝛉𝑘 ) = ∑ 𝜋𝑘𝑔 1/2
𝑒𝑥𝑝 {− (𝐱 − 𝝁𝑘𝑔 )𝚺𝑘𝑔 (𝐱 − 𝝁𝑘𝑔 ) }
(2𝜋)𝑝/2 |𝚺𝑘𝑔 | 2
𝑔=1
where 𝛉𝑘 = (𝜋𝑘1 , … , 𝜋𝑘𝐺𝑘 , 𝛍𝑘1 , … , 𝝁𝑘𝐺𝑘 , 𝚺𝑘1 , … , 𝚺𝑘𝐺𝑘 ) is the vector containing unknown
parameters of multivariate Gaussian mixture model for 𝑘th class. Where 𝜋𝑘𝑔 is mixture rate of
10
𝑘 𝐺
𝑔th subclasses in the 𝑘th class ( 𝜋𝑘𝑔 ∈ (0,1) and ∑𝑔=1 𝜋𝑘𝑔 = 1). In the 𝑘th class, 𝝁𝑘𝑔 and 𝚺𝑘𝑔
are denoted mixture rate, mean vector, and covariance matrix of 𝑔th subclass, respectively.
The prior probability 𝜋𝑘 can be estimated from the training data or other sources.62 The
estimation of the prior probability 𝜋𝑘 from the training data is defined by
𝑛𝑘
𝜋̂𝑘 =
𝑛
where 𝑛𝑘 is the number observation for the 𝑘th class of the training data. The maximum
likelihood estimations of parameters πkg , μkg and Σkg used in 𝑙𝑜𝑔𝐿(𝛉𝑘 ) calculations for 𝑘th
class can be estimated from training data using the expectation-maximization (EM)
algorithm.63,64 The EM algorithm maximizes the conditional log-likelihood, logL(θk ), for the
𝑘th class of the training data as
𝐺𝑘 𝑛𝑘
𝑙𝑜𝑔𝐿(𝛉𝑘 ) = ∑ ∑ 𝑃𝑘 (𝐺 = 𝑔|X 𝑘 = 𝐱𝑘𝑖 ){𝑙𝑜𝑔𝜋𝑘𝑔 + 𝑙𝑜𝑔𝑓𝑘𝑔 (𝐱𝑘𝑖 , 𝛉𝑘𝑔 )}
𝑔=1 𝑖=1
where 𝐱𝑘𝑖 is 1 × 𝑝 dimensional observation vector of 𝑖th in the 𝑘th class of the training data.
An observation is classified into 𝑘th class, which has the highest posterior probability, based
on Bayes rule, denoted by
𝜋𝑘 𝑓𝑘 (𝐱, 𝛉𝑘 )
𝑃(𝐾 = 𝑘|X = 𝐱) = .
𝑓(𝐱, 𝛙)
The reliability refers to the study is correct classification rate which can vary from 30% to 99%
according to the purpose of the disciplines such as medical, marketing, sociology, spectroscopy
etc., because they were used different sample size and properties in statically analysis.65,66,67,68
Therefore, it is not possible to say anything definite about the confidence interval of the correct
classification rate. However, some research has stated that the correct classification rate of 85%
or more were “reliable” or “high accuracy” in models used on spectral data from obtained plant
tissue.69,70,71,72,73,74. Thus, a conclusion was made from past research and reliability intervals
were divided into three ranges according to the correct classification rates between > 85% as
11
Result and Discussion
As a result of the measurements and sampling procedures performed in the experiment field,
the N contents of the leaf samples were homogeneously distributed into three different N
classes. Thus, the models were produced represent all the nitrogen thresholds of the peach trees.
In fact, it is advised that varying doses of the related nutrients should be formed in plants for
the estimation of plant nutrient status with spectral reflectance.4 In this study, the distribution
samples. The similarity has increased the confidence in the statistical interpretation of the
study. The characteristic curves of different N classes were drawn for hyperspectral reflectance
Examination of the mean spectral curves of leaf samples belonging to three different N classes
revealed that there was a difference in the reflectance values between 425 and 750 nm between
the classes. Considering their known characteristics, the wavelengths with the highest
correlations between N and reflectance values were found to be 425, 572, 696, and 700 nm,
12
which exhibited correlations of 0.50, 0.40, 0.43, and 0.42, respectively (Figure 4). Thus, the
This event showed that the decrease in reflectance values was resulted from increasing of N
levels, chlorophyllase enzyme activity and hence chlorophyll content.75 In addition, there is a
direct correlation between the amount of chlorophyll a and b and carotenoid pigment with
maximum absorption at 425, 455, and 485 nm.76 Studies have shown that there is a very high
increase in reflectance during N starvation, which can reach 90% depending on the degree of
deficiency.21,77-79
The reflectance curves of the orchard peach samples categorized based on the three critical N
classes exhibited similar spectral characteristics to the experiment samples. (Figure 5).
13
Fig 5. Average reflectance curves representing different N classes in orchards samples
The spectral curves show the correlation between reflectance and N content and the
wavelengths between 400 and 750 nm were similar to those in previous studies.80 It has been
reported that variations in the plant spectral reflectance between approximately 425 and 750
nm can be considered as acceptable indicators of plant nutrient stress.81 It has also been reported
that the wavelength ranges of 520–560, 650–690 nm (visible region), and 710–730 nm (red-
edge region) are useful for estimating different N levels from leaf spectra. The variation in the
photosynthetic activity, and 670 nm is the absorption band of chlorophylls a and b,20,29,82,83
whereas 425–485 nm is the reflectance zone of carotenoid pigment.76 In this study, it was
observed that the variations in the carotenoid pigment reflectance zone (approximately 425
nm), green wavelength peak (approximately 574 nm), red-edge minimum chlorophyll
absorption reflectance point (approximately 696 nm) and near-infrared region ( approximately
700 nm) caused differences in spectral reflectance, in particular, energy absorptions due to the
N–chlorophyll/carotenoids correlation.
14
These results show that different N applications result in statistically significant differences in
reflectance curves; therefore, peach trees can be used for statistical analysis of the detection of
critical N classes.
For the analysis, the wavelength reflectance values at 425, 574, 696 and 700 nm obtained from
the experiment plants given three different doses were selected as training data for each class.
Then, In the study, parameter estimates of mixed discriminant model were obtained based on
training data. Suppose we have 3 classes such as deficient, sufficient and excess in our
population and the number of subclasses in each class is 3. Thus, parameter vector 𝛙
containing all parameter of the mixture discriminant model based on multivariate Gaussian
Fig 6. The all parameters of the mixture discriminant model based on multivariate Gaussian
mixture model
The mixture discriminant analysis model based on the multivariate normal distributions used
in the study is as follows.
3
3 1 1 𝑇
−1
𝑓(x, ψ) = ∑ 𝜋𝑘 ∑ 𝜋𝑘𝑔 1/2
𝑒𝑥𝑝 {− (x − 𝜇𝑘𝑔 )Σ𝑘𝑔 (x − 𝜇𝑘𝑔 ) }
𝑘=1 (2𝜋)𝑝/2 |Σ𝑘𝑔 | 2
𝑔=1
According to the number of observations in the N% classes, the preliminary probabilities were
28 27 29
determined as 84 , 84 and 84
, respectively.
15
The GMDA model obtained in the study to show the parameter estimates for the mixture of
multivariate normal distribution in each N% classes for θ̂𝑘 was as follows.
28 27 29
̂) =
𝑓(x, ψ 𝑓1 (x, θ̂1 ) + 𝑓2 (x, θ̂2 ) + 𝑓3 (x, θ̂3 )
84 84 84
The hyperspectral reflectance at wavelengths of 425, 574, 696 and 700 nm in the all classes of
Table 4. Dataset used to obtain estimation parameters (θ̂𝑘 ) for the N classes
16
̂𝑘 ) of the Gaussian mixture model for the
The maximum likelihood estimations parameters ( 𝛉
̂1 )
Table 5. Estimations parameters for the NDeficient class ( 𝛉
𝜋̂11 0.357126
𝛍
̂11 0.040799 0.107599 0.108599 0.149999
1.06E-05 3.38E-05 1.70E-05 2.18E-05
3.38E-05 0.000315 0.000139 0.000206
̂11
𝚺
1.70E-05 0.000139 7.18E-05 0.000105
2.18E-05 0.000206 0.000105 0.000156
𝜋̂12 0.355008
𝛍
̂12 0.044806 0.170198 0.184296 0.258418
8.05E-06 4.69E-05 7.93E-05 9.90E-05
4.69E-05 0.000859 0.001238 0.001545
̂12
𝚺
7.93E-05 0.001238 0.001828 0.002278
9.90E-05 0.001545 0.002278 0.002847
𝜋̂13 0.287866
𝛍
̂13 0.038913 0.187371 0.179538 0.256611
6.69E-06 4.27E-05 4.09E-05 5.11E-05
4.27E-05 0.00108 0.000922 0.001244
̂13
𝚺
4.09E-05 0.000922 0.000939 0.001279
5.11E-05 0.001244 0.001279 0.001753
̂2 )
Table 6. Estimations parameters for the NSufficent class ( 𝛉
𝜋̂21 0.276326
𝛍
̂21 0.045226 0.142927 0.147052 0.209294
1.32E-05 3.68E-05 6.67E-05 0.000102
3.68E-05 0.000739 0.000926 0.00129
̂21
𝚺
6.67E-05 0.000926 0.001204 0.001692
0.000102 0.00129 0.001692 0.002388
𝜋̂22 0.290881
𝛍
̂22 0.04504 0.110304 0.108028 0.152263
1.31E-05 3.30E-05 2.07E-05 2.44E-05
3.30E-05 0.000104 5.80E-05 6.91E-05
̂22
𝚺
2.07E-05 5.80E-05 6.65E-05 9.80E-05
2.44E-05 6.91E-05 9.80E-05 0.000151
𝜋̂23 0.432793
𝛍
̂23 0.04132 0.123603 0.11745 0.165048
8.80E-06 6.44E-06 -1.14E-05 -2.57E-05
̂23
𝚺 6.44E-06 0.000199 5.64E-05 6.49E-05
-1.14E-05 5.64E-05 7.76E-05 0.000117
17
-2.57E-05 6.49E-05 0.000117 0.000194
̂3 )
Table 7. Estimations parameters for the NExcess class ( 𝛉
𝜋̂31 0.413787
𝛍
̂31 0.042417 0.114917 0.113833 0.163167
3.74E-06 -9.6E-06 -4.3E-06 -7.8E-06
-9.6E-06 6.31E-05 3.97E-05 6.94E-05
̂31
𝚺
-4.3E-06 3.97E-05 4.75E-05 7.7E-05
-7.8E-06 6.94E-05 7.7E-05 0.000129
𝜋̂32 0.310345
𝛍
̂32 0.046667 0.142778 0.137556 0.197667
5.78E-06 -3.5E-06 -1.5E-05 -2.2E-05
-3.5E-06 3.77E-05 4.42E-05 6.78E-05
̂32
𝚺
-1.5E-05 4.42E-05 9.49E-05 0.000145
-2.2E-05 6.78E-05 0.000145 0.000222
𝜋̂33 0.275868
𝛍
̂33 0.049125 0.124 0.110375 0.150625
4.86E-06 4.38E-06 7.45E-06 1.1E-05
4.38E-06 0.000171 0.000107 0.000153
̂33
𝚺
7.45E-06 0.000107 9.7E-05 0.000142
1.1E-05 0.000153 0.000142 0.00021
The posterior probabilities were obtained according to Bayes rule for classification using
28 ̂
𝑃(𝐾 = 1|X = 𝐱) = 84 𝑓1 (𝐱, 𝛉1 )
28 ̂ 27 ̂ 29 ̂
84 𝑓1 (𝐱, 𝛉1 ) + 84 𝑓2 (𝐱, 𝛉2 ) + 84 𝑓3 (𝐱, 𝛉3 )
27 ̂
𝑃(𝐾 = 2|X = 𝐱) = 84 𝑓2 (𝐱, 𝛉2 )
28 ̂ 27 ̂ 29 ̂
84 𝑓1 (𝐱, 𝛉1 ) + 84 𝑓2 (𝐱, 𝛉2 ) + 84 𝑓3 (𝐱, 𝛉3 )
29 ̂3 )
𝑓2 (𝐱, 𝛉
𝑃(𝐾 = 3|X = 𝐱) = 84
28 ̂1 ) + 27 𝑓2 (𝐱, 𝛉
̂2 ) + 29 𝑓3 (𝐱, 𝛉
̂3 )
𝑓1 (𝐱, 𝛉
84 84 84
18
The class assignment matrix from multivariate probability function for experiment samples
Actual classes
Deficient Sufficient Excess
Predict Deficient 27 4 0
classes Sufficient 0 21 3
Excess 1 2 26
Total 28 27 29
It was found that the feature vector X (reflectance rates separated as train data for different N
levels) was assigned to three groups, developed as train data of all reflectances obtained from
84 observations between 400 and 1000 nm in the experiment plants, as NDeficient, NSufficient, and
NExcess with an accuracy of 96.43%, 77.78%, and 89.66%, respectively, and the general correct
classification rate was found “high reliable” according to range of reliability which were
mentioned in the section of testing the reliability of method with a value of 88%.
The developed models predicted the N classes of the experiment plants with high accuracy.
After there the models were tested under field conditions. At this stage, the reflectance values
were considered as a whole without being categorized to N classes. In this way, it was
determined with which the accuracy of the reflectance values (deficient, 45; sufficient, 20; and
excess, 31) of 96 different plants between 400 and 1000 nm were categorized into three
different N classes. For this purpose, the reflectance on 425, 574, 696 and 700 nm for the actual
and prediction classes of test data according to posterior probability values were given Table
9.
Table 9. Actual and prediction Nitrogen classes of the test data in peach leaves based on the
parameter estimation by mix of multivariate normal distributions
Actual Prediction
𝑿𝟒𝟐𝟓 𝑿𝟓𝟕𝟔 𝑿𝟔𝟗𝟔 𝑿𝟕𝟎𝟎 𝑷(𝑲 = 𝟏|𝐗 = 𝐱) 𝑷(𝑲 = 𝟐|𝐗 = 𝐱) 𝑷(𝑲 = 𝟑|𝐗 = 𝐱)
Classes Classes
0.042 0.167 0.176 0.244 1 0.982 0.018 0.000 1
0.041 0.192 0.187 0.267 1 1.000 0.000 0.000 1
19
0.042 0.174 0.176 0.248 1 0.529 0.471 0.000 1
0.035 0.146 0.145 0.213 1 0.976 0.024 0.000 1
0.037 0.219 0.211 0.301 1 1.000 0.000 0.000 1
0.039 0.226 0.214 0.308 1 1.000 0.000 0.000 1
0.039 0.098 0.101 0.140 1 0.998 0.001 0.000 1
0.039 0.137 0.136 0.199 1 0.448 0.084 0.468 3*
0.044 0.150 0.128 0.180 1 0.883 0.117 0.000 1
0.040 0.141 0.133 0.199 1 0.915 0.000 0.085 1
0.036 0.158 0.133 0.191 1 0.844 0.156 0.000 1
0.040 0.099 0.111 0.154 1 0.864 0.135 0.001 1
0.037 0.095 0.103 0.143 1 1.000 0.000 0.000 1
0.040 0.107 0.112 0.154 1 0.948 0.049 0.004 1
0.045 0.101 0.106 0.145 1 0.580 0.211 0.210 1
0.045 0.103 0.107 0.144 1 0.830 0.168 0.002 1
0.040 0.179 0.195 0.276 1 1.000 0.000 0.000 1
0.048 0.167 0.189 0.264 1 1.000 0.000 0.000 1
0.043 0.230 0.202 0.282 1 1.000 0.000 0.000 1
0.036 0.095 0.097 0.135 1 1.000 0.000 0.000 1
0.046 0.168 0.191 0.268 1 1.000 0.000 0.000 1
0.045 0.192 0.215 0.291 1 1.000 0.000 0.000 1
0.049 0.245 0.290 0.394 1 1.000 0.000 0.000 1
0.038 0.095 0.104 0.143 1 1.000 0.000 0.000 1
0.044 0.133 0.117 0.162 1 0.618 0.373 0.009 1
0.046 0.138 0.138 0.201 1 0.438 0.241 0.322 1
0.046 0.163 0.180 0.251 1 0.999 0.001 0.000 1
0.045 0.160 0.168 0.240 1 0.578 0.422 0.000 1
0.049 0.123 0.131 0.185 1 0.043 0.951 0.006 2*
0.042 0.127 0.105 0.146 1 0.020 0.980 0.000 2
0.042 0.100 0.103 0.140 1 0.974 0.016 0.010 1
0.050 0.149 0.126 0.173 1 0.051 0.000 0.949 3*
0.041 0.146 0.145 0.215 1 0.999 0.000 0.001 1
0.044 0.144 0.121 0.170 1 0.635 0.365 0.000 1
0.047 0.229 0.236 0.328 1 1.000 0.000 0.000 1
0.056 0.253 0.261 0.348 1 1.000 0.000 0.000 1
0.044 0.180 0.188 0.264 1 0.304 0.696 0.000 2*
0.045 0.113 0.115 0.155 1 0.155 0.845 0.000 2*
0.049 0.139 0.114 0.161 1 0.000 0.002 0.998 3*
0.056 0.114 0.117 0.155 1 1.000 0.000 0.000 1
0.060 0.092 0.099 0.134 1 0.000 0.000 1.000 3*
0.048 0.146 0.122 0.171 1 0.417 0.028 0.555 3*
0.033 0.162 0.157 0.236 1 1.000 0.000 0.000 1
0.043 0.143 0.118 0.167 1 0.101 0.899 0.000 2*
0.042 0.142 0.144 0.209 1 0.995 0.002 0.003 1
0.042 0.139 0.115 0.160 2 0.082 0.918 0.000 2
20
0.046 0.130 0.134 0.191 2 0.037 0.933 0.031 2
0.042 0.139 0.117 0.162 2 0.037 0.962 0.001 2
0.042 0.105 0.103 0.146 2 0.000 0.934 0.066 2
0.046 0.110 0.111 0.157 2 0.000 0.970 0.030 2
0.052 0.167 0.188 0.268 2 0.008 0.992 0.000 2
0.043 0.112 0.120 0.166 2 0.212 0.760 0.028 2
0.042 0.096 0.098 0.138 2 0.000 0.994 0.006 2
0.042 0.139 0.119 0.162 2 0.000 0.995 0.005 2
0.040 0.112 0.116 0.167 2 0.004 0.596 0.399 2
0.043 0.109 0.108 0.154 2 0.000 0.345 0.655 3*
0.044 0.128 0.113 0.156 2 0.478 0.496 0.025 2
0.041 0.101 0.099 0.142 2 0.004 0.834 0.162 2
0.051 0.129 0.108 0.146 2 0.000 0.529 0.471 2
0.036 0.134 0.133 0.197 2 0.653 0.329 0.019 1*
0.044 0.141 0.126 0.175 2 0.656 0.338 0.007 1*
0.049 0.123 0.126 0.180 2 0.000 1.000 0.000 2
0.042 0.114 0.104 0.148 2 0.000 0.262 0.738 3*
0.035 0.110 0.127 0.181 2 0.002 0.998 0.000 2
0.047 0.131 0.132 0.192 2 0.153 0.751 0.095 2
0.051 0.411 0.434 0.547 3 1.000 0.000 0.000 1*
0.045 0.163 0.173 0.244 3 0.624 0.376 0.000 1*
0.042 0.109 0.108 0.155 3 0.000 0.083 0.917 3
0.037 0.086 0.094 0.134 3 0.476 0.524 0.000 2*
0.044 0.112 0.144 0.200 3 0.763 0.237 0.000 1*
0.041 0.119 0.113 0.165 3 0.020 0.046 0.935 3
0.041 0.110 0.106 0.154 3 0.006 0.309 0.684 3
0.040 0.121 0.125 0.186 3 0.028 0.172 0.801 3
0.047 0.343 0.366 0.478 3 1.000 0.000 0.000 1*
0.037 0.127 0.125 0.187 3 0.287 0.691 0.022 2*
0.038 0.139 0.138 0.205 3 0.479 0.034 0.486 3
0.041 0.088 0.099 0.142 3 0.001 0.999 0.000 2*
0.050 0.355 0.393 0.506 3 1.000 0.000 0.000 1*
0.035 0.111 0.116 0.173 3 0.294 0.706 0.000 2*
0.045 0.133 0.117 0.160 3 0.077 0.600 0.323 2*
0.052 0.137 0.115 0.156 3 0.000 0.000 1.000 3
0.041 0.121 0.121 0.176 3 0.003 0.023 0.973 3
0.048 0.121 0.102 0.139 3 0.000 0.047 0.953 3
0.049 0.137 0.126 0.182 3 0.000 0.000 1.000 3
0.041 0.114 0.110 0.157 3 0.000 0.129 0.870 3
0.049 0.133 0.128 0.183 3 0.000 0.000 1.000 3
0.041 0.108 0.110 0.158 3 0.001 0.352 0.647 3
0.045 0.113 0.112 0.160 3 0.000 0.180 0.820 3
0.046 0.146 0.147 0.212 3 0.013 0.016 0.971 3
0.045 0.140 0.140 0.201 3 0.014 0.046 0.940 3
21
0.049 0.127 0.112 0.152 3 0.006 0.005 0.989 3
0.044 0.103 0.102 0.146 3 0.000 0.158 0.842 3
0.050 0.152 0.143 0.208 3 0.000 0.000 1.000 3
0.046 0.145 0.136 0.194 3 0.000 0.000 1.000 3
0.044 0.117 0.115 0.168 3 0.029 0.128 0.843 3
0.045 0.108 0.110 0.154 3 0.000 0.079 0.921 3
* Incorrectly classified values
Reflectance of the orchard samples were assigned to the N% classes with the highest posterior
Table 10. Confusion matrix according to mixture discriminant model for test data
Actual class
Deficient Sufficient Excess
Deficient 35 1 2
Predict
class
Sufficient 6 16 8
Excess 4 3 21
Total 45 20 31
The reflectance values of the orchard samples were used as data set for the three different
models. These data were assigned to the three classes, NDeficient, NSufficient and NExcess, with an
accuracy of 77.78%, 80.00% and 67.74%, respectively and the general correct classification
rate was found “satisfactory “ according to range of reliability with a value of 75%. The fact
that the test data (96 plants) randomly selected for all classes and functioned in three different
models were assigned to their classes with satisfying accuracy was significant in terms of the
study objectives. Studies have reported that accuracy coefficient values of ≥0.70 are considered
to be "robust" in the estimation of the N contents of plants using spectral reflectance values and
that they are considered to be “reliable” for the created models.45,84 Based on the results
presented here, the success of the GMDA in studies on the classification of spectral data,85,86
of two or more components are called mixture distributions, and mixture distribution models
different aspects of natural events that are fully random in many fields.87 Thus, they are
22
considered to be useful for the analysis of spectral data, since each spectrum can be separated
from a specific spectral data.86,88,89 However, there is a lack of literature on the use of mixture
discriminant models in the categorization and estimation of nutrient levels in plants using
spectral techniques. In fact, stepwise multiple linear regression90, partial least squares
regression,77 and multivariate linear regression,14 models have been especially commonly used
in many studies conducted in this field. It has been suggested that estimates by the models
produced as a result of multiple regression analyses give results with high accuracy coefficients
(r2) in the plots and plant species (in themselves), whereas their predictive power decreases
significantly with the same plant species in different.17,20 The usage of mixture discriminant
model was ensured an assignment of samples in the N classes. Whereas in many studies,
models were set up for a determination of N content. Similarly, it has been suggested that
differential N application could be performed based on leaf spectra and discriminate analysis
(which has a coefficient of determination of 0.94–0.97) under field condition.81 This study was
showed that mixture discriminant models developed using hyperspectral reflectance data can
determine the critical class ranges of N nutrients in plants with high accuracy and be applied
under field conditions. For the farmers, the rapid prediction of the nitrogen classes in the field
analysis.
Conclusion
In this study, a non-destructive, low cost, rapid, eco-friendly and practical model was
developed and tested under the field conditions for the determination of N classes of peach
modeled using GMDA, were considerable accurate for the determination and monitoring of N
classes of peach trees in agricultural lands during the vegetation period. Many studies have
23
been conducted using spectral techniques in different plant species for determining N content
and similarly, the reflectance variations between the 400-750 nm wavelengths have been
previously associated with N content. In the present study, plants were assigned to one of three
critical N classes rather than directly estimating the N content in peach leaves. This assignment
was succeeded with high accuracy using a wider distribution model, created for experiment
samples, and used in different locations. In this way, a different approach has been presented
for the prediction of plant nutrient status using hyperspectral data. In addition, it was found that
the GMDA was a successful and powerful mathematical approach for modeling used. Thus,
the results of this study provide a different perspective for future studies. It can be suggested
that GMDA integrated with hyperspectral remote sensing is useful in the classification of
different nutrient contents. However, it was seen that some values especially NExcess class made
wrong assignments with error rates ranging from 20% to 35% in classification by the model.
This situation may have occurred due to (1) the difference between the number of observations
used in the training and the test groups, and it could be eliminated by increasing the number of
observations, (2) some critical values, which are the same or very close to the limit values of
the class ranges such as 3.40 to 3.60, (3) although the experimental samples were grown under
controlled conditions, some factors which are a necessity of working with living tissue and
which we cannot control such as instantaneous changes of temperature and radiation intensity,
and (4) orchard samples were grown in their natural environment and under traditional fertilizer
- irrigation applications, in which the error rate was expected to increase. However, the findings
showed that reasonable and remarkable rates were obtained ranging from 67.74% to 80.00%
24
Acknowledgement
I thank Dr. Murat ERİŞOĞLU for statistical comments and advices on the manuscript.
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