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A R T I C L E I N F O A B S T R A C T
Keywords: Growth and production models can help to simulate the growth of tree dimensions to predict forest productivity
Random forest at different levels. In this context, the following questions arise: (i) is it possible to recognize the growth pattern
Classification of eucalyptus species based on spectral features using machine learning (ML) for data modeling? (ii) what
Vegetation index
spectral features provides better accuracy? and (iii) what ML algorithms are most accurate for performing this
modeling? To answer these questions, the present study evaluated the use of ML techniques using breast height
and total plant height to classify the growth of five species of eucalyptus and Corymbria citriodora in an unsu
pervised learning, and the obtained classes for induce ML algorithms to recognize the species with relation to
their growth using vegetation indices (VIs) and spectral bands (SBs). It were evaluated five eucalyptus species
(E. camaldulensis, E. uroplylla, E. saligna, E. grandis e E. urograndis) and C. citriodora in experimental design of
randomized blocks with four replicates, with 20 plants inside each experimental plot. The diameter at breast
height and total plant height at stand level were obtained by measuring five trees in each experimental unit in
seven measurements. During this same period, a flight was carried out using a remotely piloted aircraft for the
acquisition of spectral variables (SBs and VIs). For recognition of eucalyptus species in relation to their growth
two machine learning approaches were employed: supervised and unsupervised. The average accuracy obtained
from 10-fold cross-validation, employing Random Forest algorithm and 24 features, was 0.76. This result shows
that the proposed approach is appropriate to recognize different eucalyptus species based on their growth.
* Corresponding author.
E-mail addresses: bruno@editorapantanal.com.br (B.R. de Oliveira), arlindo.ananias@unesp.br (A.A.P. da Silva), larissa_ribeiro@ufms.br (L.P.R. Teodoro), glauce.
azevedo@ufms.br (G.B. de Azevedo), gileno.azevedo@ufms.br (G.T.O.S. Azevedo), fabiobaio@ufms.br (F.H.R. Baio), rsobrinho@alunos.utfpr.edu.br (R.L. Sobrinho),
carlosjr@unemat.br (C.A. da Silva Junior).
https://doi.org/10.1016/j.foreco.2021.119496
Received 26 May 2021; Received in revised form 25 June 2021; Accepted 30 June 2021
Available online 9 July 2021
0378-1127/© 2021 Elsevier B.V. All rights reserved.
B.R. de Oliveira et al. Forest Ecology and Management 497 (2021) 119496
2019). Among the eucalyptus forests cultivated in the world and in Grosso do Sul (UFMS), Campus of Chapadão do Sul in January 2014. The
Brazil, 90% are made up of nine species and their hybrids: Eucalyptus soil is identified as medium-textured Red Oxisol and the climate is
camaldulensis Dehnh., E. grandis W.Hill ex Maiden, E. tereticornis Sm., tropical humid (Aw) with a rainy season from October to April and a dry
E. globulus Labill., E. nitens H. Deane & Maiden Maiden, E. urophylla S. T. season between May and September. Average rainfall varies from 750 to
Blake, E. saligna Sm., E. dunnii Maiden, E. pellita F. Muell. e Corymbia 1,800 mm/year, and average annual temperature varies from 20 to
citriodora Hook. (Binkley et al., 2017; Gallo et al., 2018; Campoe et al., 25 ◦ C.
2020; Carrijo et al., 2020). It were evaluated five eucalyptus species (E. camaldulensis,
E. grandis is a species that has excellent qualities, surpassing any E. uroplylla, E. saligna, E. grandis e E. urograndis) and Corymbria citriodora
other in increasing the volume of wood when the environmental con in experimental design of randomized blocks with four replicates, with
ditions are adequate, which is the cause of its great use (Chaín et al., 20 plants inside each experimental plot. All fertilization requirements
2020), in addition to having good wood for sawmills and excellent for were determined from soil chemical analysis. The following results were
cellulose (Mphahlele et al., 2020). C. citriodora is a species of moderate obtained: pH (CaCl2): 4.9; organic matter: 31.5 g dm− 3; phosphorus:
growth, usually ranging between 24–40 m in height and 60–120 cm in 13.6 mg dm− 3; hydrogen + aluminium (H + Al): 5.4; potassium: 0.29
diameter (Blackman et al., 2017), with excellent for sawmill, charcoal cmolc dm− 3; calcium: 2.8 cmolc dm− 3; magnesium: 0.5 cmolc dm− 3;
production, posts and sleepers (Souza et al., 2020). E. saligna provides cation exchange capacity (CEC): 9.0 cmolc dm− 3; base saturation:
light, low density wood, suitable for cellulose, firewood, coal, sawmill 39.9%. The proportions of clay, sand, and silt were 46%, 46%, and 8%,
and other purposes (Biazzon et al., 2019; Silva et al., 2020a,b,c). respectively. Crowning, weeding, ant control, and application of herbi
E. urophylla has great morphological and phenological variations in cides (glyphosate) were performed when necessary.
Brazil, according to its altitudinal distribution (Lima Costa, 2020)and
stands out for its high resistance to eucalyptus cancer, in addition to the
2.2. Data acquisition
production of cellulose (Binkley et al., 2017). E. camaldulensis is a
preferred species for planting in tropical regions subject to periods of
The diameter at breast height (DBH) and total plant height (Ht) at
drought due to its tolerance to water deficiency in the soil (Asao et al.,
stand level were obtained by measuring five trees in each experimental
2020).
unit. These trees were the same in each measurement. To obtain the DBH
Thus, different genotypes respond differently to environmental
(cm), a tape measure was used to measure the circumference at breast
changes. The interaction between these factors can affect the perfor
height, which was later converted to DBH. The Ht (m) was obtained with
mance and development of plants in different environments (Gallo et al.,
the aid of a Haglof hypsometer. Seven measurements were performed,
2018; Hakamada et al., 2020a,b). In this sense, recently, non-destructive
which occurred on the following dates: 2018-11-01, 2018-12-06, 2019-
methods are being proposed based on empirical models of crop pro
01-22, 2019-03-29, 2019-05-10, 2019-10-30, and 2019-11-28. For each
ductivity estimation, for example, those that relate values of leaf area
measurement, the average of five trees was considered.
index (LAI) with vegetation indexes (VI) derived from sensors aerial and
The characteristics related to high-throughput phenotyping were
orbital remotes (Canavesi et al., 2010). VIs enhance the spectral
obtained on the same dates. Furthermore, the flights were carried out
reflectance component of vegetation through the combination, mainly,
with Sensefly eBee RTK fixed-wing unmanned aerial vehicle (UAV), with
of the spectral bands of red (R) and near infrared (NIR), and are more
autonomous flight control. Further details on flight procedures and
sensitive to variations in the structure of the canopy than the analysis by
acquisition of wavelengths for calculating VIs can be obtained from Silva
individual bands (Borges et al., 2021; Silva et al., 2021).
et al. (2020a,b,c). The overflights were performed with 80% lateral and
Due to the easiness of acquiring spectral images, either by satellites
85% longitudinal overlap of the images, as well as the same area was
or by remotely piloted aircraft, some researches are being carried out
imaged twice using perpendicular flight lines. The overflight was per
recently to relate these variables with the phenological behavior of
formed at 100 m altitude, allowing a spatial image resolution of 0.10 m.
different forest species (Sanchini and Grosjean, 2020; Vali et al., 2020;
The increase of the overlap between the images was necessary in order
Borges et al., 2021; Silva et al., 2021). Knowledge of the volumetric
to obtain a greater number of scenes containing the same control points,
production and the biomass of the stem of forest plantations is essential.
allowing greater accuracy in the mosaic of the images by the Pix4D
It makes it possible to define the productive capacity of the place and
mapper software. This need occurs according to the plant height, which
specify the application of wood that is used as a raw material in the
is subject to the oscillations of the stem as a function of the wind,
forest products industry. In addition, this knowledge enables decision-
because regardless of its speed, it interferes in the mosaicking process.
making in forest improvement programs (Hakamada et al., 2020a,b;
The overflights were carried out near the zenith due to the minimization
Rocha et al., 2020).
of the shadows of the trees, at 11 a.m., given that the multispectral
Growth and production models can help to simulate the growth of
sensor is passive type, that is, dependent on the solar luminosity. A
tree dimensions (height and diameter) to predict forest productivity at
calibration reference plaque is also used, in the Pix4DMapper software,
different levels. In this context, the following questions arise: (i) is it
to convert the digital number of the pixels into reflectance values. The
possible to recognize the growth pattern of eucalyptus species based on
spectral regions registered by this sensor correspond to green (550 nm),
spectral features using machine learning (ML) for data modeling? ii)
red (660 nm), red-edge (735 nm), and near-infrared (NIR) (790 nm).
what spectral features provides better accuracy? and (iii) what ML al
Table 1 presents all the VIs used in later experiments.
gorithms are most accurate for performing this modeling? To answer
A Pearson correlation analysis between the evaluated variables
these questions, the present study evaluated the use of ML techniques
(DBH, HT, SBs and VIs) was performed. The results were expressed
using breast height and total plant height to classify the growth of five
graphically, where positive correlations were expressed in gray circles,
species of eucalyptus and Corymbria citriodora in an unsupervised
while negative correlations were represented by black circles. The size of
learning, and the obtained classes for induce ML algorithms to recognize
the circle is proportional to the magnitude of the correlation.
the species with relation to their growth using spectral bands and VIs.
2.1. Experiment conducting Due to the characteristics of the problem investigated, two machine
learning approaches were employed: supervised and unsupervised. In
The experiment was installed in the experimental area (18◦ 41′ 33′′ S, the supervised way are implemented algorithms for recognition of the
52◦ 40′ 45′′ W, with altitude is 820 m) of the Federal University of Mato patterns x ∈ RN labeled as y ∈ { − 1, +1}, wherexis a feature vector and
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B.R. de Oliveira et al. Forest Ecology and Management 497 (2021) 119496
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B.R. de Oliveira et al. Forest Ecology and Management 497 (2021) 119496
as measure of the degree of membership of classes. distintic subsets provided by cross-validation. Then, average accuracy is
For the unsupervised way, a clustering algorithm is performed for calculated for performance evaluation.
classification, namely, K-means. This algorithm is based only two steps
that are repeated: (1) an instance is assigned to the clusters whose 3. Results
centroid is closest to this instance; (2) the centroids are updated such
that the new centroids represent the mean center of assigned instances Pearson’s correlations between the evaluated variables are shown in
(Awad and Khanna, 2015). Fig. 2. The growth variables (DBH and Ht) did not present a high
magnitude linear relationship with any spectral variable evaluated.
2.4. Proposed methodology However, most of the spectral variables evaluated are positively corre
lated (grey circles).
In order to recognize eucalyptus species in relation to its growth, it is The first step of the proposed methodology is the instance classifi
necessary to classify each instance, since the dataset is not labeled. For cation using K-means clustering method. For each measurement, in
this, the K-means clustering method is used to group the instances based different dates, this method is executed taking two clusters representing
on the similarities of the samples in relation to the DAP and Ht values, in low- and fast-growth. Figure shows the instances per date, represented
an unsupervised approach. However, as the species were observed on by growth features Ht and DBH, for only three first measurements. The
different dates, this approach must be done for each date separately. instances are limited by circles whose centers is the K-means clusters and
After classifying (groups) the instances, ML methods for recognition the radius is the distance between each center (marked with a red x) and
were implemented in a supervised manner. Since many VIs have been the most distant instance associated with this center.
measured and some of them are linear combination from others (see From clustering shown in Fig. 3, the species 1 (E. camaldulensis), 4
Table 1), then a method for spectral feature selection based on F sta (E. urophylla) and 6 (Corymbia citriodora) are assigned to slow growth
tistics, provided by analysis of variance (ANOVA), was performed. Thus, class and the others are assigned to fast growth class, taking into account
for each feature subgroup, the ML methods are trained and tested. To the distance from the center of the circle.
avoid overfitting when choosing data for training and testing, cross- After classification, spectral features were selected from higher F-
validation approach was performed using 10-fold and the average ac score and lowest p-value using ANOVA statistical test. Table 2 shows
curacy calculated. Following, Fig. 1 illustrate the proposed theses values for each feature. Through the results from Table 2, the
methodology. selection of the features for ML training was done, cumulatively, i.e., for
In the “Features” block, the features of dataset are split to be used in one feature it is used only NormR1, for two features, it is used NormR1
the algorithms that implement two approaches: unsupervised and su and Norm R2 and so on. The first three features selected were NormR1,
pervised learning. In the first approach, the K-means method groups the NormR2 and GSAVI. Of these, the first stood out for presenting a
instances based on their Euclidean distances from a cluster. As the negative correlation with most spectral variables, while the last two
objective is to group the species in fast- and low-growth, two clusters are presented positive correlations.
used. As there is variability in species growth between data collection By varying the numbers of features and hyperparameters of ML al
dates, the clustering method is used for each date separately. Each group gorithms, several models were induced from subsets generated by 10-
corresponds to a class label which is after used for ML algorithms that fold cross-validation. To choose the best hyperparameters, the Grid
employing supervised approach. In this step, the best VI features are Search approach was implemented, which performs the training and
selected, according to ANOVA statistical test, in relation to the variance. testing steps and selects those hyperparameters that provide higher
For the best features, ML algorithms are induced and tested using accuracy.
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B.R. de Oliveira et al. Forest Ecology and Management 497 (2021) 119496
Fig. 2. Pearson correlation’s between the variables diameter at breast height (DBH) and total height (Ht) with the spectral variables described in Table 1. Positive
correlations were expressed in gray circles, while negative correlations were represented by black circles. The size of the circle is proportional to the magnitude of the
correlation.
Fig. 3. Clusters obtained for each date using K-means method based on diameter at breast height (DBH) and total plant height (Ht) of five species of eucalyptus and
C. citriodora. Grey circles grouped the instances. The colors and numbers of bullets mean the species. Red × is the center of circles (cluster). (For interpretation of the
references to colour in this figure legend, the reader is referred to the web version of this article.)
The four best results of each ML algorithm and hyperparameter balanced, entropy as measure of a split and number of trees equal to 10.
configuration employed by scikit-learn library (Pedregosa et al., 2011) Considering the best algorithm (Random Forest) according Table 2,
are described in Table 3. It is possible to observe that the Random Forest Figure shows how the accuracy changes when we vary the number of
algorithm showed the best performance among the others evaluated. virtual trees, keeping the other hyperparameters fixed. As we can see,
The greatest accuracy was obtained with 24 features, weight class the best result is achieved with 10 virtual trees. From this value, the
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B.R. de Oliveira et al. Forest Ecology and Management 497 (2021) 119496
Table 2 Table 3
Selected spectral features according to analysis of variance (ANOVA), F-score Average accuracy obtained by 10-fold cross-validation for several algorithms
and p-value. taking into account different features, provided in Table 2.
Number of selected features Feature* F-score p-Value Number of features Algorithm (hyperparameters) Average accuracy
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B.R. de Oliveira et al. Forest Ecology and Management 497 (2021) 119496
content and photosynthetic efficiency (Scolforo et al., 2019; Chen et al., 5. Conclusion
2020; Reis et al., 2021), which can be observed in phenological attri
butes such as stem diametric growth and plant height (Banks, 2018; Our results show that it is possible to recognize different eucalyptus
Pšidová et al., 2018). Unlike the empirical spectral variables (Lich species in terms of slow- and fast-growth patterns. The best three fea
tenthaler, 1987; Zhou et al., 2021), which are often developed at the leaf tures were Norm R1, Norm R2 and GSAVI. Overall, all ML algorithms
level and can be species, location and time specific, a process modeling had good accuracy (superior to 0.66), but the Random Forest using 24
approach may be responsible for varying other variables that affect features stand out by the highest accuracy (0.76). Therefore, the accu
canopy reflectance, therefore providing a more accurate estimate of the racy in recognizing growth patterns in eucalyptus species is dependent
chlorophyll content, and consequently growth in various cultivated on the ML algorithm and the number of features used in the model.
species, time periods and in broader spatial extensions (Spafford et al., Our results show that ML algorithms applied to spectral data are an
2021). appropriate approach to classify different eucalyptus species based on
Due to the importance of pigments for photosynthesis, variations in growth and to recognize theses species using spectral variables. This
pigment levels can provide information on the physiological state of the approach, supported by unsupervised and supervised learning, may be
plant and therefore on its growth (Zargar et al., 2017; Santos et al., an important strategy in monitoring and management of forest planta
2019). Chlorophylls have strong absorbance peaks in the red and blue tions for providing good accuracy and saving time and labor.
regions of the electromagnetic spectrum (Sanchini and Grosjean, 2020),
however, the reflectance at these wavelengths was not as useful for
classifying the growth of species, since they are closely related to plant Declaration of Competing Interest
development, as the reflectance at longer or shorter wavelengths. This is
because the relatively low chlorophyll contents are sufficient to saturate The authors declare that they have no known competing financial
the absorption in the 660–680 nm region, thus reducing the sensitivity interests or personal relationships that could have appeared to influence
to high chlorophyll contents of spectral variables based on these wave the work reported in this paper.
lengths (Lichtenthaler, 1987; Oliveira et al., 2017).
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