Abstract
StemAnalysis R package is a tool for designed to reconstruct stem
growth profiles, construct height-diameter relationships, and
consequently to compute growth trends in terms of diameter at breast
height (DBH), tree height, stem volume, tree biomass and carbon storage
for an individual tree. This vignette provides an overview of this
package functions and options. We provide a working examples that
demonstrates the basic functionality and use of the package.
Purpose
Accurate information about age dynamics of timber production and
carbon storage in forest ecosystems is frequently required by
scientists, stakeholders, and policymakers. Stem analysis is a technique
for measuring tree growth (Salas-Eljatib, 2021). The computational
burden of reconstructing temporal, radial, and longitudinal patterns of
tree growth, fitting height-diameter relationships, and calculating
outside-bark diameter from radial annual-ring increment sequences
measured on multiple cross-sectional discs, may present a hindrance to
application of stem analysis methodology in forest research
investigations and operational forest multifunctional management
(Newton, 2019). Therefore, a standardized tool, StemAnalysis R package,
is developed to calculate tree growth dynamics and then make the stem
analysis technique more conveniently applied to forest multifunctional
investigation.
3. Load the stem analysis data stored in the package
The list of input variables and their description in stemdata
dataset
No: The line number
Treeno: The tree number for the sampled tree, the same number
represents the same tree
TreeTH: Tree total height (m)
stemheight: The stem height that the cross-sectional discs were
obtained (m). The detail information see Figure 1
stemage: The age at the stem height, namely the number of growth
rings of the cross-sectional disc (year)
Dwithbark: The maximum outside-bark diameter of the cross-sectional
disc (cm)
Dnobark0: The maximum inside-bark diameter of the cross-sectional
disc without bark (cm)
Dnobark1: The diameter for the 1th age class inner growth ring of
the cross-sectional disc (cm). The detail information see Figure 2
Dnobark2: The diameter for the 2th age class inner growth ring of
the cross-sectional disc (cm)
Dnobark3: The diameter for the 3th age class inner growth ring of
the cross-sectional disc (cm)
Dnobark4: The diameter for the 4th age class inner growth ring of
the cross-sectional disc (cm)
Dnobark5: The diameter for the 5th age class inner growth ring of
the cross-sectional disc (cm)
Dnobark6: The diameter for the 6th age class inner growth ring of
the cross-sectional disc (cm)
Dnobark7: The diameter for the 7th age class inner growth ring of
the cross-sectional disc (cm)
Dnobark8: The diameter for the 8th age class inner growth ring of
the cross-sectional disc (cm)
Dnobark9: The diameter for the 9th age class inner growth ring of
the cross-sectional disc (cm)
Dnobark10: The diameter for the 10th age class inner growth ring of
the cross-sectional disc (cm)
Dnobark11: The diameter for the 11th age class inner growth ring of
the cross-sectional disc (cm)
4. Load the allompardata dataset stored in the package
5. Load the biomass conversion factor data stored in the
package
6. Application of StemAnalysis package
6.1 Stem growth analysis
Reconstructed stem growth patterns and calculated DBH and tree
height growth trends, and outside-bark stem volume increment trends
using stem analysis data.
stemgrowth <- stemanalysism(xtree = 8, stemgrowth = TRUE, stemdata = stemdata)
knitr::kable(stemgrowth)
0 |
0 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
Dnobark9 |
2 |
0.000 |
0.839 |
0.000 |
0.000 |
0.000 |
0.419 |
0.419 |
0.000 |
0.000 |
Dnobark8 |
4 |
2.093 |
2.200 |
0.001 |
1.046 |
0.523 |
0.681 |
0.550 |
0.001 |
0.000 |
Dnobark7 |
6 |
5.134 |
4.787 |
0.008 |
1.520 |
0.856 |
1.294 |
0.798 |
0.003 |
0.001 |
Dnobark6 |
8 |
6.111 |
6.720 |
0.011 |
0.489 |
0.764 |
0.966 |
0.840 |
0.002 |
0.001 |
Dnobark5 |
10 |
7.197 |
8.826 |
0.017 |
0.543 |
0.720 |
1.053 |
0.883 |
0.003 |
0.002 |
Dnobark4 |
12 |
8.392 |
10.908 |
0.027 |
0.597 |
0.699 |
1.041 |
0.909 |
0.005 |
0.002 |
Dnobark3 |
14 |
9.043 |
11.333 |
0.034 |
0.326 |
0.646 |
0.213 |
0.810 |
0.003 |
0.002 |
Dnobark2 |
16 |
9.586 |
12.446 |
0.040 |
0.272 |
0.599 |
0.556 |
0.778 |
0.003 |
0.002 |
Dnobark1 |
18 |
9.695 |
12.467 |
0.044 |
0.054 |
0.539 |
0.010 |
0.693 |
0.002 |
0.002 |
Dnobark0 |
20 |
10.347 |
12.600 |
0.052 |
0.326 |
0.517 |
0.067 |
0.630 |
0.004 |
0.003 |
|
Table 1 The tree age chronosequence and the corresponding growth
data of DBH, stem height, and stem volume. stemdj is the age class of a
tree growths (year); DBHt is the tree diameter at breast height (cm);
Height is the tree height (m); Volume is the tree stem volume (m3);
AnincreD is the mean annual increment of diameter at breast height (cm);
AvincreD is the current annual increment of diameter at breast height
(cm); AnincreH is the mean annual increment of tree height (m); AvincreH
is the current annual increment of tree height (m); AnincreV is the mean
annual increment of tree stem volume (m3); AvincreV is the current
annual increment of tree stem volume (m3).
Figure 3 Stem growth patterns of an individual tree. (a) shows the
stem growth pattern; (b), (c), and (d) are the cumulative growth and
(e), (f), and (g) are the mean annual increment (red dotted line) and
current annual increment (blue dashed line) of DBH, tree height, and
stem volume, respectively.
6.2 Estimation Of tree carbon accumulation
6.2.1 Tree biomass and carbon accumulation estimated by allometric
models
If set ‘treecarbon = TRUE’ and provide allompardata data, tree
biomass and carbon accumulation estimated by allometric models.
allomcarbon <- stemanalysism(xtree = 8, treecarbon = TRUE, stemdata = stemdata, allompardata = allomPardata)
knitr::kable(allomcarbon)
0 |
0 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
Dnobark9 |
2 |
0.000 |
0.839 |
0.000 |
0.000 |
0.000 |
0.419 |
0.419 |
0.000 |
0.000 |
Dnobark8 |
4 |
2.093 |
2.200 |
0.001 |
1.046 |
0.523 |
0.681 |
0.550 |
0.001 |
0.000 |
Dnobark7 |
6 |
5.134 |
4.787 |
0.008 |
1.520 |
0.856 |
1.294 |
0.798 |
0.003 |
0.001 |
Dnobark6 |
8 |
6.111 |
6.720 |
0.011 |
0.489 |
0.764 |
0.966 |
0.840 |
0.002 |
0.001 |
Dnobark5 |
10 |
7.197 |
8.826 |
0.017 |
0.543 |
0.720 |
1.053 |
0.883 |
0.003 |
0.002 |
Dnobark4 |
12 |
8.392 |
10.908 |
0.027 |
0.597 |
0.699 |
1.041 |
0.909 |
0.005 |
0.002 |
Dnobark3 |
14 |
9.043 |
11.333 |
0.034 |
0.326 |
0.646 |
0.213 |
0.810 |
0.003 |
0.002 |
Dnobark2 |
16 |
9.586 |
12.446 |
0.040 |
0.272 |
0.599 |
0.556 |
0.778 |
0.003 |
0.002 |
Dnobark1 |
18 |
9.695 |
12.467 |
0.044 |
0.054 |
0.539 |
0.010 |
0.693 |
0.002 |
0.002 |
Dnobark0 |
20 |
10.347 |
12.600 |
0.052 |
0.326 |
0.517 |
0.067 |
0.630 |
0.004 |
0.003 |
|
0 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
2 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
4 |
0.765 |
0.145 |
0.910 |
0.382 |
0.071 |
0.453 |
6 |
3.844 |
0.854 |
4.698 |
1.923 |
0.417 |
2.340 |
8 |
6.461 |
1.276 |
7.736 |
3.232 |
0.622 |
3.855 |
10 |
10.283 |
1.868 |
12.151 |
5.145 |
0.912 |
6.056 |
12 |
15.564 |
2.688 |
18.252 |
7.787 |
1.312 |
9.098 |
14 |
18.444 |
3.233 |
21.677 |
9.228 |
1.578 |
10.805 |
16 |
21.730 |
3.705 |
25.435 |
10.871 |
1.808 |
12.680 |
18 |
22.247 |
3.812 |
26.059 |
11.130 |
1.860 |
12.990 |
20 |
25.501 |
4.488 |
29.989 |
12.758 |
2.190 |
14.948 |
|
Table 2 The stem growth data (the same to Table 1) and tree biomass
and carbon storage that estimated by allometric models. treeage is the
age class of a tree growths (year); abovegroundB is the aboveground
biomass of a sampled tree (kg); belowgroundB is the belowground biomass
of a sampled tree (kg); totalB is the total tree biomass of a sampled
tree (kg); abovegroundC is the aboveground carbon storage of a sampled
tree (kg); belowgroundC is the belowground carbon storage of a sampled
tree (kg); totalC is the total tree carbon storage of a sampled tree
(kg).
Figure 4 The age dynamics of total tree biomass (a) and carbon
storage (b) for the 20-year-old Chinese fir tree estimated using
allometric models.
6.2.2 Tree biomass and carbon accumulation estimated by volume
model
If set ‘treecarbon = TRUE’ and provide biomass conversion factor
data, tree biomass and carbon accumulation estimated by volume
model.
volumecarbon <- stemanalysism(xtree = 8, treecarbon = TRUE, stemdata = stemdata, volumepardata = volumePardata)
knitr::kable(volumecarbon)
0 |
0 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
Dnobark9 |
2 |
0.000 |
0.839 |
0.000 |
0.000 |
0.000 |
0.419 |
0.419 |
0.000 |
0.000 |
Dnobark8 |
4 |
2.093 |
2.200 |
0.001 |
1.046 |
0.523 |
0.681 |
0.550 |
0.001 |
0.000 |
Dnobark7 |
6 |
5.134 |
4.787 |
0.008 |
1.520 |
0.856 |
1.294 |
0.798 |
0.003 |
0.001 |
Dnobark6 |
8 |
6.111 |
6.720 |
0.011 |
0.489 |
0.764 |
0.966 |
0.840 |
0.002 |
0.001 |
Dnobark5 |
10 |
7.197 |
8.826 |
0.017 |
0.543 |
0.720 |
1.053 |
0.883 |
0.003 |
0.002 |
Dnobark4 |
12 |
8.392 |
10.908 |
0.027 |
0.597 |
0.699 |
1.041 |
0.909 |
0.005 |
0.002 |
Dnobark3 |
14 |
9.043 |
11.333 |
0.034 |
0.326 |
0.646 |
0.213 |
0.810 |
0.003 |
0.002 |
Dnobark2 |
16 |
9.586 |
12.446 |
0.040 |
0.272 |
0.599 |
0.556 |
0.778 |
0.003 |
0.002 |
Dnobark1 |
18 |
9.695 |
12.467 |
0.044 |
0.054 |
0.539 |
0.010 |
0.693 |
0.002 |
0.002 |
Dnobark0 |
20 |
10.347 |
12.600 |
0.052 |
0.326 |
0.517 |
0.067 |
0.630 |
0.004 |
0.003 |
|
0 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
2 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
0.000 |
4 |
0.765 |
0.190 |
0.944 |
0.179 |
1.123 |
0.471 |
0.089 |
0.561 |
6 |
0.586 |
0.222 |
4.724 |
1.050 |
5.774 |
2.357 |
0.524 |
2.881 |
8 |
0.510 |
0.197 |
5.744 |
1.134 |
6.878 |
2.866 |
0.566 |
3.432 |
10 |
0.458 |
0.182 |
7.885 |
1.433 |
9.318 |
3.935 |
0.715 |
4.650 |
12 |
0.423 |
0.173 |
11.291 |
1.950 |
13.241 |
5.634 |
0.973 |
6.607 |
14 |
0.420 |
0.175 |
14.142 |
2.479 |
16.621 |
7.057 |
1.237 |
8.294 |
16 |
0.405 |
0.171 |
16.085 |
2.743 |
18.828 |
8.026 |
1.369 |
9.395 |
18 |
0.406 |
0.171 |
17.985 |
3.082 |
21.066 |
8.974 |
1.538 |
10.512 |
20 |
0.408 |
0.176 |
21.176 |
3.727 |
24.903 |
10.567 |
1.860 |
12.427 |
|
Table 3 The stem growth data (the same to Table 1) and tree biomass
and carbon storage that estimated by volume model. treeage is the age
class of a tree growths (year); BCF is the estimated Biomass Conversion
Factor; RSR is the estimated Root-to-Shoot Ratio; abovegroundB is the
aboveground biomass of a sampled tree (kg); belowgroundB is the
belowground biomass of a sampled tree (kg); totalB is the total tree
biomass of a sampled tree (kg); abovegroundC is the aboveground carbon
storage of a sampled tree (kg); belowgroundC is the belowground carbon
storage of a sampled tree (kg); totalC is the total tree carbon storage
of a sampled tree (kg).
Figure 5 The age dynamics of total tree biomass (a) and carbon
storage (b) for the 20-year-old Chinese fir tree estimated using volume
model.
6.3 Construction of height-diameter relationship
If set ‘HDmodel = TRUE’, tree height-diameter relationship will be
constructed by nonlinear models, and the fitted statistics are showed in
a graph.
stemgrowth <- stemanalysism(xtree = 8, HDmodel = TRUE, stemdata = stemdata)
Figure 6 Tree height-diameter relationships for the 20-year-old
Chinese fir tree. The fitted curves of the Chapman-Richards model (red
line), Logistic model (blue line), Weibull model (green line), and
Gomperz model (yellow line) as well as their fitted statistics. a, b and
C are the parameters of the nonlinear models; R2 is the coefficient of
determination; RSS is the residual sum of squares; AIC is the akaike
information criterion; logLik is the Log-Likelihood value.
References
IPCC. (2003) Good Practice Guidance for Land Use, Land-Use Change
and Forestry; IPCC/IGES: Hayama, Japan.
Newton, P.F. (2019) Examining naturogenic processes and
anthropogenic influences on tree growth and development via stem
analysis: data processing and computational analytics. Forests 10,
1058.
Salas-Eljatib, C. (2021) A new algorithm for reconstructing the
height growth with stem analysis data. Methods Ecol. Evol. 12,
2008–2016.
National Forestry and Grassland Administration. (2014) Tree biomass
models and related parameters to carbon accounting for Cunninghamria
lanceolata. Forestry industry standards of the People’s Republic of
China, Beijing, LY/T 2264—2014.