buffer: Identify the buffer zone in the point pattern
In forestSAS: Forest Spatial Structure Analysis Systems
Description
Usage
Arguments
Value
Author(s)
References
Examples
Description
To eliminate edge effects and improve the accuracy of the
Calculation,such as analyzing the forest spatial structure
parameters, we always established a buffer
zone around the plot. In the statistical analysis, only the
trees in the reduced window are used as
reference trees, and the individual trees in the buffer zone
are only considered to be the nearest neighbors of the
trees in the reduced window. This edge
correction can individually evaluate each tree to determine
whether all n nearest neighbors are truly located within
the plot.
Usage
1
buffer(X, buf.xwid = 5, buf.ywid = 5)
Arguments
X
A point pattern (object of class "ppp").
buf.xwid
The width of buffer zone in the x coordinates of data points
buf.ywid
The width of buffer zone in the y coordinates of data points
Value
An object of class "ppp", which add a marks "zone" in the orginal point pattern
Author(s)
Zongzheng Chai, chaizz@126.com
References
Chai ZZ, Sun CL, Wang DX, Liu WZ, and Zhang CS.2016.
Spatial structure and dynamics of predominant populations in a virgin
old-growthoak forest in the Qinling Mountains, China. Scandinavian Journal of Forest Research. DOI:
10.1080/02827581.2016.1183703
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
library(spatstat)
####Based on the simulated data####
# Creating a simulated point pattern
x <- runif(20)
y <- runif(20)
X <- ppp(x, y, c(0,1), c(0,1))
X
# Identifing the buffer zone and core zone in the point pattern
# The width of buffer zone in the x coordinates of data points is 0.2
# The width of buffer zone in the y coordinates of data points is 0.3
X_buf<-buffer(X,buf.xwid =0.2,buf.ywid=0.3)
X_buf
as.data.frame(X_buf)
####Based on the example data####
data(finpines)
finpines
# Marked planar point pattern: 126 points
# Mark variables: diameter, height
# window: rectangle = [-5, 5] x [-8, 2] metres
# Identifing the buffer zone and core zone in the finpines
# The width of buffer zone in the x coordinates of finpines is 2
# The width of buffer zone in the y coordinates of finpines is 3
finpines_buf<-buffer(finpines,buf.xwid =2,buf.ywid=3)
finpines_buf
as.data.frame(finpines_buf)
Example output
Loading required package: spatstat.data
Loading required package: nlme
Loading required package: rpart
spatstat 1.64-1 (nickname: ‘Help you I can, yes!’)
For an introduction to spatstat, type ‘beginner’
Note: spatstat version 1.64-1 is out of date by more than 8 months; we recommend upgrading to the latest version.
Planar point pattern: 20 points
window: rectangle = [0, 1] x [0, 1] units
Marked planar point pattern: 20 points
marks are of storage type ‘character’
window: rectangle = [0, 1] x [0, 1] units
x y marks
1 0.786061556 0.3560393145 core
2 0.883954267 0.0004149135 buffer
3 0.765444344 0.2705544846 buffer
4 0.652685593 0.5836955821 core
5 0.588980209 0.4279244677 core
6 0.188390202 0.3399326128 buffer
7 0.017174433 0.8572971914 buffer
8 0.453981719 0.2106998689 buffer
9 0.498548838 0.0433045919 buffer
10 0.710189351 0.9995242043 buffer
11 0.487205357 0.1595071384 buffer
12 0.815430560 0.3164006171 buffer
13 0.029421117 0.1073130299 buffer
14 0.588426327 0.2176640797 buffer
15 0.644737532 0.7045785759 buffer
16 0.519787660 0.8722142342 buffer
17 0.734523239 0.5549636772 core
18 0.443493712 0.2916929885 buffer
19 0.004635065 0.5046903468 buffer
20 0.445850483 0.5065684102 core
Marked planar point pattern: 126 points
Mark variables: diameter, height
window: rectangle = [-5, 5] x [-8, 2] metres
Marked planar point pattern: 126 points
Mark variables: diameter, height, zone
window: rectangle = [-5, 5] x [-8, 2] units
x y diameter height zone
1 -1.993875e+00 9.297642e-01 1 1.70 buffer
2 -1.019901e+00 4.120694e-01 1 1.70 buffer
3 -4.914071e+00 1.985425e+00 1 1.60 buffer
4 -4.469962e+00 1.452390e+00 5 4.10 buffer
5 -4.303847e+00 9.148214e-01 3 3.10 buffer
6 -3.814774e+00 8.108644e-01 4 4.30 buffer
7 -3.423515e+00 7.276988e-01 2 2.30 buffer
8 -3.130071e+00 6.653246e-01 4 4.00 buffer
9 -4.431633e+00 7.814268e-01 7 5.40 buffer
10 -9.000000e-01 2.067087e-06 2 1.80 buffer
11 -3.899406e+00 6.807388e-02 3 3.20 buffer
12 -1.315571e+00 -4.788248e-01 1 1.30 buffer
13 -2.499282e+00 -7.166504e-01 5 3.80 buffer
14 -2.704594e+00 -7.246863e-01 1 1.50 buffer
15 -4.510529e+00 -1.641685e+00 2 2.10 buffer
16 -4.134652e+00 -1.504878e+00 3 3.30 buffer
17 -4.107759e+00 -1.576808e+00 3 3.00 buffer
18 -4.040682e+00 -1.470676e+00 4 3.20 buffer
19 -3.174177e+00 -1.218442e+00 1 1.50 buffer
20 -3.150349e+00 -2.124924e+00 1 1.60 buffer
21 -4.948165e+00 -3.213357e+00 2 2.10 buffer
22 -5.656871e-01 -5.656838e-01 1 1.40 buffer
23 -3.217394e+00 -2.699698e+00 3 2.80 buffer
24 -2.877367e+00 -2.778625e+00 4 4.00 core
25 -4.027665e+00 -4.973723e+00 1 1.40 buffer
26 -4.847309e+00 -7.464154e+00 1 1.60 buffer
27 -4.738381e+00 -7.296420e+00 3 4.00 buffer
28 -3.914369e-01 -5.803250e-01 1 1.90 buffer
29 -3.444492e+00 -5.512302e+00 7 4.80 buffer
30 -1.960709e+00 -3.019208e+00 1 1.60 core
31 -2.225672e+00 -3.561795e+00 3 3.00 core
32 -9.000050e-01 -1.558843e+00 3 3.10 core
33 -2.450014e+00 -4.243516e+00 6 4.40 core
34 -3.102800e+00 -5.597556e+00 1 2.10 buffer
35 -3.248244e+00 -5.859941e+00 2 3.00 buffer
36 -3.400019e+00 -5.888962e+00 1 2.40 buffer
37 -3.286322e+00 -6.180622e+00 1 1.90 buffer
38 -3.393688e+00 -6.122327e+00 2 2.30 buffer
39 -3.700021e+00 -6.408576e+00 6 4.80 buffer
40 -4.600026e+00 -7.967419e+00 1 1.80 buffer
41 -1.436497e+00 -3.946704e+00 1 2.00 core
42 -2.701983e+00 -7.423563e+00 3 3.50 buffer
43 -1.941167e+00 -7.244437e+00 3 3.30 buffer
44 -1.967049e+00 -7.341030e+00 2 2.80 buffer
45 -1.669284e+00 -6.695035e+00 1 1.65 buffer
46 -1.475744e+00 -5.918799e+00 2 2.40 buffer
47 -1.268229e+00 -4.733033e+00 3 3.50 core
48 -6.531979e-01 -2.619796e+00 0 1.00 core
49 -7.119707e-01 -4.037709e+00 3 3.00 core
50 -1.007178e+00 -5.711882e+00 1 2.40 buffer
51 -9.506087e-01 -7.741857e+00 3 3.40 buffer
52 -7.212717e-01 -6.862198e+00 0 0.80 buffer
53 -2.361414e-05 -7.100000e+00 2 2.30 buffer
54 -2.261636e-05 -6.800000e+00 7 5.00 buffer
55 -1.962302e-05 -5.900000e+00 4 3.60 buffer
56 3.820261e-01 -7.289998e+00 3 3.40 buffer
57 3.506266e-01 -6.690819e+00 2 4.00 buffer
58 5.939180e-01 -6.674507e+00 1 1.50 buffer
59 5.839180e-01 -6.684507e+00 4 4.70 buffer
60 5.752028e-01 -6.574887e+00 6 5.00 buffer
61 4.254918e-01 -6.085142e+00 2 2.80 buffer
62 5.229116e-01 -5.977170e+00 1 1.40 buffer
63 7.839378e-01 -7.458917e+00 2 2.90 buffer
64 7.734853e-01 -7.359465e+00 5 4.60 buffer
65 6.376027e-01 -6.066586e+00 1 1.60 buffer
66 6.271502e-01 -5.967134e+00 1 2.30 buffer
67 6.166977e-01 -5.867682e+00 3 4.40 buffer
68 5.957927e-01 -5.668777e+00 2 3.60 buffer
69 6.580755e-01 -5.359752e+00 6 4.90 buffer
70 3.149265e-01 -1.364119e+00 1 2.10 core
71 7.741384e-01 -3.104949e+00 1 1.50 core
72 8.709057e-01 -3.493068e+00 3 3.00 core
73 1.204589e+00 -3.498423e+00 3 3.00 core
74 1.530154e+00 -4.443943e+00 3 3.20 core
75 1.953639e+00 -4.602531e+00 3 3.20 core
76 1.992711e+00 -4.694582e+00 2 3.00 core
77 2.031784e+00 -4.786633e+00 2 3.00 core
78 2.198075e+00 -5.154835e+00 1 1.90 buffer
79 2.188075e+00 -5.154835e+00 3 3.60 buffer
80 2.237032e+00 -5.024508e+00 3 3.30 buffer
81 2.318379e+00 -5.207218e+00 1 2.40 buffer
82 3.634487e+00 -7.794261e+00 7 4.90 buffer
83 2.323348e+00 -4.763618e+00 2 2.50 core
84 2.411021e+00 -4.943377e+00 1 1.60 core
85 4.302621e+00 -6.625516e+00 7 3.90 buffer
86 4.106847e+00 -6.572390e+00 4 4.00 buffer
87 2.384621e+00 -3.816226e+00 4 4.20 core
88 1.539145e+00 -1.970033e+00 3 3.10 core
89 4.719881e+00 -5.828613e+00 1 1.40 buffer
90 3.583619e+00 -3.341807e+00 4 3.80 buffer
91 2.120918e+00 -1.977804e+00 1 1.80 core
92 4.457258e+00 -2.678217e+00 2 2.90 buffer
93 3.221761e+00 -1.367573e+00 1 2.20 buffer
94 3.129711e+00 -1.328499e+00 3 3.50 buffer
95 1.933057e+00 -8.205435e-01 3 3.20 buffer
96 4.079437e+00 -4.996840e-01 1 2.10 buffer
97 4.069437e+00 -5.096840e-01 6 5.20 buffer
98 2.757459e+00 -4.862275e-01 3 3.50 buffer
99 2.673722e+00 -3.757801e-01 5 3.90 buffer
100 2.382109e+00 -2.924980e-01 1 1.50 buffer
101 2.696299e+00 -1.413200e-01 0 0.90 buffer
102 3.305476e+00 -1.727244e-01 2 2.80 buffer
103 3.295476e+00 -1.627244e-01 1 1.50 buffer
104 3.595065e+00 -1.884266e-01 1 2.30 buffer
105 3.894654e+00 -2.041288e-01 4 4.00 buffer
106 4.397319e+00 -1.535792e-01 0 0.90 buffer
107 2.490487e+00 2.178892e-01 2 2.30 buffer
108 4.881354e+00 4.270628e-01 1 1.20 buffer
109 3.366912e+00 4.731882e-01 2 2.50 buffer
110 3.862046e+00 5.427747e-01 3 3.70 buffer
111 4.159126e+00 5.845266e-01 1 2.00 buffer
112 4.037712e+00 7.119570e-01 4 3.80 buffer
113 3.325702e+00 7.068992e-01 0 1.30 buffer
114 2.934443e+00 6.237346e-01 3 3.20 buffer
115 4.733037e+00 1.268212e+00 2 2.70 buffer
116 4.698464e+00 1.710100e+00 5 4.80 buffer
117 3.296725e+00 1.679764e+00 2 2.30 buffer
118 6.709366e-01 4.357109e-01 6 4.50 buffer
119 2.289731e+00 1.430781e+00 0 1.30 buffer
120 7.372370e-01 5.162184e-01 0 1.30 buffer
121 2.374739e+00 1.992640e+00 3 3.10 buffer
122 1.198207e+00 1.845074e+00 5 4.30 buffer
123 8.714234e-01 1.341872e+00 1 2.10 buffer
124 6.180466e-01 1.028600e+00 6 4.80 buffer
125 2.079127e-01 9.781474e-01 2 2.50 buffer
126 -1.395106e-01 1.995128e+00 0 1.20 buffer
forestSAS documentation built on May 1, 2019, 10:15 p.m.
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Description Usage Arguments Value Author(s) References Examples
Description
To eliminate edge effects and improve the accuracy of the Calculation,such as analyzing the forest spatial structure parameters, we always established a buffer zone around the plot. In the statistical analysis, only the trees in the reduced window are used as reference trees, and the individual trees in the buffer zone are only considered to be the nearest neighbors of the trees in the reduced window. This edge correction can individually evaluate each tree to determine whether all n nearest neighbors are truly located within the plot.
Usage
1 | buffer(X, buf.xwid = 5, buf.ywid = 5)
|
Arguments
X |
A point pattern (object of class "ppp"). |
buf.xwid |
The width of buffer zone in the x coordinates of data points |
buf.ywid |
The width of buffer zone in the y coordinates of data points |
Value
An object of class "ppp", which add a marks "zone" in the orginal point pattern
Author(s)
Zongzheng Chai, chaizz@126.com
References
Chai ZZ, Sun CL, Wang DX, Liu WZ, and Zhang CS.2016. Spatial structure and dynamics of predominant populations in a virgin old-growthoak forest in the Qinling Mountains, China. Scandinavian Journal of Forest Research. DOI: 10.1080/02827581.2016.1183703
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | library(spatstat)
####Based on the simulated data####
# Creating a simulated point pattern
x <- runif(20)
y <- runif(20)
X <- ppp(x, y, c(0,1), c(0,1))
X
# Identifing the buffer zone and core zone in the point pattern
# The width of buffer zone in the x coordinates of data points is 0.2
# The width of buffer zone in the y coordinates of data points is 0.3
X_buf<-buffer(X,buf.xwid =0.2,buf.ywid=0.3)
X_buf
as.data.frame(X_buf)
####Based on the example data####
data(finpines)
finpines
# Marked planar point pattern: 126 points
# Mark variables: diameter, height
# window: rectangle = [-5, 5] x [-8, 2] metres
# Identifing the buffer zone and core zone in the finpines
# The width of buffer zone in the x coordinates of finpines is 2
# The width of buffer zone in the y coordinates of finpines is 3
finpines_buf<-buffer(finpines,buf.xwid =2,buf.ywid=3)
finpines_buf
as.data.frame(finpines_buf)
|
Example output
Loading required package: spatstat.data
Loading required package: nlme
Loading required package: rpart
spatstat 1.64-1 (nickname: ‘Help you I can, yes!’)
For an introduction to spatstat, type ‘beginner’
Note: spatstat version 1.64-1 is out of date by more than 8 months; we recommend upgrading to the latest version.
Planar point pattern: 20 points
window: rectangle = [0, 1] x [0, 1] units
Marked planar point pattern: 20 points
marks are of storage type ‘character’
window: rectangle = [0, 1] x [0, 1] units
x y marks
1 0.786061556 0.3560393145 core
2 0.883954267 0.0004149135 buffer
3 0.765444344 0.2705544846 buffer
4 0.652685593 0.5836955821 core
5 0.588980209 0.4279244677 core
6 0.188390202 0.3399326128 buffer
7 0.017174433 0.8572971914 buffer
8 0.453981719 0.2106998689 buffer
9 0.498548838 0.0433045919 buffer
10 0.710189351 0.9995242043 buffer
11 0.487205357 0.1595071384 buffer
12 0.815430560 0.3164006171 buffer
13 0.029421117 0.1073130299 buffer
14 0.588426327 0.2176640797 buffer
15 0.644737532 0.7045785759 buffer
16 0.519787660 0.8722142342 buffer
17 0.734523239 0.5549636772 core
18 0.443493712 0.2916929885 buffer
19 0.004635065 0.5046903468 buffer
20 0.445850483 0.5065684102 core
Marked planar point pattern: 126 points
Mark variables: diameter, height
window: rectangle = [-5, 5] x [-8, 2] metres
Marked planar point pattern: 126 points
Mark variables: diameter, height, zone
window: rectangle = [-5, 5] x [-8, 2] units
x y diameter height zone
1 -1.993875e+00 9.297642e-01 1 1.70 buffer
2 -1.019901e+00 4.120694e-01 1 1.70 buffer
3 -4.914071e+00 1.985425e+00 1 1.60 buffer
4 -4.469962e+00 1.452390e+00 5 4.10 buffer
5 -4.303847e+00 9.148214e-01 3 3.10 buffer
6 -3.814774e+00 8.108644e-01 4 4.30 buffer
7 -3.423515e+00 7.276988e-01 2 2.30 buffer
8 -3.130071e+00 6.653246e-01 4 4.00 buffer
9 -4.431633e+00 7.814268e-01 7 5.40 buffer
10 -9.000000e-01 2.067087e-06 2 1.80 buffer
11 -3.899406e+00 6.807388e-02 3 3.20 buffer
12 -1.315571e+00 -4.788248e-01 1 1.30 buffer
13 -2.499282e+00 -7.166504e-01 5 3.80 buffer
14 -2.704594e+00 -7.246863e-01 1 1.50 buffer
15 -4.510529e+00 -1.641685e+00 2 2.10 buffer
16 -4.134652e+00 -1.504878e+00 3 3.30 buffer
17 -4.107759e+00 -1.576808e+00 3 3.00 buffer
18 -4.040682e+00 -1.470676e+00 4 3.20 buffer
19 -3.174177e+00 -1.218442e+00 1 1.50 buffer
20 -3.150349e+00 -2.124924e+00 1 1.60 buffer
21 -4.948165e+00 -3.213357e+00 2 2.10 buffer
22 -5.656871e-01 -5.656838e-01 1 1.40 buffer
23 -3.217394e+00 -2.699698e+00 3 2.80 buffer
24 -2.877367e+00 -2.778625e+00 4 4.00 core
25 -4.027665e+00 -4.973723e+00 1 1.40 buffer
26 -4.847309e+00 -7.464154e+00 1 1.60 buffer
27 -4.738381e+00 -7.296420e+00 3 4.00 buffer
28 -3.914369e-01 -5.803250e-01 1 1.90 buffer
29 -3.444492e+00 -5.512302e+00 7 4.80 buffer
30 -1.960709e+00 -3.019208e+00 1 1.60 core
31 -2.225672e+00 -3.561795e+00 3 3.00 core
32 -9.000050e-01 -1.558843e+00 3 3.10 core
33 -2.450014e+00 -4.243516e+00 6 4.40 core
34 -3.102800e+00 -5.597556e+00 1 2.10 buffer
35 -3.248244e+00 -5.859941e+00 2 3.00 buffer
36 -3.400019e+00 -5.888962e+00 1 2.40 buffer
37 -3.286322e+00 -6.180622e+00 1 1.90 buffer
38 -3.393688e+00 -6.122327e+00 2 2.30 buffer
39 -3.700021e+00 -6.408576e+00 6 4.80 buffer
40 -4.600026e+00 -7.967419e+00 1 1.80 buffer
41 -1.436497e+00 -3.946704e+00 1 2.00 core
42 -2.701983e+00 -7.423563e+00 3 3.50 buffer
43 -1.941167e+00 -7.244437e+00 3 3.30 buffer
44 -1.967049e+00 -7.341030e+00 2 2.80 buffer
45 -1.669284e+00 -6.695035e+00 1 1.65 buffer
46 -1.475744e+00 -5.918799e+00 2 2.40 buffer
47 -1.268229e+00 -4.733033e+00 3 3.50 core
48 -6.531979e-01 -2.619796e+00 0 1.00 core
49 -7.119707e-01 -4.037709e+00 3 3.00 core
50 -1.007178e+00 -5.711882e+00 1 2.40 buffer
51 -9.506087e-01 -7.741857e+00 3 3.40 buffer
52 -7.212717e-01 -6.862198e+00 0 0.80 buffer
53 -2.361414e-05 -7.100000e+00 2 2.30 buffer
54 -2.261636e-05 -6.800000e+00 7 5.00 buffer
55 -1.962302e-05 -5.900000e+00 4 3.60 buffer
56 3.820261e-01 -7.289998e+00 3 3.40 buffer
57 3.506266e-01 -6.690819e+00 2 4.00 buffer
58 5.939180e-01 -6.674507e+00 1 1.50 buffer
59 5.839180e-01 -6.684507e+00 4 4.70 buffer
60 5.752028e-01 -6.574887e+00 6 5.00 buffer
61 4.254918e-01 -6.085142e+00 2 2.80 buffer
62 5.229116e-01 -5.977170e+00 1 1.40 buffer
63 7.839378e-01 -7.458917e+00 2 2.90 buffer
64 7.734853e-01 -7.359465e+00 5 4.60 buffer
65 6.376027e-01 -6.066586e+00 1 1.60 buffer
66 6.271502e-01 -5.967134e+00 1 2.30 buffer
67 6.166977e-01 -5.867682e+00 3 4.40 buffer
68 5.957927e-01 -5.668777e+00 2 3.60 buffer
69 6.580755e-01 -5.359752e+00 6 4.90 buffer
70 3.149265e-01 -1.364119e+00 1 2.10 core
71 7.741384e-01 -3.104949e+00 1 1.50 core
72 8.709057e-01 -3.493068e+00 3 3.00 core
73 1.204589e+00 -3.498423e+00 3 3.00 core
74 1.530154e+00 -4.443943e+00 3 3.20 core
75 1.953639e+00 -4.602531e+00 3 3.20 core
76 1.992711e+00 -4.694582e+00 2 3.00 core
77 2.031784e+00 -4.786633e+00 2 3.00 core
78 2.198075e+00 -5.154835e+00 1 1.90 buffer
79 2.188075e+00 -5.154835e+00 3 3.60 buffer
80 2.237032e+00 -5.024508e+00 3 3.30 buffer
81 2.318379e+00 -5.207218e+00 1 2.40 buffer
82 3.634487e+00 -7.794261e+00 7 4.90 buffer
83 2.323348e+00 -4.763618e+00 2 2.50 core
84 2.411021e+00 -4.943377e+00 1 1.60 core
85 4.302621e+00 -6.625516e+00 7 3.90 buffer
86 4.106847e+00 -6.572390e+00 4 4.00 buffer
87 2.384621e+00 -3.816226e+00 4 4.20 core
88 1.539145e+00 -1.970033e+00 3 3.10 core
89 4.719881e+00 -5.828613e+00 1 1.40 buffer
90 3.583619e+00 -3.341807e+00 4 3.80 buffer
91 2.120918e+00 -1.977804e+00 1 1.80 core
92 4.457258e+00 -2.678217e+00 2 2.90 buffer
93 3.221761e+00 -1.367573e+00 1 2.20 buffer
94 3.129711e+00 -1.328499e+00 3 3.50 buffer
95 1.933057e+00 -8.205435e-01 3 3.20 buffer
96 4.079437e+00 -4.996840e-01 1 2.10 buffer
97 4.069437e+00 -5.096840e-01 6 5.20 buffer
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