bootstrap: Bootstraps a community matrix
In fsfrazao/SharedS: Assessing the influence of occasional species on shared-species metrics
Description
Usage
Arguments
Value
Examples
Description
This function bootstraps a community matrix. The output can be used by 'conservation_value_seq_CI',
which computes confidence intervals for conservation value curves.
Usage
1
Arguments
data
The community matrix, with species in columns and samples in rows.
n
The number of bootstraped communities.
Value
A r x c x n array, whith the same number of rows (r) and columns (c) as data.
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
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
data(community_data)
#Select all samples in Evironment 'A'
comm.A<-community_data[which(community_data$environment == "A"),]
# Select only the abundance matrix (columns 1 and 2 contain the 'environment' and 'sample' data)
comm.A <- comm.A[, 3:ncol(comm.A)]
bootstrap(comm.A, 3)
, , 1
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1 2 5 6 1 7 1 5 6 0 0 10 9 8
[2,] 5 2 6 2 0 6 6 10 3 0 2 2 1 6
[3,] 1 2 3 6 1 10 3 2 3 0 2 8 1 6
[4,] 6 3 6 2 1 6 3 5 1 0 2 2 10 6
[5,] 5 2 4 6 1 7 6 10 6 0 7 3 9 10
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
[1,] 8 8 0 3 5 5 1 10 0 0 6 7
[2,] 0 2 5 7 1 5 8 0 0 9 2 7
[3,] 2 8 0 4 10 2 8 0 10 8 9 7
[4,] 0 2 8 9 5 2 1 4 0 9 9 7
[5,] 2 2 9 7 4 10 8 2 10 8 9 9
[,27] [,28] [,29] [,30]
[1,] 10 2 8 4
[2,] 7 8 3 7
[3,] 2 2 3 2
[4,] 7 10 6 4
[5,] 7 2 3 4
, , 2
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 6 8 5 5 1 10 6 5 3 0 7 8 6 6
[2,] 5 2 6 6 0 7 6 10 8 0 2 2 10 6
[3,] 6 2 6 2 1 7 3 10 7 0 7 3 9 2
[4,] 5 3 6 2 1 6 6 7 6 0 0 10 1 10
[5,] 5 8 5 2 1 7 3 10 1 0 7 3 9 2
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
[1,] 8 1 4 3 4 2 8 4 0 8 9 9
[2,] 0 2 5 9 5 5 0 4 10 9 2 9
[3,] 0 8 8 9 1 2 0 4 0 3 5 9
[4,] 3 8 4 3 4 3 1 2 10 0 9 7
[5,] 0 1 5 9 5 3 8 2 0 9 5 4
[,27] [,28] [,29] [,30]
[1,] 6 10 2 4
[2,] 6 2 3 4
[3,] 10 10 3 2
[4,] 2 8 8 4
[5,] 2 10 6 8
, , 3
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1 3 6 2 1 6 3 7 1 0 7 2 10 10
[2,] 5 2 4 2 1 6 3 2 8 0 2 10 10 2
[3,] 5 2 5 2 1 6 6 5 7 0 2 8 1 8
[4,] 6 3 6 2 0 6 6 10 8 0 0 5 6 10
[5,] 5 2 5 2 0 6 1 7 6 0 7 3 1 6
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
[1,] 0 8 9 3 1 3 0 10 5 3 2 7
[2,] 0 1 5 3 4 5 8 4 0 9 2 9
[3,] 3 8 0 3 10 2 1 10 0 3 9 7
[4,] 3 8 0 3 1 3 8 10 0 0 9 9
[5,] 8 8 0 9 4 2 0 10 0 3 5 9
[,27] [,28] [,29] [,30]
[1,] 2 10 3 4
[2,] 2 10 8 7
[3,] 6 2 2 4
[4,] 10 8 6 4
[5,] 2 8 3 4
fsfrazao/SharedS documentation built on July 1, 2019, 6:24 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Examples
Description
This function bootstraps a community matrix. The output can be used by 'conservation_value_seq_CI', which computes confidence intervals for conservation value curves.
Usage
1 |
Arguments
data |
The community matrix, with species in columns and samples in rows. |
n |
The number of bootstraped communities. |
Value
A r x c x n array, whith the same number of rows (r) and columns (c) as data.
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 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | data(community_data)
#Select all samples in Evironment 'A'
comm.A<-community_data[which(community_data$environment == "A"),]
# Select only the abundance matrix (columns 1 and 2 contain the 'environment' and 'sample' data)
comm.A <- comm.A[, 3:ncol(comm.A)]
bootstrap(comm.A, 3)
, , 1
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1 2 5 6 1 7 1 5 6 0 0 10 9 8
[2,] 5 2 6 2 0 6 6 10 3 0 2 2 1 6
[3,] 1 2 3 6 1 10 3 2 3 0 2 8 1 6
[4,] 6 3 6 2 1 6 3 5 1 0 2 2 10 6
[5,] 5 2 4 6 1 7 6 10 6 0 7 3 9 10
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
[1,] 8 8 0 3 5 5 1 10 0 0 6 7
[2,] 0 2 5 7 1 5 8 0 0 9 2 7
[3,] 2 8 0 4 10 2 8 0 10 8 9 7
[4,] 0 2 8 9 5 2 1 4 0 9 9 7
[5,] 2 2 9 7 4 10 8 2 10 8 9 9
[,27] [,28] [,29] [,30]
[1,] 10 2 8 4
[2,] 7 8 3 7
[3,] 2 2 3 2
[4,] 7 10 6 4
[5,] 7 2 3 4
, , 2
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 6 8 5 5 1 10 6 5 3 0 7 8 6 6
[2,] 5 2 6 6 0 7 6 10 8 0 2 2 10 6
[3,] 6 2 6 2 1 7 3 10 7 0 7 3 9 2
[4,] 5 3 6 2 1 6 6 7 6 0 0 10 1 10
[5,] 5 8 5 2 1 7 3 10 1 0 7 3 9 2
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
[1,] 8 1 4 3 4 2 8 4 0 8 9 9
[2,] 0 2 5 9 5 5 0 4 10 9 2 9
[3,] 0 8 8 9 1 2 0 4 0 3 5 9
[4,] 3 8 4 3 4 3 1 2 10 0 9 7
[5,] 0 1 5 9 5 3 8 2 0 9 5 4
[,27] [,28] [,29] [,30]
[1,] 6 10 2 4
[2,] 6 2 3 4
[3,] 10 10 3 2
[4,] 2 8 8 4
[5,] 2 10 6 8
, , 3
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1 3 6 2 1 6 3 7 1 0 7 2 10 10
[2,] 5 2 4 2 1 6 3 2 8 0 2 10 10 2
[3,] 5 2 5 2 1 6 6 5 7 0 2 8 1 8
[4,] 6 3 6 2 0 6 6 10 8 0 0 5 6 10
[5,] 5 2 5 2 0 6 1 7 6 0 7 3 1 6
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
[1,] 0 8 9 3 1 3 0 10 5 3 2 7
[2,] 0 1 5 3 4 5 8 4 0 9 2 9
[3,] 3 8 0 3 10 2 1 10 0 3 9 7
[4,] 3 8 0 3 1 3 8 10 0 0 9 9
[5,] 8 8 0 9 4 2 0 10 0 3 5 9
[,27] [,28] [,29] [,30]
[1,] 2 10 3 4
[2,] 2 10 8 7
[3,] 6 2 2 4
[4,] 10 8 6 4
[5,] 2 8 3 4
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.