check: Checks the input data
In Traitspace: A Predictive Model for Trait Based Community Assembly of Plant Species
Description
Usage
Arguments
Details
Value
Examples
Description
Performs basic checks on the data and arranges it in a format that can be used as an input into the remaining functions of this package.
Usage
1
check(level_1, level_2, level_3, site, N)
Arguments
level_1
A column containing the names of the tree species
level_2
Column/s containing the trait values
level_3
Column/s containing enviromental gradient/s
site
A column containing the site names.
N
Size of the simulated trait sample.
Details
Transforms the existing data into appropriate format. This includes: 1) transform level_1 into factors; 2) transform level_2 and level_3 into dataframes; 3) generate a new factor site.name and a new dataframe site by the input site; 4) check the dimentions of these data and 5) make sure level_2 does not has negative value.
Value
A list of transformed data that can be used as an input in the remaining functions of this package.
Examples
1
2
3
4
5
6
7
Example output
Loading required package: permute
Loading required package: mclust
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.
Attaching package: 'Traitspace'
The following object is masked from 'package:permute':
check
[[1]]
function (...) .Primitive("c")
$level_1
[1] S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S2 S2
[26] S2 S2 S2 S2 S2 S1 S1 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2
[51] S3 S3 S3 S3 S3 S3 S3 S3 S3 S4 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3
[76] S3 S4 S4 S4 S4 S4 S4 S4 S4 S4 S4 S4 S4 S4 S5 S4 S4 S4 S4 S4 S4 S4 S4 S4 S4
[101] S4 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S6 S5 S5 S5 S5 S5
[126] S5 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6
Levels: S1 S2 S3 S4 S5 S6
$level_2
X1 X2
1 2.946034 5.004824
2 3.547296 5.722181
3 4.086488 7.065948
4 4.105366 4.943454
5 4.251024 4.006488
6 4.475151 4.993972
7 4.599768 6.146829
8 4.614724 5.434410
9 4.619417 7.761296
10 4.642999 4.882122
11 4.672121 7.433204
12 4.692398 6.907608
13 5.054456 6.000039
14 5.071702 5.207787
15 5.082598 6.400480
16 5.223502 6.958805
17 5.280443 6.652254
18 5.458624 5.623033
19 5.491165 6.843411
20 5.746547 7.396170
21 5.760980 7.127937
22 5.808336 4.961989
23 5.827577 5.130873
24 5.257517 7.959685
25 5.732289 9.165939
26 5.783733 6.971162
27 5.793769 8.958164
28 5.843718 9.336589
29 5.891362 8.537796
30 5.959888 8.902222
31 6.281674 5.419445
32 6.772223 7.082431
33 6.009708 8.957679
34 6.245035 9.984002
35 6.417271 7.934921
36 6.493327 8.430911
37 6.541460 8.636992
38 6.644222 7.731258
39 6.692799 8.770749
40 6.720194 8.220537
41 6.908725 8.062681
42 7.004628 9.470326
43 7.070169 10.250541
44 7.247096 8.374253
45 7.528539 10.021130
46 7.586631 8.495496
47 7.845378 7.766778
48 8.213386 8.473631
49 8.649114 8.397238
50 8.770022 10.605025
51 7.623625 10.913938
52 7.719718 10.194121
53 8.128304 9.564487
54 8.206739 9.821173
55 8.486968 9.460773
56 8.762987 9.784287
57 8.789266 9.780123
58 8.796299 10.084569
59 8.822942 9.372920
60 8.802934 10.357419
61 8.886963 9.480469
62 8.968593 10.050940
63 9.119584 10.443279
64 9.185302 10.732225
65 9.203466 10.463474
66 9.364184 9.421486
67 9.364757 10.827401
68 9.404546 9.837392
69 9.414028 10.286528
70 9.415862 10.594962
71 9.418365 11.011999
72 9.450735 10.400626
73 9.658704 10.669254
74 9.689912 10.106111
75 10.307492 9.940054
76 10.627168 10.595116
77 9.148014 11.466184
78 9.324388 11.757395
79 9.333042 10.076335
80 9.587423 10.653052
81 9.771300 10.684167
82 9.912056 12.158460
83 9.941582 10.622721
84 10.072111 10.965875
85 10.304350 11.025887
86 10.359436 10.717654
87 10.367958 10.842586
88 10.452452 9.808926
89 10.713106 11.192349
90 10.864452 12.341652
91 10.898042 11.036234
92 11.163786 10.281470
93 11.399734 11.302819
94 11.475345 11.241835
95 11.518800 10.800547
96 11.661366 10.469046
97 11.800935 12.342269
98 11.915488 11.148556
99 11.948678 11.278631
100 12.258031 12.249537
101 12.658123 11.549046
102 10.939685 11.851198
103 11.106496 12.049388
104 11.562507 12.785763
105 11.929991 12.009394
106 12.208205 11.490699
107 12.367024 11.862392
108 12.390038 10.663974
109 12.468644 11.596261
110 12.864142 11.261727
111 12.879569 14.207176
112 13.015491 12.738648
113 13.059130 11.100994
114 13.217858 12.922046
115 13.322798 12.432716
116 13.443887 11.194670
117 13.451328 11.970098
118 13.629800 11.667843
119 13.718139 12.559174
120 13.853664 13.444435
121 14.279416 11.044450
122 14.302831 11.045198
123 14.316537 11.616775
124 14.343774 10.961157
125 14.743183 13.463603
126 16.097230 12.793834
127 14.166375 13.396658
128 14.283739 14.313544
129 14.592881 12.584306
130 14.602419 13.917633
131 14.659908 14.090429
132 14.668648 12.672649
133 14.695203 12.708527
134 14.720432 12.614696
135 14.809481 14.859236
136 14.929831 14.548171
137 14.931365 14.009907
138 15.038374 14.300392
139 15.205888 12.045660
140 15.260843 13.282750
141 15.272496 15.173164
142 15.314267 13.425861
143 15.350324 12.795827
144 15.448281 14.823059
145 15.739390 15.213066
146 15.802834 14.146520
147 16.113317 12.486896
148 16.337760 14.003174
149 16.750573 14.376392
150 16.916515 14.536384
$level_3
level_3
1 -3.0
2 -3.0
3 -3.0
4 -3.0
5 -3.0
6 -3.0
7 -3.0
8 -3.0
9 -3.0
10 -3.0
11 -3.0
12 -3.0
13 -3.0
14 -3.0
15 -3.0
16 -3.0
17 -3.0
18 -3.0
19 -3.0
20 -3.0
21 -3.0
22 -3.0
23 -3.0
24 -3.0
25 -3.0
26 -3.0
27 -3.0
28 -3.0
29 -3.0
30 -3.0
31 -1.5
32 -1.5
33 -1.5
34 -1.5
35 -1.5
36 -1.5
37 -1.5
38 -1.5
39 -1.5
40 -1.5
41 -1.5
42 -1.5
43 -1.5
44 -1.5
45 -1.5
46 -1.5
47 -1.5
48 -1.5
49 -1.5
50 -1.5
51 -1.5
52 -1.5
53 -1.5
54 -1.5
55 -1.5
56 -1.5
57 -1.5
58 -1.5
59 -1.5
60 -1.5
61 0.0
62 0.0
63 0.0
64 0.0
65 0.0
66 0.0
67 0.0
68 0.0
69 0.0
70 0.0
71 0.0
72 0.0
73 0.0
74 0.0
75 0.0
76 0.0
77 0.0
78 0.0
79 0.0
80 0.0
81 0.0
82 0.0
83 0.0
84 0.0
85 0.0
86 0.0
87 0.0
88 0.0
89 0.0
90 0.0
91 1.5
92 1.5
93 1.5
94 1.5
95 1.5
96 1.5
97 1.5
98 1.5
99 1.5
100 1.5
101 1.5
102 1.5
103 1.5
104 1.5
105 1.5
106 1.5
107 1.5
108 1.5
109 1.5
110 1.5
111 1.5
112 1.5
113 1.5
114 1.5
115 1.5
116 1.5
117 1.5
118 1.5
119 1.5
120 1.5
121 3.0
122 3.0
123 3.0
124 3.0
125 3.0
126 3.0
127 3.0
128 3.0
129 3.0
130 3.0
131 3.0
132 3.0
133 3.0
134 3.0
135 3.0
136 3.0
137 3.0
138 3.0
139 3.0
140 3.0
141 3.0
142 3.0
143 3.0
144 3.0
145 3.0
146 3.0
147 3.0
148 3.0
149 3.0
150 3.0
$site.name
[1] A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A B B B B B B B
[38] B B B B B B B B B B B B B B B B B B B B B B B C C C C C C C C C C C C C C
[75] C C C C C C C C C C C C C C C C D D D D D D D D D D D D D D D D D D D D D
[112] D D D D D D D D D E E E E E E E E E E E E E E E E E E E E E E E E E E E E
[149] E E
Levels: A B C D E
$site
site
1 A
2 A
3 A
4 A
5 A
6 A
7 A
8 A
9 A
10 A
11 A
12 A
13 A
14 A
15 A
16 A
17 A
18 A
19 A
20 A
21 A
22 A
23 A
24 A
25 A
26 A
27 A
28 A
29 A
30 A
31 B
32 B
33 B
34 B
35 B
36 B
37 B
38 B
39 B
40 B
41 B
42 B
43 B
44 B
45 B
46 B
47 B
48 B
49 B
50 B
51 B
52 B
53 B
54 B
55 B
56 B
57 B
58 B
59 B
60 B
61 C
62 C
63 C
64 C
65 C
66 C
67 C
68 C
69 C
70 C
71 C
72 C
73 C
74 C
75 C
76 C
77 C
78 C
79 C
80 C
81 C
82 C
83 C
84 C
85 C
86 C
87 C
88 C
89 C
90 C
91 D
92 D
93 D
94 D
95 D
96 D
97 D
98 D
99 D
100 D
101 D
102 D
103 D
104 D
105 D
106 D
107 D
108 D
109 D
110 D
111 D
112 D
113 D
114 D
115 D
116 D
117 D
118 D
119 D
120 D
121 E
122 E
123 E
124 E
125 E
126 E
127 E
128 E
129 E
130 E
131 E
132 E
133 E
134 E
135 E
136 E
137 E
138 E
139 E
140 E
141 E
142 E
143 E
144 E
145 E
146 E
147 E
148 E
149 E
150 E
Traitspace documentation built on May 2, 2019, 4:10 a.m.
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Description Usage Arguments Details Value Examples
Description
Performs basic checks on the data and arranges it in a format that can be used as an input into the remaining functions of this package.
Usage
1 | check(level_1, level_2, level_3, site, N)
|
Arguments
level_1 |
A column containing the names of the tree species |
level_2 |
Column/s containing the trait values |
level_3 |
Column/s containing enviromental gradient/s |
site |
A column containing the site names. |
N |
Size of the simulated trait sample. |
Details
Transforms the existing data into appropriate format. This includes: 1) transform level_1 into factors; 2) transform level_2 and level_3 into dataframes; 3) generate a new factor site.name and a new dataframe site by the input site; 4) check the dimentions of these data and 5) make sure level_2 does not has negative value.
Value
A list of transformed data that can be used as an input in the remaining functions of this package.
Examples
1 2 3 4 5 6 7 |
Example output
Loading required package: permute
Loading required package: mclust
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.
Attaching package: 'Traitspace'
The following object is masked from 'package:permute':
check
[[1]]
function (...) .Primitive("c")
$level_1
[1] S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S2 S2
[26] S2 S2 S2 S2 S2 S1 S1 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2
[51] S3 S3 S3 S3 S3 S3 S3 S3 S3 S4 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3 S3
[76] S3 S4 S4 S4 S4 S4 S4 S4 S4 S4 S4 S4 S4 S4 S5 S4 S4 S4 S4 S4 S4 S4 S4 S4 S4
[101] S4 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S5 S6 S5 S5 S5 S5 S5
[126] S5 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6 S6
Levels: S1 S2 S3 S4 S5 S6
$level_2
X1 X2
1 2.946034 5.004824
2 3.547296 5.722181
3 4.086488 7.065948
4 4.105366 4.943454
5 4.251024 4.006488
6 4.475151 4.993972
7 4.599768 6.146829
8 4.614724 5.434410
9 4.619417 7.761296
10 4.642999 4.882122
11 4.672121 7.433204
12 4.692398 6.907608
13 5.054456 6.000039
14 5.071702 5.207787
15 5.082598 6.400480
16 5.223502 6.958805
17 5.280443 6.652254
18 5.458624 5.623033
19 5.491165 6.843411
20 5.746547 7.396170
21 5.760980 7.127937
22 5.808336 4.961989
23 5.827577 5.130873
24 5.257517 7.959685
25 5.732289 9.165939
26 5.783733 6.971162
27 5.793769 8.958164
28 5.843718 9.336589
29 5.891362 8.537796
30 5.959888 8.902222
31 6.281674 5.419445
32 6.772223 7.082431
33 6.009708 8.957679
34 6.245035 9.984002
35 6.417271 7.934921
36 6.493327 8.430911
37 6.541460 8.636992
38 6.644222 7.731258
39 6.692799 8.770749
40 6.720194 8.220537
41 6.908725 8.062681
42 7.004628 9.470326
43 7.070169 10.250541
44 7.247096 8.374253
45 7.528539 10.021130
46 7.586631 8.495496
47 7.845378 7.766778
48 8.213386 8.473631
49 8.649114 8.397238
50 8.770022 10.605025
51 7.623625 10.913938
52 7.719718 10.194121
53 8.128304 9.564487
54 8.206739 9.821173
55 8.486968 9.460773
56 8.762987 9.784287
57 8.789266 9.780123
58 8.796299 10.084569
59 8.822942 9.372920
60 8.802934 10.357419
61 8.886963 9.480469
62 8.968593 10.050940
63 9.119584 10.443279
64 9.185302 10.732225
65 9.203466 10.463474
66 9.364184 9.421486
67 9.364757 10.827401
68 9.404546 9.837392
69 9.414028 10.286528
70 9.415862 10.594962
71 9.418365 11.011999
72 9.450735 10.400626
73 9.658704 10.669254
74 9.689912 10.106111
75 10.307492 9.940054
76 10.627168 10.595116
77 9.148014 11.466184
78 9.324388 11.757395
79 9.333042 10.076335
80 9.587423 10.653052
81 9.771300 10.684167
82 9.912056 12.158460
83 9.941582 10.622721
84 10.072111 10.965875
85 10.304350 11.025887
86 10.359436 10.717654
87 10.367958 10.842586
88 10.452452 9.808926
89 10.713106 11.192349
90 10.864452 12.341652
91 10.898042 11.036234
92 11.163786 10.281470
93 11.399734 11.302819
94 11.475345 11.241835
95 11.518800 10.800547
96 11.661366 10.469046
97 11.800935 12.342269
98 11.915488 11.148556
99 11.948678 11.278631
100 12.258031 12.249537
101 12.658123 11.549046
102 10.939685 11.851198
103 11.106496 12.049388
104 11.562507 12.785763
105 11.929991 12.009394
106 12.208205 11.490699
107 12.367024 11.862392
108 12.390038 10.663974
109 12.468644 11.596261
110 12.864142 11.261727
111 12.879569 14.207176
112 13.015491 12.738648
113 13.059130 11.100994
114 13.217858 12.922046
115 13.322798 12.432716
116 13.443887 11.194670
117 13.451328 11.970098
118 13.629800 11.667843
119 13.718139 12.559174
120 13.853664 13.444435
121 14.279416 11.044450
122 14.302831 11.045198
123 14.316537 11.616775
124 14.343774 10.961157
125 14.743183 13.463603
126 16.097230 12.793834
127 14.166375 13.396658
128 14.283739 14.313544
129 14.592881 12.584306
130 14.602419 13.917633
131 14.659908 14.090429
132 14.668648 12.672649
133 14.695203 12.708527
134 14.720432 12.614696
135 14.809481 14.859236
136 14.929831 14.548171
137 14.931365 14.009907
138 15.038374 14.300392
139 15.205888 12.045660
140 15.260843 13.282750
141 15.272496 15.173164
142 15.314267 13.425861
143 15.350324 12.795827
144 15.448281 14.823059
145 15.739390 15.213066
146 15.802834 14.146520
147 16.113317 12.486896
148 16.337760 14.003174
149 16.750573 14.376392
150 16.916515 14.536384
$level_3
level_3
1 -3.0
2 -3.0
3 -3.0
4 -3.0
5 -3.0
6 -3.0
7 -3.0
8 -3.0
9 -3.0
10 -3.0
11 -3.0
12 -3.0
13 -3.0
14 -3.0
15 -3.0
16 -3.0
17 -3.0
18 -3.0
19 -3.0
20 -3.0
21 -3.0
22 -3.0
23 -3.0
24 -3.0
25 -3.0
26 -3.0
27 -3.0
28 -3.0
29 -3.0
30 -3.0
31 -1.5
32 -1.5
33 -1.5
34 -1.5
35 -1.5
36 -1.5
37 -1.5
38 -1.5
39 -1.5
40 -1.5
41 -1.5
42 -1.5
43 -1.5
44 -1.5
45 -1.5
46 -1.5
47 -1.5
48 -1.5
49 -1.5
50 -1.5
51 -1.5
52 -1.5
53 -1.5
54 -1.5
55 -1.5
56 -1.5
57 -1.5
58 -1.5
59 -1.5
60 -1.5
61 0.0
62 0.0
63 0.0
64 0.0
65 0.0
66 0.0
67 0.0
68 0.0
69 0.0
70 0.0
71 0.0
72 0.0
73 0.0
74 0.0
75 0.0
76 0.0
77 0.0
78 0.0
79 0.0
80 0.0
81 0.0
82 0.0
83 0.0
84 0.0
85 0.0
86 0.0
87 0.0
88 0.0
89 0.0
90 0.0
91 1.5
92 1.5
93 1.5
94 1.5
95 1.5
96 1.5
97 1.5
98 1.5
99 1.5
100 1.5
101 1.5
102 1.5
103 1.5
104 1.5
105 1.5
106 1.5
107 1.5
108 1.5
109 1.5
110 1.5
111 1.5
112 1.5
113 1.5
114 1.5
115 1.5
116 1.5
117 1.5
118 1.5
119 1.5
120 1.5
121 3.0
122 3.0
123 3.0
124 3.0
125 3.0
126 3.0
127 3.0
128 3.0
129 3.0
130 3.0
131 3.0
132 3.0
133 3.0
134 3.0
135 3.0
136 3.0
137 3.0
138 3.0
139 3.0
140 3.0
141 3.0
142 3.0
143 3.0
144 3.0
145 3.0
146 3.0
147 3.0
148 3.0
149 3.0
150 3.0
$site.name
[1] A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A B B B B B B B
[38] B B B B B B B B B B B B B B B B B B B B B B B C C C C C C C C C C C C C C
[75] C C C C C C C C C C C C C C C C D D D D D D D D D D D D D D D D D D D D D
[112] D D D D D D D D D E E E E E E E E E E E E E E E E E E E E E E E E E E E E
[149] E E
Levels: A B C D E
$site
site
1 A
2 A
3 A
4 A
5 A
6 A
7 A
8 A
9 A
10 A
11 A
12 A
13 A
14 A
15 A
16 A
17 A
18 A
19 A
20 A
21 A
22 A
23 A
24 A
25 A
26 A
27 A
28 A
29 A
30 A
31 B
32 B
33 B
34 B
35 B
36 B
37 B
38 B
39 B
40 B
41 B
42 B
43 B
44 B
45 B
46 B
47 B
48 B
49 B
50 B
51 B
52 B
53 B
54 B
55 B
56 B
57 B
58 B
59 B
60 B
61 C
62 C
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65 C
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68 C
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76 C
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85 C
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88 C
89 C
90 C
91 D
92 D
93 D
94 D
95 D
96 D
97 D
98 D
99 D
100 D
101 D
102 D
103 D
104 D
105 D
106 D
107 D
108 D
109 D
110 D
111 D
112 D
113 D
114 D
115 D
116 D
117 D
118 D
119 D
120 D
121 E
122 E
123 E
124 E
125 E
126 E
127 E
128 E
129 E
130 E
131 E
132 E
133 E
134 E
135 E
136 E
137 E
138 E
139 E
140 E
141 E
142 E
143 E
144 E
145 E
146 E
147 E
148 E
149 E
150 E
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