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tests/testthat/_snaps/fortify-ordination-methods.md
In ggvegan: 'ggplot2' Plots for the 'vegan' Package
fortify works for cca like objects
Code
fortify(dune_pca)
Output
# A tibble: 50 x 8
score label pc1 pc2 pc3 pc4 pc5 pc6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.604 -0.124 0.00846 0.160 -0.409 -0.128
2 species Agrostol -1.37 0.964 0.167 0.266 0.0877 -0.0474
3 species Airaprae -0.0234 -0.251 -0.195 -0.326 -0.0557 0.0796
4 species Alopgeni -0.531 1.43 -0.505 -0.0429 0.443 -0.279
5 species Anthodor 0.559 -0.568 -0.476 0.0158 -0.344 0.136
6 species Bellpere 0.334 0.189 0.141 -0.0842 -0.125 -0.135
7 species Bromhord 0.523 0.197 0.164 0.00567 -0.386 -0.258
8 species Chenalbu -0.0175 0.0546 -0.0553 -0.0106 -0.0266 -0.0164
9 species Cirsarve -0.00240 0.102 0.0637 -0.0487 0.0321 0.0361
10 species Comapalu -0.169 -0.105 0.0636 0.0524 -0.131 -0.108
# i 40 more rows
Code
fortify(dune_ca)
Output
# A tibble: 50 x 8
score label ca1 ca2 ca3 ca4 ca5 ca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.909 -0.0846 0.586 -0.00892 -0.660 -0.189
2 species Agrostol -0.934 0.207 -0.282 0.0243 -0.139 -0.0226
3 species Airaprae 1.00 -3.07 -1.34 0.194 -1.08 -0.537
4 species Alopgeni -0.401 0.618 -0.850 0.347 0.0165 0.102
5 species Anthodor 0.967 -1.08 0.172 0.460 -0.608 -0.304
6 species Bellpere 0.500 0.355 0.152 -0.704 -0.0585 0.0731
7 species Bromhord 0.658 0.406 0.307 -0.497 -0.561 0.0700
8 species Chenalbu -0.424 0.844 -1.59 1.25 -0.207 0.876
9 species Cirsarve 0.0565 0.764 -0.918 -1.18 -0.384 -0.140
10 species Comapalu -1.92 -0.522 1.18 -0.0217 -1.36 1.31
# i 40 more rows
Code
fortify(dune_rda)
Output
# A tibble: 90 x 8
score label rda1 rda2 rda3 rda4 rda5 rda6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.598 -0.111 0.0923 0.0490 -0.0751 0.272
2 species Agrostol -1.18 0.963 0.194 0.227 0.261 0.108
3 species Airaprae -0.111 -0.205 0.0183 -0.180 0.0796 0.108
4 species Alopgeni -0.491 1.42 0.0492 -0.210 -0.126 -0.121
5 species Anthodor 0.421 -0.369 -0.219 0.0134 0.214 0.483
6 species Bellpere 0.375 -0.00458 0.133 -0.0719 0.0840 0.227
7 species Bromhord 0.547 0.0669 0.263 0.0629 -0.109 0.347
8 species Chenalbu -0.0333 0.0454 0.0000779 0.0106 0.0194 0.0362
9 species Cirsarve 0.0205 0.0912 0.0664 -0.0236 0.0943 0.00858
10 species Comapalu -0.198 -0.107 -0.00589 0.183 -0.0969 -0.0371
# i 80 more rows
Code
fortify(dune_cca)
Output
# A tibble: 90 x 8
score label cca1 cca2 cca3 cca4 cca5 cca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.841 -0.438 -0.150 0.275 0.0510 0.236
2 species Agrostol -0.765 0.481 0.0317 0.147 0.221 0.0954
3 species Airaprae -0.733 -1.75 1.15 -0.109 0.246 0.482
4 species Alopgeni -0.345 1.03 0.364 0.113 -0.0402 -0.0165
5 species Anthodor 0.390 -0.830 0.0306 -0.167 0.316 0.447
6 species Bellpere 0.707 -0.251 0.0109 0.490 0.158 0.409
7 species Bromhord 0.832 -0.119 -0.145 0.655 0.0944 0.283
8 species Chenalbu -0.973 1.30 0.517 0.0117 1.37 -0.252
9 species Cirsarve 0.429 0.741 0.495 0.977 1.07 0.601
10 species Comapalu -2.01 -0.351 -2.28 0.110 -0.485 1.20
# i 80 more rows
Code
fortify(dune_pco)
Output
# A tibble: 20 x 8
score label mds1 mds2 mds3 mds4 mds5 mds6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 -0.857 0.172 -2.61 1.13 -0.451 2.49
2 sites 2 -1.64 1.23 -0.887 0.986 -2.03 -1.81
3 sites 3 -0.440 2.38 -0.930 0.460 1.03 0.0518
4 sites 4 0.0479 2.05 -1.27 0.974 0.642 0.721
5 sites 5 -1.62 -0.290 1.59 -1.54 -1.86 2.21
6 sites 6 -1.97 -1.08 1.15 -3.35 1.52 -0.0313
7 sites 7 -1.79 -0.322 0.220 -1.47 -0.0125 0.426
8 sites 8 0.890 1.09 -0.925 -0.516 1.09 -0.948
9 sites 9 0.00904 1.66 0.466 0.283 0.108 2.17
10 sites 10 -1.91 -0.494 -0.706 -0.268 -1.37 -2.62
11 sites 11 -1.04 -1.21 -1.42 0.957 2.72 -1.11
12 sites 12 1.02 1.46 3.25 0.325 1.75 -1.02
13 sites 13 0.699 2.18 2.21 0.423 -1.07 -0.656
14 sites 14 1.49 -0.977 -0.545 -0.273 -2.39 -2.48
15 sites 15 1.89 -1.13 -0.727 -0.773 -0.221 0.318
16 sites 16 2.85 0.208 -0.704 -2.10 -0.293 0.0812
17 sites 17 0.0467 -1.73 0.914 1.67 -1.80 1.56
18 sites 18 -0.269 -1.72 -0.165 0.577 2.10 -0.339
19 sites 19 0.281 -2.19 1.99 3.23 0.458 0.0239
20 sites 20 2.34 -1.30 -0.903 -0.718 0.0757 0.969
Code
fortify(dune_dbrda)
Output
# A tibble: 69 x 8
score label dbrda1 dbrda2 dbrda3 dbrda4 dbrda5 dbrda6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 -0.980 0.00752 -1.73 1.12 2.75 2.35
2 sites 2 -1.73 -0.845 -1.80 0.409 -2.33 -3.44
3 sites 3 -0.597 -2.49 -1.58 0.989 1.22 0.711
4 sites 4 -0.0978 -2.15 -1.93 1.05 2.34 -0.873
5 sites 5 -1.72 0.329 3.40 -0.987 1.73 -2.40
6 sites 6 -2.11 0.831 2.75 -2.75 -0.481 2.33
7 sites 7 -1.91 0.305 0.812 -1.46 0.562 0.955
8 sites 8 0.811 -1.27 -1.23 -1.47 -0.894 0.227
9 sites 9 -0.0647 -1.75 2.16 1.63 -1.84 -0.109
10 sites 10 -1.97 0.718 -1.87 -1.08 -1.78 -2.89
# i 59 more rows
tidy works for cca like objects
Code
tidy(dune_pca)
Output
# A tibble: 50 x 8
score label pc1 pc2 pc3 pc4 pc5 pc6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.604 -0.124 0.00846 0.160 -0.409 -0.128
2 species Agrostol -1.37 0.964 0.167 0.266 0.0877 -0.0474
3 species Airaprae -0.0234 -0.251 -0.195 -0.326 -0.0557 0.0796
4 species Alopgeni -0.531 1.43 -0.505 -0.0429 0.443 -0.279
5 species Anthodor 0.559 -0.568 -0.476 0.0158 -0.344 0.136
6 species Bellpere 0.334 0.189 0.141 -0.0842 -0.125 -0.135
7 species Bromhord 0.523 0.197 0.164 0.00567 -0.386 -0.258
8 species Chenalbu -0.0175 0.0546 -0.0553 -0.0106 -0.0266 -0.0164
9 species Cirsarve -0.00240 0.102 0.0637 -0.0487 0.0321 0.0361
10 species Comapalu -0.169 -0.105 0.0636 0.0524 -0.131 -0.108
# i 40 more rows
Code
tidy(dune_ca)
Output
# A tibble: 50 x 8
score label ca1 ca2 ca3 ca4 ca5 ca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.909 -0.0846 0.586 -0.00892 -0.660 -0.189
2 species Agrostol -0.934 0.207 -0.282 0.0243 -0.139 -0.0226
3 species Airaprae 1.00 -3.07 -1.34 0.194 -1.08 -0.537
4 species Alopgeni -0.401 0.618 -0.850 0.347 0.0165 0.102
5 species Anthodor 0.967 -1.08 0.172 0.460 -0.608 -0.304
6 species Bellpere 0.500 0.355 0.152 -0.704 -0.0585 0.0731
7 species Bromhord 0.658 0.406 0.307 -0.497 -0.561 0.0700
8 species Chenalbu -0.424 0.844 -1.59 1.25 -0.207 0.876
9 species Cirsarve 0.0565 0.764 -0.918 -1.18 -0.384 -0.140
10 species Comapalu -1.92 -0.522 1.18 -0.0217 -1.36 1.31
# i 40 more rows
Code
tidy(dune_rda)
Output
# A tibble: 99 x 8
score label rda1 rda2 rda3 rda4 rda5 rda6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.598 -0.111 0.0923 0.0490 -0.0751 0.272
2 species Agrostol -1.18 0.963 0.194 0.227 0.261 0.108
3 species Airaprae -0.111 -0.205 0.0183 -0.180 0.0796 0.108
4 species Alopgeni -0.491 1.42 0.0492 -0.210 -0.126 -0.121
5 species Anthodor 0.421 -0.369 -0.219 0.0134 0.214 0.483
6 species Bellpere 0.375 -0.00458 0.133 -0.0719 0.0840 0.227
7 species Bromhord 0.547 0.0669 0.263 0.0629 -0.109 0.347
8 species Chenalbu -0.0333 0.0454 0.0000779 0.0106 0.0194 0.0362
9 species Cirsarve 0.0205 0.0912 0.0664 -0.0236 0.0943 0.00858
10 species Comapalu -0.198 -0.107 -0.00589 0.183 -0.0969 -0.0371
# i 89 more rows
Code
tidy(dune_cca)
Output
# A tibble: 90 x 8
score label cca1 cca2 cca3 cca4 cca5 cca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.841 -0.438 -0.150 0.275 0.0510 0.236
2 species Agrostol -0.765 0.481 0.0317 0.147 0.221 0.0954
3 species Airaprae -0.733 -1.75 1.15 -0.109 0.246 0.482
4 species Alopgeni -0.345 1.03 0.364 0.113 -0.0402 -0.0165
5 species Anthodor 0.390 -0.830 0.0306 -0.167 0.316 0.447
6 species Bellpere 0.707 -0.251 0.0109 0.490 0.158 0.409
7 species Bromhord 0.832 -0.119 -0.145 0.655 0.0944 0.283
8 species Chenalbu -0.973 1.30 0.517 0.0117 1.37 -0.252
9 species Cirsarve 0.429 0.741 0.495 0.977 1.07 0.601
10 species Comapalu -2.01 -0.351 -2.28 0.110 -0.485 1.20
# i 80 more rows
Code
tidy(dune_pco)
Output
# A tibble: 20 x 8
score label mds1 mds2 mds3 mds4 mds5 mds6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 -0.857 0.172 -2.61 1.13 -0.451 2.49
2 sites 2 -1.64 1.23 -0.887 0.986 -2.03 -1.81
3 sites 3 -0.440 2.38 -0.930 0.460 1.03 0.0518
4 sites 4 0.0479 2.05 -1.27 0.974 0.642 0.721
5 sites 5 -1.62 -0.290 1.59 -1.54 -1.86 2.21
6 sites 6 -1.97 -1.08 1.15 -3.35 1.52 -0.0313
7 sites 7 -1.79 -0.322 0.220 -1.47 -0.0125 0.426
8 sites 8 0.890 1.09 -0.925 -0.516 1.09 -0.948
9 sites 9 0.00904 1.66 0.466 0.283 0.108 2.17
10 sites 10 -1.91 -0.494 -0.706 -0.268 -1.37 -2.62
11 sites 11 -1.04 -1.21 -1.42 0.957 2.72 -1.11
12 sites 12 1.02 1.46 3.25 0.325 1.75 -1.02
13 sites 13 0.699 2.18 2.21 0.423 -1.07 -0.656
14 sites 14 1.49 -0.977 -0.545 -0.273 -2.39 -2.48
15 sites 15 1.89 -1.13 -0.727 -0.773 -0.221 0.318
16 sites 16 2.85 0.208 -0.704 -2.10 -0.293 0.0812
17 sites 17 0.0467 -1.73 0.914 1.67 -1.80 1.56
18 sites 18 -0.269 -1.72 -0.165 0.577 2.10 -0.339
19 sites 19 0.281 -2.19 1.99 3.23 0.458 0.0239
20 sites 20 2.34 -1.30 -0.903 -0.718 0.0757 0.969
Code
tidy(dune_dbrda)
Output
# A tibble: 69 x 8
score label dbrda1 dbrda2 dbrda3 dbrda4 dbrda5 dbrda6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 -0.980 0.00752 -1.73 1.12 2.75 2.35
2 sites 2 -1.73 -0.845 -1.80 0.409 -2.33 -3.44
3 sites 3 -0.597 -2.49 -1.58 0.989 1.22 0.711
4 sites 4 -0.0978 -2.15 -1.93 1.05 2.34 -0.873
5 sites 5 -1.72 0.329 3.40 -0.987 1.73 -2.40
6 sites 6 -2.11 0.831 2.75 -2.75 -0.481 2.33
7 sites 7 -1.91 0.305 0.812 -1.46 0.562 0.955
8 sites 8 0.811 -1.27 -1.23 -1.47 -0.894 0.227
9 sites 9 -0.0647 -1.75 2.16 1.63 -1.84 -0.109
10 sites 10 -1.97 0.718 -1.87 -1.08 -1.78 -2.89
# i 59 more rows
fortify works for cca with layers length 1
Code
fortify(dune_cca, layers = "sites")
Output
# A tibble: 20 x 8
score label cca1 cca2 cca3 cca4 cca5 cca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 1.22 0.422 0.546 1.09 0.790 -2.12
2 sites 2 0.862 0.177 0.0575 1.50 0.144 1.15
3 sites 3 0.317 0.969 0.648 0.900 0.544 -0.314
4 sites 4 0.243 0.872 0.812 1.51 1.38 1.18
5 sites 5 1.14 -0.283 -0.774 -1.34 1.01 1.17
6 sites 6 1.03 -0.371 -1.34 -2.05 0.494 -0.983
7 sites 7 1.03 -0.153 -0.743 -0.918 -0.0579 -0.832
8 sites 8 -0.696 0.670 -0.0344 0.263 0.515 -1.17
9 sites 9 0.0576 1.10 0.832 -1.18 -1.47 0.728
10 sites 10 0.963 -0.646 -0.595 1.48 -0.194 0.951
11 sites 11 0.508 -0.826 -0.0477 1.28 -2.62 -2.67
12 sites 12 -0.342 1.60 1.05 -0.827 -2.31 0.772
13 sites 13 -0.469 1.60 0.965 -0.0778 0.471 0.205
14 sites 14 -2.02 -0.300 -2.84 1.03 -0.915 0.736
15 sites 15 -1.96 -0.103 -2.33 -0.321 0.129 1.49
16 sites 16 -1.93 0.588 -1.01 0.136 1.45 -1.70
17 sites 17 0.391 -2.69 1.15 -0.128 1.25 3.54
18 sites 18 0.302 -1.40 0.352 0.139 -1.74 -1.26
19 sites 19 -0.671 -2.69 3.08 -0.652 -0.278 1.65
20 sites 20 -2.02 -1.04 0.346 -1.03 1.22 -1.93
Code
tidy(dune_cca, layers = "sites")
Output
# A tibble: 20 x 8
score label cca1 cca2 cca3 cca4 cca5 cca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 1.22 0.422 0.546 1.09 0.790 -2.12
2 sites 2 0.862 0.177 0.0575 1.50 0.144 1.15
3 sites 3 0.317 0.969 0.648 0.900 0.544 -0.314
4 sites 4 0.243 0.872 0.812 1.51 1.38 1.18
5 sites 5 1.14 -0.283 -0.774 -1.34 1.01 1.17
6 sites 6 1.03 -0.371 -1.34 -2.05 0.494 -0.983
7 sites 7 1.03 -0.153 -0.743 -0.918 -0.0579 -0.832
8 sites 8 -0.696 0.670 -0.0344 0.263 0.515 -1.17
9 sites 9 0.0576 1.10 0.832 -1.18 -1.47 0.728
10 sites 10 0.963 -0.646 -0.595 1.48 -0.194 0.951
11 sites 11 0.508 -0.826 -0.0477 1.28 -2.62 -2.67
12 sites 12 -0.342 1.60 1.05 -0.827 -2.31 0.772
13 sites 13 -0.469 1.60 0.965 -0.0778 0.471 0.205
14 sites 14 -2.02 -0.300 -2.84 1.03 -0.915 0.736
15 sites 15 -1.96 -0.103 -2.33 -0.321 0.129 1.49
16 sites 16 -1.93 0.588 -1.01 0.136 1.45 -1.70
17 sites 17 0.391 -2.69 1.15 -0.128 1.25 3.54
18 sites 18 0.302 -1.40 0.352 0.139 -1.74 -1.26
19 sites 19 -0.671 -2.69 3.08 -0.652 -0.278 1.65
20 sites 20 -2.02 -1.04 0.346 -1.03 1.22 -1.93
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fortify works for cca like objects
Code
fortify(dune_pca)
Output
# A tibble: 50 x 8
score label pc1 pc2 pc3 pc4 pc5 pc6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.604 -0.124 0.00846 0.160 -0.409 -0.128
2 species Agrostol -1.37 0.964 0.167 0.266 0.0877 -0.0474
3 species Airaprae -0.0234 -0.251 -0.195 -0.326 -0.0557 0.0796
4 species Alopgeni -0.531 1.43 -0.505 -0.0429 0.443 -0.279
5 species Anthodor 0.559 -0.568 -0.476 0.0158 -0.344 0.136
6 species Bellpere 0.334 0.189 0.141 -0.0842 -0.125 -0.135
7 species Bromhord 0.523 0.197 0.164 0.00567 -0.386 -0.258
8 species Chenalbu -0.0175 0.0546 -0.0553 -0.0106 -0.0266 -0.0164
9 species Cirsarve -0.00240 0.102 0.0637 -0.0487 0.0321 0.0361
10 species Comapalu -0.169 -0.105 0.0636 0.0524 -0.131 -0.108
# i 40 more rows
Code
fortify(dune_ca)
Output
# A tibble: 50 x 8
score label ca1 ca2 ca3 ca4 ca5 ca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.909 -0.0846 0.586 -0.00892 -0.660 -0.189
2 species Agrostol -0.934 0.207 -0.282 0.0243 -0.139 -0.0226
3 species Airaprae 1.00 -3.07 -1.34 0.194 -1.08 -0.537
4 species Alopgeni -0.401 0.618 -0.850 0.347 0.0165 0.102
5 species Anthodor 0.967 -1.08 0.172 0.460 -0.608 -0.304
6 species Bellpere 0.500 0.355 0.152 -0.704 -0.0585 0.0731
7 species Bromhord 0.658 0.406 0.307 -0.497 -0.561 0.0700
8 species Chenalbu -0.424 0.844 -1.59 1.25 -0.207 0.876
9 species Cirsarve 0.0565 0.764 -0.918 -1.18 -0.384 -0.140
10 species Comapalu -1.92 -0.522 1.18 -0.0217 -1.36 1.31
# i 40 more rows
Code
fortify(dune_rda)
Output
# A tibble: 90 x 8
score label rda1 rda2 rda3 rda4 rda5 rda6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.598 -0.111 0.0923 0.0490 -0.0751 0.272
2 species Agrostol -1.18 0.963 0.194 0.227 0.261 0.108
3 species Airaprae -0.111 -0.205 0.0183 -0.180 0.0796 0.108
4 species Alopgeni -0.491 1.42 0.0492 -0.210 -0.126 -0.121
5 species Anthodor 0.421 -0.369 -0.219 0.0134 0.214 0.483
6 species Bellpere 0.375 -0.00458 0.133 -0.0719 0.0840 0.227
7 species Bromhord 0.547 0.0669 0.263 0.0629 -0.109 0.347
8 species Chenalbu -0.0333 0.0454 0.0000779 0.0106 0.0194 0.0362
9 species Cirsarve 0.0205 0.0912 0.0664 -0.0236 0.0943 0.00858
10 species Comapalu -0.198 -0.107 -0.00589 0.183 -0.0969 -0.0371
# i 80 more rows
Code
fortify(dune_cca)
Output
# A tibble: 90 x 8
score label cca1 cca2 cca3 cca4 cca5 cca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.841 -0.438 -0.150 0.275 0.0510 0.236
2 species Agrostol -0.765 0.481 0.0317 0.147 0.221 0.0954
3 species Airaprae -0.733 -1.75 1.15 -0.109 0.246 0.482
4 species Alopgeni -0.345 1.03 0.364 0.113 -0.0402 -0.0165
5 species Anthodor 0.390 -0.830 0.0306 -0.167 0.316 0.447
6 species Bellpere 0.707 -0.251 0.0109 0.490 0.158 0.409
7 species Bromhord 0.832 -0.119 -0.145 0.655 0.0944 0.283
8 species Chenalbu -0.973 1.30 0.517 0.0117 1.37 -0.252
9 species Cirsarve 0.429 0.741 0.495 0.977 1.07 0.601
10 species Comapalu -2.01 -0.351 -2.28 0.110 -0.485 1.20
# i 80 more rows
Code
fortify(dune_pco)
Output
# A tibble: 20 x 8
score label mds1 mds2 mds3 mds4 mds5 mds6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 -0.857 0.172 -2.61 1.13 -0.451 2.49
2 sites 2 -1.64 1.23 -0.887 0.986 -2.03 -1.81
3 sites 3 -0.440 2.38 -0.930 0.460 1.03 0.0518
4 sites 4 0.0479 2.05 -1.27 0.974 0.642 0.721
5 sites 5 -1.62 -0.290 1.59 -1.54 -1.86 2.21
6 sites 6 -1.97 -1.08 1.15 -3.35 1.52 -0.0313
7 sites 7 -1.79 -0.322 0.220 -1.47 -0.0125 0.426
8 sites 8 0.890 1.09 -0.925 -0.516 1.09 -0.948
9 sites 9 0.00904 1.66 0.466 0.283 0.108 2.17
10 sites 10 -1.91 -0.494 -0.706 -0.268 -1.37 -2.62
11 sites 11 -1.04 -1.21 -1.42 0.957 2.72 -1.11
12 sites 12 1.02 1.46 3.25 0.325 1.75 -1.02
13 sites 13 0.699 2.18 2.21 0.423 -1.07 -0.656
14 sites 14 1.49 -0.977 -0.545 -0.273 -2.39 -2.48
15 sites 15 1.89 -1.13 -0.727 -0.773 -0.221 0.318
16 sites 16 2.85 0.208 -0.704 -2.10 -0.293 0.0812
17 sites 17 0.0467 -1.73 0.914 1.67 -1.80 1.56
18 sites 18 -0.269 -1.72 -0.165 0.577 2.10 -0.339
19 sites 19 0.281 -2.19 1.99 3.23 0.458 0.0239
20 sites 20 2.34 -1.30 -0.903 -0.718 0.0757 0.969
Code
fortify(dune_dbrda)
Output
# A tibble: 69 x 8
score label dbrda1 dbrda2 dbrda3 dbrda4 dbrda5 dbrda6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 -0.980 0.00752 -1.73 1.12 2.75 2.35
2 sites 2 -1.73 -0.845 -1.80 0.409 -2.33 -3.44
3 sites 3 -0.597 -2.49 -1.58 0.989 1.22 0.711
4 sites 4 -0.0978 -2.15 -1.93 1.05 2.34 -0.873
5 sites 5 -1.72 0.329 3.40 -0.987 1.73 -2.40
6 sites 6 -2.11 0.831 2.75 -2.75 -0.481 2.33
7 sites 7 -1.91 0.305 0.812 -1.46 0.562 0.955
8 sites 8 0.811 -1.27 -1.23 -1.47 -0.894 0.227
9 sites 9 -0.0647 -1.75 2.16 1.63 -1.84 -0.109
10 sites 10 -1.97 0.718 -1.87 -1.08 -1.78 -2.89
# i 59 more rows
tidy works for cca like objects
Code
tidy(dune_pca)
Output
# A tibble: 50 x 8
score label pc1 pc2 pc3 pc4 pc5 pc6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.604 -0.124 0.00846 0.160 -0.409 -0.128
2 species Agrostol -1.37 0.964 0.167 0.266 0.0877 -0.0474
3 species Airaprae -0.0234 -0.251 -0.195 -0.326 -0.0557 0.0796
4 species Alopgeni -0.531 1.43 -0.505 -0.0429 0.443 -0.279
5 species Anthodor 0.559 -0.568 -0.476 0.0158 -0.344 0.136
6 species Bellpere 0.334 0.189 0.141 -0.0842 -0.125 -0.135
7 species Bromhord 0.523 0.197 0.164 0.00567 -0.386 -0.258
8 species Chenalbu -0.0175 0.0546 -0.0553 -0.0106 -0.0266 -0.0164
9 species Cirsarve -0.00240 0.102 0.0637 -0.0487 0.0321 0.0361
10 species Comapalu -0.169 -0.105 0.0636 0.0524 -0.131 -0.108
# i 40 more rows
Code
tidy(dune_ca)
Output
# A tibble: 50 x 8
score label ca1 ca2 ca3 ca4 ca5 ca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.909 -0.0846 0.586 -0.00892 -0.660 -0.189
2 species Agrostol -0.934 0.207 -0.282 0.0243 -0.139 -0.0226
3 species Airaprae 1.00 -3.07 -1.34 0.194 -1.08 -0.537
4 species Alopgeni -0.401 0.618 -0.850 0.347 0.0165 0.102
5 species Anthodor 0.967 -1.08 0.172 0.460 -0.608 -0.304
6 species Bellpere 0.500 0.355 0.152 -0.704 -0.0585 0.0731
7 species Bromhord 0.658 0.406 0.307 -0.497 -0.561 0.0700
8 species Chenalbu -0.424 0.844 -1.59 1.25 -0.207 0.876
9 species Cirsarve 0.0565 0.764 -0.918 -1.18 -0.384 -0.140
10 species Comapalu -1.92 -0.522 1.18 -0.0217 -1.36 1.31
# i 40 more rows
Code
tidy(dune_rda)
Output
# A tibble: 99 x 8
score label rda1 rda2 rda3 rda4 rda5 rda6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.598 -0.111 0.0923 0.0490 -0.0751 0.272
2 species Agrostol -1.18 0.963 0.194 0.227 0.261 0.108
3 species Airaprae -0.111 -0.205 0.0183 -0.180 0.0796 0.108
4 species Alopgeni -0.491 1.42 0.0492 -0.210 -0.126 -0.121
5 species Anthodor 0.421 -0.369 -0.219 0.0134 0.214 0.483
6 species Bellpere 0.375 -0.00458 0.133 -0.0719 0.0840 0.227
7 species Bromhord 0.547 0.0669 0.263 0.0629 -0.109 0.347
8 species Chenalbu -0.0333 0.0454 0.0000779 0.0106 0.0194 0.0362
9 species Cirsarve 0.0205 0.0912 0.0664 -0.0236 0.0943 0.00858
10 species Comapalu -0.198 -0.107 -0.00589 0.183 -0.0969 -0.0371
# i 89 more rows
Code
tidy(dune_cca)
Output
# A tibble: 90 x 8
score label cca1 cca2 cca3 cca4 cca5 cca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 species Achimill 0.841 -0.438 -0.150 0.275 0.0510 0.236
2 species Agrostol -0.765 0.481 0.0317 0.147 0.221 0.0954
3 species Airaprae -0.733 -1.75 1.15 -0.109 0.246 0.482
4 species Alopgeni -0.345 1.03 0.364 0.113 -0.0402 -0.0165
5 species Anthodor 0.390 -0.830 0.0306 -0.167 0.316 0.447
6 species Bellpere 0.707 -0.251 0.0109 0.490 0.158 0.409
7 species Bromhord 0.832 -0.119 -0.145 0.655 0.0944 0.283
8 species Chenalbu -0.973 1.30 0.517 0.0117 1.37 -0.252
9 species Cirsarve 0.429 0.741 0.495 0.977 1.07 0.601
10 species Comapalu -2.01 -0.351 -2.28 0.110 -0.485 1.20
# i 80 more rows
Code
tidy(dune_pco)
Output
# A tibble: 20 x 8
score label mds1 mds2 mds3 mds4 mds5 mds6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 -0.857 0.172 -2.61 1.13 -0.451 2.49
2 sites 2 -1.64 1.23 -0.887 0.986 -2.03 -1.81
3 sites 3 -0.440 2.38 -0.930 0.460 1.03 0.0518
4 sites 4 0.0479 2.05 -1.27 0.974 0.642 0.721
5 sites 5 -1.62 -0.290 1.59 -1.54 -1.86 2.21
6 sites 6 -1.97 -1.08 1.15 -3.35 1.52 -0.0313
7 sites 7 -1.79 -0.322 0.220 -1.47 -0.0125 0.426
8 sites 8 0.890 1.09 -0.925 -0.516 1.09 -0.948
9 sites 9 0.00904 1.66 0.466 0.283 0.108 2.17
10 sites 10 -1.91 -0.494 -0.706 -0.268 -1.37 -2.62
11 sites 11 -1.04 -1.21 -1.42 0.957 2.72 -1.11
12 sites 12 1.02 1.46 3.25 0.325 1.75 -1.02
13 sites 13 0.699 2.18 2.21 0.423 -1.07 -0.656
14 sites 14 1.49 -0.977 -0.545 -0.273 -2.39 -2.48
15 sites 15 1.89 -1.13 -0.727 -0.773 -0.221 0.318
16 sites 16 2.85 0.208 -0.704 -2.10 -0.293 0.0812
17 sites 17 0.0467 -1.73 0.914 1.67 -1.80 1.56
18 sites 18 -0.269 -1.72 -0.165 0.577 2.10 -0.339
19 sites 19 0.281 -2.19 1.99 3.23 0.458 0.0239
20 sites 20 2.34 -1.30 -0.903 -0.718 0.0757 0.969
Code
tidy(dune_dbrda)
Output
# A tibble: 69 x 8
score label dbrda1 dbrda2 dbrda3 dbrda4 dbrda5 dbrda6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 -0.980 0.00752 -1.73 1.12 2.75 2.35
2 sites 2 -1.73 -0.845 -1.80 0.409 -2.33 -3.44
3 sites 3 -0.597 -2.49 -1.58 0.989 1.22 0.711
4 sites 4 -0.0978 -2.15 -1.93 1.05 2.34 -0.873
5 sites 5 -1.72 0.329 3.40 -0.987 1.73 -2.40
6 sites 6 -2.11 0.831 2.75 -2.75 -0.481 2.33
7 sites 7 -1.91 0.305 0.812 -1.46 0.562 0.955
8 sites 8 0.811 -1.27 -1.23 -1.47 -0.894 0.227
9 sites 9 -0.0647 -1.75 2.16 1.63 -1.84 -0.109
10 sites 10 -1.97 0.718 -1.87 -1.08 -1.78 -2.89
# i 59 more rows
fortify works for cca with layers length 1
Code
fortify(dune_cca, layers = "sites")
Output
# A tibble: 20 x 8
score label cca1 cca2 cca3 cca4 cca5 cca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 1.22 0.422 0.546 1.09 0.790 -2.12
2 sites 2 0.862 0.177 0.0575 1.50 0.144 1.15
3 sites 3 0.317 0.969 0.648 0.900 0.544 -0.314
4 sites 4 0.243 0.872 0.812 1.51 1.38 1.18
5 sites 5 1.14 -0.283 -0.774 -1.34 1.01 1.17
6 sites 6 1.03 -0.371 -1.34 -2.05 0.494 -0.983
7 sites 7 1.03 -0.153 -0.743 -0.918 -0.0579 -0.832
8 sites 8 -0.696 0.670 -0.0344 0.263 0.515 -1.17
9 sites 9 0.0576 1.10 0.832 -1.18 -1.47 0.728
10 sites 10 0.963 -0.646 -0.595 1.48 -0.194 0.951
11 sites 11 0.508 -0.826 -0.0477 1.28 -2.62 -2.67
12 sites 12 -0.342 1.60 1.05 -0.827 -2.31 0.772
13 sites 13 -0.469 1.60 0.965 -0.0778 0.471 0.205
14 sites 14 -2.02 -0.300 -2.84 1.03 -0.915 0.736
15 sites 15 -1.96 -0.103 -2.33 -0.321 0.129 1.49
16 sites 16 -1.93 0.588 -1.01 0.136 1.45 -1.70
17 sites 17 0.391 -2.69 1.15 -0.128 1.25 3.54
18 sites 18 0.302 -1.40 0.352 0.139 -1.74 -1.26
19 sites 19 -0.671 -2.69 3.08 -0.652 -0.278 1.65
20 sites 20 -2.02 -1.04 0.346 -1.03 1.22 -1.93
Code
tidy(dune_cca, layers = "sites")
Output
# A tibble: 20 x 8
score label cca1 cca2 cca3 cca4 cca5 cca6
<fct> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 sites 1 1.22 0.422 0.546 1.09 0.790 -2.12
2 sites 2 0.862 0.177 0.0575 1.50 0.144 1.15
3 sites 3 0.317 0.969 0.648 0.900 0.544 -0.314
4 sites 4 0.243 0.872 0.812 1.51 1.38 1.18
5 sites 5 1.14 -0.283 -0.774 -1.34 1.01 1.17
6 sites 6 1.03 -0.371 -1.34 -2.05 0.494 -0.983
7 sites 7 1.03 -0.153 -0.743 -0.918 -0.0579 -0.832
8 sites 8 -0.696 0.670 -0.0344 0.263 0.515 -1.17
9 sites 9 0.0576 1.10 0.832 -1.18 -1.47 0.728
10 sites 10 0.963 -0.646 -0.595 1.48 -0.194 0.951
11 sites 11 0.508 -0.826 -0.0477 1.28 -2.62 -2.67
12 sites 12 -0.342 1.60 1.05 -0.827 -2.31 0.772
13 sites 13 -0.469 1.60 0.965 -0.0778 0.471 0.205
14 sites 14 -2.02 -0.300 -2.84 1.03 -0.915 0.736
15 sites 15 -1.96 -0.103 -2.33 -0.321 0.129 1.49
16 sites 16 -1.93 0.588 -1.01 0.136 1.45 -1.70
17 sites 17 0.391 -2.69 1.15 -0.128 1.25 3.54
18 sites 18 0.302 -1.40 0.352 0.139 -1.74 -1.26
19 sites 19 -0.671 -2.69 3.08 -0.652 -0.278 1.65
20 sites 20 -2.02 -1.04 0.346 -1.03 1.22 -1.93
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