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tests/testthat/_snaps/metrics.md
In BioTIMEr: Tools to Use and Explore the 'BioTIME' Database
getAlpha works consistently
Code
getAlpha(x = data, id = "TestID")
Output
assemblageID YEAR S N maxN Shannon Simpson invSimpson PIE
1 TestID 2010 4 51 15 1.374722 0.7443291 3.911278 0.7592157
2 TestID 2011 4 47 22 1.259384 0.6808511 3.133333 0.6956522
3 TestID 2012 4 41 13 1.368895 0.7412255 3.864368 0.7597561
4 TestID 2013 4 34 12 1.320670 0.7179931 3.546012 0.7397504
5 TestID 2014 4 39 11 1.377299 0.7455621 3.930233 0.7651822
6 TestID 2015 4 34 9 1.384563 0.7491349 3.986207 0.7718360
7 TestID 2010 4 48 15 1.350205 0.7335069 3.752443 0.7491135
8 TestID 2011 4 34 10 1.369700 0.7422145 3.879195 0.7647059
9 TestID 2012 4 39 16 1.310762 0.7100592 3.448980 0.7287449
10 TestID 2013 4 40 15 1.334575 0.7237500 3.619910 0.7423077
11 TestID 2014 4 47 14 1.339754 0.7297420 3.700168 0.7456059
12 TestID 2015 4 46 17 1.314793 0.7155009 3.514950 0.7314010
13 TestID 2010 4 30 11 1.340860 0.7266667 3.658537 0.7517241
14 TestID 2011 4 41 14 1.331201 0.7233789 3.615054 0.7414634
15 TestID 2012 4 39 13 1.365068 0.7389875 3.831234 0.7584345
16 TestID 2013 4 45 14 1.371850 0.7427160 3.886756 0.7595960
17 TestID 2014 4 43 14 1.368789 0.7409410 3.860125 0.7585825
18 TestID 2015 4 38 13 1.334030 0.7243767 3.628141 0.7439545
19 TestID 2010 4 35 15 1.282139 0.6971429 3.301887 0.7176471
20 TestID 2011 4 30 9 1.364755 0.7400000 3.846154 0.7655172
21 TestID 2012 4 29 12 1.307434 0.7086801 3.432653 0.7339901
22 TestID 2013 4 36 15 1.308605 0.7083333 3.428571 0.7285714
23 TestID 2014 4 58 21 1.331969 0.7229489 3.609442 0.7356322
24 TestID 2015 4 31 10 1.368397 0.7408949 3.859438 0.7655914
25 TestID 2010 4 44 14 1.367462 0.7407025 3.856574 0.7579281
26 TestID 2011 4 35 12 1.355920 0.7346939 3.769231 0.7563025
27 TestID 2012 4 42 14 1.343810 0.7301587 3.705882 0.7479675
28 TestID 2013 4 27 11 1.324660 0.7160494 3.521739 0.7435897
29 TestID 2014 4 36 11 1.357414 0.7361111 3.789474 0.7571429
30 TestID 2015 4 48 14 1.363951 0.7395833 3.840000 0.7553191
31 TestID 2010 4 46 13 1.377400 0.7457467 3.933086 0.7623188
32 TestID 2011 4 32 11 1.359976 0.7363281 3.792593 0.7600806
33 TestID 2012 4 42 14 1.363046 0.7380952 3.818182 0.7560976
34 TestID 2013 4 55 19 1.362162 0.7371901 3.805031 0.7508418
35 TestID 2014 4 49 19 1.332135 0.7213661 3.588939 0.7363946
36 TestID 2015 4 46 14 1.373912 0.7438563 3.904059 0.7603865
37 TestID 2010 4 47 17 1.336186 0.7252150 3.639209 0.7409806
38 TestID 2011 4 45 14 1.367150 0.7407407 3.857143 0.7575758
39 TestID 2012 4 42 14 1.368082 0.7403628 3.851528 0.7584204
40 TestID 2013 4 48 17 1.354860 0.7335069 3.752443 0.7491135
41 TestID 2014 4 37 12 1.319925 0.7216947 3.593176 0.7417417
42 TestID 2015 4 42 14 1.343668 0.7290249 3.690377 0.7468060
43 TestID 2010 4 53 18 1.337430 0.7276611 3.671895 0.7416546
44 TestID 2011 4 37 12 1.357666 0.7363039 3.792244 0.7567568
45 TestID 2012 4 32 10 1.370502 0.7421875 3.878788 0.7661290
46 TestID 2013 4 36 11 1.363289 0.7391975 3.834320 0.7603175
47 TestID 2014 4 39 12 1.374965 0.7442472 3.910026 0.7638327
48 TestID 2015 4 38 10 1.381979 0.7479224 3.967033 0.7681366
49 TestID 2010 4 35 13 1.332431 0.7232653 3.613569 0.7445378
50 TestID 2011 4 33 11 1.359423 0.7364555 3.794425 0.7594697
51 TestID 2012 4 33 10 1.333723 0.7272727 3.666667 0.7500000
52 TestID 2013 4 36 11 1.373845 0.7438272 3.903614 0.7650794
53 TestID 2014 4 37 15 1.244500 0.6822498 3.147126 0.7012012
54 TestID 2015 4 26 11 1.289874 0.7011834 3.346535 0.7292308
55 TestID 2010 4 35 10 1.375102 0.7444898 3.913738 0.7663866
56 TestID 2011 4 48 14 1.377579 0.7456597 3.931741 0.7615248
57 TestID 2012 4 52 22 1.313154 0.7093195 3.440204 0.7232278
58 TestID 2013 4 35 11 1.361383 0.7379592 3.816199 0.7596639
59 TestID 2014 4 35 12 1.355920 0.7346939 3.769231 0.7563025
60 TestID 2015 4 48 15 1.370502 0.7421875 3.878788 0.7579787
61 TestID 2010 4 34 12 1.334793 0.7249135 3.635220 0.7468806
62 TestID 2011 4 44 15 1.360122 0.7365702 3.796078 0.7536998
63 TestID 2012 4 34 11 1.342396 0.7283737 3.681529 0.7504456
64 TestID 2013 4 48 15 1.374486 0.7439236 3.905085 0.7597518
65 TestID 2014 4 36 11 1.363289 0.7391975 3.834320 0.7603175
66 TestID 2015 4 36 16 1.241728 0.6805556 3.130435 0.7000000
67 TestID 2010 4 37 11 1.379501 0.7465303 3.945245 0.7672673
68 TestID 2011 4 39 15 1.329390 0.7205786 3.578824 0.7395412
69 TestID 2012 4 34 15 1.293693 0.6989619 3.321839 0.7201426
70 TestID 2013 4 39 11 1.377299 0.7455621 3.930233 0.7651822
71 TestID 2014 4 34 13 1.331641 0.7214533 3.590062 0.7433155
72 TestID 2015 4 35 12 1.343459 0.7297959 3.700906 0.7512605
73 TestID 2010 4 38 12 1.355447 0.7354571 3.780105 0.7553343
74 TestID 2011 4 35 12 1.355920 0.7346939 3.769231 0.7563025
75 TestID 2012 4 34 12 1.334793 0.7249135 3.635220 0.7468806
76 TestID 2013 4 46 14 1.373912 0.7438563 3.904059 0.7603865
77 TestID 2014 4 38 12 1.371381 0.7423823 3.881720 0.7624467
78 TestID 2015 4 39 12 1.351681 0.7337278 3.755556 0.7530364
79 TestID 2010 4 50 14 1.371764 0.7432000 3.894081 0.7583673
80 TestID 2011 4 29 9 1.370342 0.7419738 3.875576 0.7684729
81 TestID 2012 4 36 12 1.336895 0.7268519 3.661017 0.7476190
82 TestID 2013 4 49 17 1.347709 0.7305289 3.710974 0.7457483
83 TestID 2014 4 47 13 1.376050 0.7451335 3.923623 0.7613321
84 TestID 2015 4 41 13 1.368895 0.7412255 3.864368 0.7597561
85 TestID 2010 4 29 12 1.320152 0.7134364 3.489627 0.7389163
86 TestID 2011 4 26 10 1.249083 0.6893491 3.219048 0.7169231
87 TestID 2012 4 32 11 1.359976 0.7363281 3.792593 0.7600806
88 TestID 2013 4 31 10 1.337807 0.7284079 3.681992 0.7526882
89 TestID 2014 4 39 15 1.339134 0.7245233 3.630072 0.7435897
90 TestID 2015 4 47 15 1.365765 0.7397012 3.841739 0.7557817
91 TestID 2010 4 51 19 1.347219 0.7289504 3.689362 0.7435294
92 TestID 2011 4 47 19 1.323940 0.7161612 3.523126 0.7317299
93 TestID 2012 4 42 14 1.357411 0.7358277 3.785408 0.7537747
94 TestID 2013 4 41 16 1.337779 0.7233789 3.615054 0.7414634
95 TestID 2014 4 34 10 1.366425 0.7404844 3.853333 0.7629234
96 TestID 2015 4 30 13 1.292482 0.7000000 3.333333 0.7241379
DomMc expShannon
1 0.5686275 3.953977
2 0.7021277 3.523252
3 0.5853659 3.931006
4 0.6764706 3.745931
5 0.5641026 3.964179
6 0.5294118 3.993082
7 0.6041667 3.858217
8 0.5588235 3.934171
9 0.6666667 3.708998
10 0.6250000 3.798381
11 0.5957447 3.818104
12 0.6739130 3.723982
13 0.6333333 3.822329
14 0.6585366 3.785585
15 0.5897436 3.915989
16 0.5777778 3.942638
17 0.5813953 3.930586
18 0.6578947 3.796310
19 0.6857143 3.604341
20 0.5666667 3.914763
21 0.6551724 3.696677
22 0.6666667 3.701009
23 0.6551724 3.788497
24 0.5806452 3.929046
25 0.5681818 3.925374
26 0.6000000 3.880328
27 0.6190476 3.833623
28 0.6296296 3.760905
29 0.6111111 3.886130
30 0.5833333 3.911616
31 0.5434783 3.964579
32 0.5937500 3.896101
33 0.5952381 3.908078
34 0.5818182 3.904626
35 0.6326531 3.789123
36 0.5652174 3.950776
37 0.6382979 3.804506
38 0.5777778 3.924151
39 0.5714286 3.927808
40 0.6041667 3.876217
41 0.6216216 3.743139
42 0.6428571 3.833079
43 0.6037736 3.809242
44 0.5945946 3.887111
45 0.5625000 3.937328
46 0.5833333 3.909029
47 0.5641026 3.954937
48 0.5263158 3.982774
49 0.6285714 3.790248
50 0.6060606 3.893945
51 0.6060606 3.795145
52 0.5555556 3.950511
53 0.7567568 3.471199
54 0.6538462 3.632327
55 0.5714286 3.955481
56 0.5625000 3.965291
57 0.6346154 3.717882
58 0.6000000 3.901584
59 0.6000000 3.880328
60 0.5625000 3.937328
61 0.6470588 3.799210
62 0.5909091 3.896668
63 0.6470588 3.828203
64 0.5625000 3.953043
65 0.5833333 3.909029
66 0.7222222 3.461589
67 0.5405405 3.972919
68 0.6410256 3.778738
69 0.6470588 3.646228
70 0.5641026 3.964179
71 0.6470588 3.787252
72 0.6000000 3.832277
73 0.6052632 3.878492
74 0.6000000 3.880328
75 0.6470588 3.799210
76 0.5652174 3.950776
77 0.5789474 3.940789
78 0.6153846 3.863916
79 0.5600000 3.942297
80 0.5862069 3.936696
81 0.6388889 3.807205
82 0.6326531 3.848597
83 0.5531915 3.959232
84 0.5853659 3.931006
85 0.6206897 3.743989
86 0.7307692 3.487143
87 0.5937500 3.896101
88 0.6129032 3.810678
89 0.6153846 3.815738
90 0.5957447 3.918721
91 0.6078431 3.846714
92 0.6382979 3.758201
93 0.5952381 3.886118
94 0.6097561 3.810572
95 0.5882353 3.921309
96 0.6666667 3.641816
getAlphaMetrics works correctly for Abundance
Code
getAlphaMetrics(x = dataMetrics, measure = "ABUNDANCE")
Output
assemblageID YEAR S N maxN Shannon Simpson invSimpson PIE
1 A 2010 4 34 14 1.318024 0.7128028 3.481928 0.7344029
2 A 2011 4 40 15 1.344075 0.7275000 3.669725 0.7461538
3 A 2012 4 35 12 1.355920 0.7346939 3.769231 0.7563025
4 A 2013 4 34 14 1.318024 0.7128028 3.481928 0.7344029
5 A 2014 4 36 14 1.322282 0.7175926 3.540984 0.7380952
6 A 2015 4 45 14 1.343094 0.7308642 3.715596 0.7474747
7 B 2010 4 45 14 1.371850 0.7427160 3.886756 0.7595960
8 B 2011 4 38 14 1.296892 0.7091413 3.438095 0.7283073
9 B 2012 4 36 11 1.363289 0.7391975 3.834320 0.7603175
10 B 2013 4 39 11 1.379867 0.7468771 3.950649 0.7665317
11 B 2014 4 27 9 1.362721 0.7379973 3.816754 0.7663818
12 B 2015 4 42 13 1.366865 0.7403628 3.851528 0.7584204
13 C 2010 4 42 15 1.322869 0.7210884 3.585366 0.7386760
14 C 2011 4 37 15 1.267203 0.6968590 3.298795 0.7162162
15 C 2012 4 38 15 1.308673 0.7105263 3.454545 0.7297297
16 C 2013 4 32 12 1.328497 0.7207031 3.580420 0.7439516
17 C 2014 4 44 14 1.372269 0.7427686 3.887550 0.7600423
18 C 2015 4 41 14 1.320563 0.7198096 3.569002 0.7378049
19 D 2010 4 37 12 1.340163 0.7289993 3.690027 0.7492492
20 D 2011 4 48 19 1.315262 0.7135417 3.490909 0.7287234
21 D 2012 4 41 14 1.362762 0.7376562 3.811791 0.7560976
22 D 2013 4 36 13 1.340682 0.7268519 3.661017 0.7476190
23 D 2014 4 30 9 1.360577 0.7377778 3.813559 0.7632184
24 D 2015 4 25 7 1.383954 0.7488000 3.980892 0.7800000
25 E 2010 4 30 8 1.379292 0.7466667 3.947368 0.7724138
26 E 2011 4 34 14 1.283173 0.6989619 3.321839 0.7201426
27 E 2012 4 45 21 1.274065 0.6864198 3.188976 0.7020202
28 E 2013 4 40 14 1.349366 0.7312500 3.720930 0.7500000
29 E 2014 4 37 12 1.351950 0.7333820 3.750685 0.7537538
30 E 2015 4 37 12 1.364928 0.7392257 3.834734 0.7597598
31 F 2010 4 51 17 1.358035 0.7358708 3.786026 0.7505882
32 F 2011 4 59 18 1.367156 0.7405918 3.854928 0.7533606
33 F 2012 4 34 9 1.384563 0.7491349 3.986207 0.7718360
34 F 2013 4 32 9 1.373982 0.7441406 3.908397 0.7681452
35 F 2014 4 38 13 1.345289 0.7299169 3.702564 0.7496444
36 F 2015 4 41 11 1.382973 0.7483641 3.973995 0.7670732
37 G 2010 4 32 10 1.366586 0.7402344 3.849624 0.7641129
38 G 2011 4 36 11 1.363289 0.7391975 3.834320 0.7603175
39 G 2012 4 42 15 1.347336 0.7301587 3.705882 0.7479675
40 G 2013 4 32 12 1.336893 0.7246094 3.631206 0.7479839
41 G 2014 4 38 12 1.374311 0.7437673 3.902703 0.7638691
42 G 2015 4 35 12 1.355920 0.7346939 3.769231 0.7563025
43 H 2010 4 30 10 1.362447 0.7377778 3.813559 0.7632184
44 H 2011 4 38 15 1.296355 0.7077562 3.421801 0.7268848
45 H 2012 4 40 11 1.378502 0.7462500 3.940887 0.7653846
46 H 2013 4 44 13 1.371108 0.7427686 3.887550 0.7600423
47 H 2014 4 42 12 1.375572 0.7448980 3.920000 0.7630662
48 H 2015 4 48 15 1.363525 0.7387153 3.827243 0.7544326
DomMc expShannon
1 0.6470588 3.736031
2 0.6000000 3.834639
3 0.6000000 3.880328
4 0.6470588 3.736031
5 0.6388889 3.751972
6 0.6000000 3.830878
7 0.5777778 3.942638
8 0.6842105 3.657909
9 0.5833333 3.909029
10 0.5384615 3.974374
11 0.5925926 3.906808
12 0.5952381 3.923034
13 0.6190476 3.754176
14 0.6756757 3.550906
15 0.6842105 3.701257
16 0.6562500 3.775364
17 0.5681818 3.944289
18 0.6585366 3.745531
19 0.6216216 3.819665
20 0.6666667 3.725727
21 0.5853659 3.906970
22 0.6388889 3.821650
23 0.6000000 3.898443
24 0.5200000 3.990650
25 0.5333333 3.972089
26 0.7058824 3.608069
27 0.6666667 3.575356
28 0.6250000 3.854979
29 0.6216216 3.864954
30 0.5945946 3.915440
31 0.6078431 3.888547
32 0.5932203 3.924174
33 0.5294118 3.993082
34 0.5625000 3.951052
35 0.6315789 3.839297
36 0.5365854 3.986736
37 0.5937500 3.921938
38 0.5833333 3.909029
39 0.6190476 3.847165
40 0.6250000 3.807196
41 0.5526316 3.952353
42 0.6000000 3.880328
43 0.6000000 3.905741
44 0.6578947 3.655945
45 0.5500000 3.968954
46 0.5681818 3.939713
47 0.5476190 3.957339
48 0.6041667 3.909953
getAlphaMetrics works correctly for Biomass
Code
getAlphaMetrics(x = dataMetrics, measure = "BIOMASS")
Output
assemblageID YEAR S N maxN Shannon Simpson invSimpson PIE
1 A 2010 4 4051 1034 1.386206 0.7499555 3.999288 0.7501406
2 A 2011 4 4064 1049 1.385816 0.7497608 3.996177 0.7499454
3 A 2012 4 4107 1076 1.385474 0.7495905 3.993459 0.7497731
4 A 2013 4 3964 1014 1.386140 0.7499230 3.998768 0.7501122
5 A 2014 4 4048 1044 1.385972 0.7498395 3.997434 0.7500248
6 A 2015 4 3935 991 1.386227 0.7499664 3.999462 0.7501570
7 B 2010 4 3935 1007 1.386155 0.7499301 3.998881 0.7501207
8 B 2011 4 4002 1044 1.385871 0.7497876 3.996605 0.7499750
9 B 2012 4 3887 1009 1.385983 0.7498439 3.997504 0.7500368
10 B 2013 4 3863 1008 1.385833 0.7497689 3.996306 0.7499630
11 B 2014 4 3847 1014 1.385609 0.7496567 3.994515 0.7498516
12 B 2015 4 3954 1028 1.385803 0.7497551 3.996085 0.7499448
13 C 2010 4 3933 1014 1.386011 0.7498586 3.997739 0.7500493
14 C 2011 4 3932 1014 1.385825 0.7497674 3.996282 0.7499581
15 C 2012 4 4020 1025 1.386051 0.7498792 3.998068 0.7500658
16 C 2013 4 3991 1030 1.386114 0.7499094 3.998551 0.7500974
17 C 2014 4 4030 1023 1.386213 0.7499594 3.999351 0.7501456
18 C 2015 4 4034 1042 1.385888 0.7497978 3.996767 0.7499837
19 D 2010 4 4035 1066 1.385637 0.7496695 3.994719 0.7498553
20 D 2011 4 4021 1041 1.385371 0.7495455 3.992741 0.7497319
21 D 2012 4 3863 1001 1.385787 0.7497473 3.995961 0.7499415
22 D 2013 4 4033 1026 1.386179 0.7499424 3.999079 0.7501284
23 D 2014 4 4053 1040 1.385972 0.7498396 3.997435 0.7500247
24 D 2015 4 3986 1017 1.386145 0.7499257 3.998811 0.7501139
25 E 2010 4 3976 1025 1.386112 0.7499085 3.998537 0.7500972
26 E 2011 4 3978 1058 1.385497 0.7495975 3.993571 0.7497860
27 E 2012 4 3958 1005 1.386178 0.7499417 3.999068 0.7501312
28 E 2013 4 3919 989 1.386231 0.7499683 3.999493 0.7501597
29 E 2014 4 4082 1070 1.385042 0.7493789 3.990087 0.7495625
30 E 2015 4 3928 1010 1.386088 0.7498969 3.998352 0.7500879
31 F 2010 4 4121 1102 1.385123 0.7494143 3.990651 0.7495962
32 F 2011 4 3964 1016 1.386096 0.7499010 3.998416 0.7500902
33 F 2012 4 3994 1014 1.386206 0.7499558 3.999293 0.7501436
34 F 2013 4 3893 1018 1.385713 0.7497090 3.995349 0.7499016
35 F 2014 4 4063 1043 1.386040 0.7498735 3.997977 0.7500581
36 F 2015 4 3886 1027 1.385755 0.7497268 3.995634 0.7499198
37 G 2010 4 4030 1047 1.385674 0.7496924 3.995085 0.7498785
38 G 2011 4 4094 1041 1.386061 0.7498838 3.998142 0.7500670
39 G 2012 4 3892 1020 1.385449 0.7495783 3.993264 0.7497709
40 G 2013 4 4049 1050 1.385988 0.7498462 3.997541 0.7500315
41 G 2014 4 3895 1000 1.385836 0.7497728 3.996368 0.7499654
42 G 2015 4 3929 997 1.386236 0.7499707 3.999531 0.7501616
43 H 2010 4 3929 1035 1.385340 0.7495233 3.992387 0.7497141
44 H 2011 4 4020 1018 1.386264 0.7499850 3.999760 0.7501716
45 H 2012 4 4009 1040 1.385847 0.7497770 3.996435 0.7499640
46 H 2013 4 3970 1031 1.385565 0.7496389 3.994231 0.7498278
47 H 2014 4 4060 1065 1.385746 0.7497245 3.995596 0.7499092
48 H 2015 4 4011 1032 1.386086 0.7498954 3.998327 0.7500824
DomMc expShannon
1 0.5055542 3.999645
2 0.5152559 3.998086
3 0.5191137 3.996718
4 0.5063068 3.999383
5 0.5101285 3.998712
6 0.5034307 3.999730
7 0.5077510 3.999441
8 0.5129935 3.998308
9 0.5109339 3.998756
10 0.5135905 3.998156
11 0.5144268 3.997259
12 0.5131512 3.998035
13 0.5105517 3.998868
14 0.5116989 3.998124
15 0.5089552 3.999028
16 0.5063894 3.999280
17 0.5057072 3.999675
18 0.5116510 3.998374
19 0.5142503 3.997372
20 0.5138025 3.996308
21 0.5146259 3.997973
22 0.5058269 3.999538
23 0.5102393 3.998709
24 0.5075263 3.999404
25 0.5077968 3.999272
26 0.5170940 3.996810
27 0.5075796 3.999534
28 0.5039551 3.999745
29 0.5227829 3.994995
30 0.5089104 3.999176
31 0.5171075 3.995319
32 0.5090817 3.999207
33 0.5055083 3.999646
34 0.5163113 3.997677
35 0.5087374 3.998984
36 0.5102934 3.997842
37 0.5136476 3.997521
38 0.5085491 3.999065
39 0.5195272 3.996620
40 0.5102494 3.998773
41 0.5116816 3.998166
42 0.5047086 3.999765
43 0.5209977 3.996186
44 0.5029851 3.999880
45 0.5125967 3.998210
46 0.5148615 3.997082
47 0.5150246 3.997806
48 0.5095986 3.999165
getBetaMetrics works correctly for Abundance
Code
getBetaMetrics(x = dataMetrics, measure = "ABUNDANCE")
Output
YEAR assemblageID JaccardDiss MorisitaHornDiss BrayCurtisDiss
1 2010 A 1 1 1
2 2011 A 1 1 1
3 2012 A 1 1 1
4 2013 A 1 1 1
5 2014 A 1 1 1
6 2015 A 1 1 1
7 2010 B 1 1 1
8 2011 B 1 1 1
9 2012 B 1 1 1
10 2013 B 1 1 1
11 2014 B 1 1 1
12 2015 B 1 1 1
13 2010 C 1 1 1
14 2011 C 1 1 1
15 2012 C 1 1 1
16 2013 C 1 1 1
17 2014 C 1 1 1
18 2015 C 1 1 1
19 2010 D 1 1 1
20 2011 D 1 1 1
21 2012 D 1 1 1
22 2013 D 1 1 1
23 2014 D 1 1 1
24 2015 D 1 1 1
25 2010 E 1 1 1
26 2011 E 1 1 1
27 2012 E 1 1 1
28 2013 E 1 1 1
29 2014 E 1 1 1
30 2015 E 1 1 1
31 2010 F 1 1 1
32 2011 F 1 1 1
33 2012 F 1 1 1
34 2013 F 1 1 1
35 2014 F 1 1 1
36 2015 F 1 1 1
37 2010 G 1 1 1
38 2011 G 1 1 1
39 2012 G 1 1 1
40 2013 G 1 1 1
41 2014 G 1 1 1
42 2015 G 1 1 1
43 2010 H 1 1 1
44 2011 H 1 1 1
45 2012 H 1 1 1
46 2013 H 1 1 1
47 2014 H 1 1 1
48 2015 H 1 1 1
getBetaMetrics works correctly for Biomass
Code
getBetaMetrics(x = dataMetrics, measure = "BIOMASS")
Output
YEAR assemblageID JaccardDiss MorisitaHornDiss BrayCurtisDiss
1 2010 A 1 1 1
2 2011 A 1 1 1
3 2012 A 1 1 1
4 2013 A 1 1 1
5 2014 A 1 1 1
6 2015 A 1 1 1
7 2010 B 1 1 1
8 2011 B 1 1 1
9 2012 B 1 1 1
10 2013 B 1 1 1
11 2014 B 1 1 1
12 2015 B 1 1 1
13 2010 C 1 1 1
14 2011 C 1 1 1
15 2012 C 1 1 1
16 2013 C 1 1 1
17 2014 C 1 1 1
18 2015 C 1 1 1
19 2010 D 1 1 1
20 2011 D 1 1 1
21 2012 D 1 1 1
22 2013 D 1 1 1
23 2014 D 1 1 1
24 2015 D 1 1 1
25 2010 E 1 1 1
26 2011 E 1 1 1
27 2012 E 1 1 1
28 2013 E 1 1 1
29 2014 E 1 1 1
30 2015 E 1 1 1
31 2010 F 1 1 1
32 2011 F 1 1 1
33 2012 F 1 1 1
34 2013 F 1 1 1
35 2014 F 1 1 1
36 2015 F 1 1 1
37 2010 G 1 1 1
38 2011 G 1 1 1
39 2012 G 1 1 1
40 2013 G 1 1 1
41 2014 G 1 1 1
42 2015 G 1 1 1
43 2010 H 1 1 1
44 2011 H 1 1 1
45 2012 H 1 1 1
46 2013 H 1 1 1
47 2014 H 1 1 1
48 2015 H 1 1 1
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BioTIMEr documentation built on Sept. 14, 2024, 9:09 a.m.
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getAlpha works consistently
Code
getAlpha(x = data, id = "TestID")
Output
assemblageID YEAR S N maxN Shannon Simpson invSimpson PIE
1 TestID 2010 4 51 15 1.374722 0.7443291 3.911278 0.7592157
2 TestID 2011 4 47 22 1.259384 0.6808511 3.133333 0.6956522
3 TestID 2012 4 41 13 1.368895 0.7412255 3.864368 0.7597561
4 TestID 2013 4 34 12 1.320670 0.7179931 3.546012 0.7397504
5 TestID 2014 4 39 11 1.377299 0.7455621 3.930233 0.7651822
6 TestID 2015 4 34 9 1.384563 0.7491349 3.986207 0.7718360
7 TestID 2010 4 48 15 1.350205 0.7335069 3.752443 0.7491135
8 TestID 2011 4 34 10 1.369700 0.7422145 3.879195 0.7647059
9 TestID 2012 4 39 16 1.310762 0.7100592 3.448980 0.7287449
10 TestID 2013 4 40 15 1.334575 0.7237500 3.619910 0.7423077
11 TestID 2014 4 47 14 1.339754 0.7297420 3.700168 0.7456059
12 TestID 2015 4 46 17 1.314793 0.7155009 3.514950 0.7314010
13 TestID 2010 4 30 11 1.340860 0.7266667 3.658537 0.7517241
14 TestID 2011 4 41 14 1.331201 0.7233789 3.615054 0.7414634
15 TestID 2012 4 39 13 1.365068 0.7389875 3.831234 0.7584345
16 TestID 2013 4 45 14 1.371850 0.7427160 3.886756 0.7595960
17 TestID 2014 4 43 14 1.368789 0.7409410 3.860125 0.7585825
18 TestID 2015 4 38 13 1.334030 0.7243767 3.628141 0.7439545
19 TestID 2010 4 35 15 1.282139 0.6971429 3.301887 0.7176471
20 TestID 2011 4 30 9 1.364755 0.7400000 3.846154 0.7655172
21 TestID 2012 4 29 12 1.307434 0.7086801 3.432653 0.7339901
22 TestID 2013 4 36 15 1.308605 0.7083333 3.428571 0.7285714
23 TestID 2014 4 58 21 1.331969 0.7229489 3.609442 0.7356322
24 TestID 2015 4 31 10 1.368397 0.7408949 3.859438 0.7655914
25 TestID 2010 4 44 14 1.367462 0.7407025 3.856574 0.7579281
26 TestID 2011 4 35 12 1.355920 0.7346939 3.769231 0.7563025
27 TestID 2012 4 42 14 1.343810 0.7301587 3.705882 0.7479675
28 TestID 2013 4 27 11 1.324660 0.7160494 3.521739 0.7435897
29 TestID 2014 4 36 11 1.357414 0.7361111 3.789474 0.7571429
30 TestID 2015 4 48 14 1.363951 0.7395833 3.840000 0.7553191
31 TestID 2010 4 46 13 1.377400 0.7457467 3.933086 0.7623188
32 TestID 2011 4 32 11 1.359976 0.7363281 3.792593 0.7600806
33 TestID 2012 4 42 14 1.363046 0.7380952 3.818182 0.7560976
34 TestID 2013 4 55 19 1.362162 0.7371901 3.805031 0.7508418
35 TestID 2014 4 49 19 1.332135 0.7213661 3.588939 0.7363946
36 TestID 2015 4 46 14 1.373912 0.7438563 3.904059 0.7603865
37 TestID 2010 4 47 17 1.336186 0.7252150 3.639209 0.7409806
38 TestID 2011 4 45 14 1.367150 0.7407407 3.857143 0.7575758
39 TestID 2012 4 42 14 1.368082 0.7403628 3.851528 0.7584204
40 TestID 2013 4 48 17 1.354860 0.7335069 3.752443 0.7491135
41 TestID 2014 4 37 12 1.319925 0.7216947 3.593176 0.7417417
42 TestID 2015 4 42 14 1.343668 0.7290249 3.690377 0.7468060
43 TestID 2010 4 53 18 1.337430 0.7276611 3.671895 0.7416546
44 TestID 2011 4 37 12 1.357666 0.7363039 3.792244 0.7567568
45 TestID 2012 4 32 10 1.370502 0.7421875 3.878788 0.7661290
46 TestID 2013 4 36 11 1.363289 0.7391975 3.834320 0.7603175
47 TestID 2014 4 39 12 1.374965 0.7442472 3.910026 0.7638327
48 TestID 2015 4 38 10 1.381979 0.7479224 3.967033 0.7681366
49 TestID 2010 4 35 13 1.332431 0.7232653 3.613569 0.7445378
50 TestID 2011 4 33 11 1.359423 0.7364555 3.794425 0.7594697
51 TestID 2012 4 33 10 1.333723 0.7272727 3.666667 0.7500000
52 TestID 2013 4 36 11 1.373845 0.7438272 3.903614 0.7650794
53 TestID 2014 4 37 15 1.244500 0.6822498 3.147126 0.7012012
54 TestID 2015 4 26 11 1.289874 0.7011834 3.346535 0.7292308
55 TestID 2010 4 35 10 1.375102 0.7444898 3.913738 0.7663866
56 TestID 2011 4 48 14 1.377579 0.7456597 3.931741 0.7615248
57 TestID 2012 4 52 22 1.313154 0.7093195 3.440204 0.7232278
58 TestID 2013 4 35 11 1.361383 0.7379592 3.816199 0.7596639
59 TestID 2014 4 35 12 1.355920 0.7346939 3.769231 0.7563025
60 TestID 2015 4 48 15 1.370502 0.7421875 3.878788 0.7579787
61 TestID 2010 4 34 12 1.334793 0.7249135 3.635220 0.7468806
62 TestID 2011 4 44 15 1.360122 0.7365702 3.796078 0.7536998
63 TestID 2012 4 34 11 1.342396 0.7283737 3.681529 0.7504456
64 TestID 2013 4 48 15 1.374486 0.7439236 3.905085 0.7597518
65 TestID 2014 4 36 11 1.363289 0.7391975 3.834320 0.7603175
66 TestID 2015 4 36 16 1.241728 0.6805556 3.130435 0.7000000
67 TestID 2010 4 37 11 1.379501 0.7465303 3.945245 0.7672673
68 TestID 2011 4 39 15 1.329390 0.7205786 3.578824 0.7395412
69 TestID 2012 4 34 15 1.293693 0.6989619 3.321839 0.7201426
70 TestID 2013 4 39 11 1.377299 0.7455621 3.930233 0.7651822
71 TestID 2014 4 34 13 1.331641 0.7214533 3.590062 0.7433155
72 TestID 2015 4 35 12 1.343459 0.7297959 3.700906 0.7512605
73 TestID 2010 4 38 12 1.355447 0.7354571 3.780105 0.7553343
74 TestID 2011 4 35 12 1.355920 0.7346939 3.769231 0.7563025
75 TestID 2012 4 34 12 1.334793 0.7249135 3.635220 0.7468806
76 TestID 2013 4 46 14 1.373912 0.7438563 3.904059 0.7603865
77 TestID 2014 4 38 12 1.371381 0.7423823 3.881720 0.7624467
78 TestID 2015 4 39 12 1.351681 0.7337278 3.755556 0.7530364
79 TestID 2010 4 50 14 1.371764 0.7432000 3.894081 0.7583673
80 TestID 2011 4 29 9 1.370342 0.7419738 3.875576 0.7684729
81 TestID 2012 4 36 12 1.336895 0.7268519 3.661017 0.7476190
82 TestID 2013 4 49 17 1.347709 0.7305289 3.710974 0.7457483
83 TestID 2014 4 47 13 1.376050 0.7451335 3.923623 0.7613321
84 TestID 2015 4 41 13 1.368895 0.7412255 3.864368 0.7597561
85 TestID 2010 4 29 12 1.320152 0.7134364 3.489627 0.7389163
86 TestID 2011 4 26 10 1.249083 0.6893491 3.219048 0.7169231
87 TestID 2012 4 32 11 1.359976 0.7363281 3.792593 0.7600806
88 TestID 2013 4 31 10 1.337807 0.7284079 3.681992 0.7526882
89 TestID 2014 4 39 15 1.339134 0.7245233 3.630072 0.7435897
90 TestID 2015 4 47 15 1.365765 0.7397012 3.841739 0.7557817
91 TestID 2010 4 51 19 1.347219 0.7289504 3.689362 0.7435294
92 TestID 2011 4 47 19 1.323940 0.7161612 3.523126 0.7317299
93 TestID 2012 4 42 14 1.357411 0.7358277 3.785408 0.7537747
94 TestID 2013 4 41 16 1.337779 0.7233789 3.615054 0.7414634
95 TestID 2014 4 34 10 1.366425 0.7404844 3.853333 0.7629234
96 TestID 2015 4 30 13 1.292482 0.7000000 3.333333 0.7241379
DomMc expShannon
1 0.5686275 3.953977
2 0.7021277 3.523252
3 0.5853659 3.931006
4 0.6764706 3.745931
5 0.5641026 3.964179
6 0.5294118 3.993082
7 0.6041667 3.858217
8 0.5588235 3.934171
9 0.6666667 3.708998
10 0.6250000 3.798381
11 0.5957447 3.818104
12 0.6739130 3.723982
13 0.6333333 3.822329
14 0.6585366 3.785585
15 0.5897436 3.915989
16 0.5777778 3.942638
17 0.5813953 3.930586
18 0.6578947 3.796310
19 0.6857143 3.604341
20 0.5666667 3.914763
21 0.6551724 3.696677
22 0.6666667 3.701009
23 0.6551724 3.788497
24 0.5806452 3.929046
25 0.5681818 3.925374
26 0.6000000 3.880328
27 0.6190476 3.833623
28 0.6296296 3.760905
29 0.6111111 3.886130
30 0.5833333 3.911616
31 0.5434783 3.964579
32 0.5937500 3.896101
33 0.5952381 3.908078
34 0.5818182 3.904626
35 0.6326531 3.789123
36 0.5652174 3.950776
37 0.6382979 3.804506
38 0.5777778 3.924151
39 0.5714286 3.927808
40 0.6041667 3.876217
41 0.6216216 3.743139
42 0.6428571 3.833079
43 0.6037736 3.809242
44 0.5945946 3.887111
45 0.5625000 3.937328
46 0.5833333 3.909029
47 0.5641026 3.954937
48 0.5263158 3.982774
49 0.6285714 3.790248
50 0.6060606 3.893945
51 0.6060606 3.795145
52 0.5555556 3.950511
53 0.7567568 3.471199
54 0.6538462 3.632327
55 0.5714286 3.955481
56 0.5625000 3.965291
57 0.6346154 3.717882
58 0.6000000 3.901584
59 0.6000000 3.880328
60 0.5625000 3.937328
61 0.6470588 3.799210
62 0.5909091 3.896668
63 0.6470588 3.828203
64 0.5625000 3.953043
65 0.5833333 3.909029
66 0.7222222 3.461589
67 0.5405405 3.972919
68 0.6410256 3.778738
69 0.6470588 3.646228
70 0.5641026 3.964179
71 0.6470588 3.787252
72 0.6000000 3.832277
73 0.6052632 3.878492
74 0.6000000 3.880328
75 0.6470588 3.799210
76 0.5652174 3.950776
77 0.5789474 3.940789
78 0.6153846 3.863916
79 0.5600000 3.942297
80 0.5862069 3.936696
81 0.6388889 3.807205
82 0.6326531 3.848597
83 0.5531915 3.959232
84 0.5853659 3.931006
85 0.6206897 3.743989
86 0.7307692 3.487143
87 0.5937500 3.896101
88 0.6129032 3.810678
89 0.6153846 3.815738
90 0.5957447 3.918721
91 0.6078431 3.846714
92 0.6382979 3.758201
93 0.5952381 3.886118
94 0.6097561 3.810572
95 0.5882353 3.921309
96 0.6666667 3.641816
getAlphaMetrics works correctly for Abundance
Code
getAlphaMetrics(x = dataMetrics, measure = "ABUNDANCE")
Output
assemblageID YEAR S N maxN Shannon Simpson invSimpson PIE
1 A 2010 4 34 14 1.318024 0.7128028 3.481928 0.7344029
2 A 2011 4 40 15 1.344075 0.7275000 3.669725 0.7461538
3 A 2012 4 35 12 1.355920 0.7346939 3.769231 0.7563025
4 A 2013 4 34 14 1.318024 0.7128028 3.481928 0.7344029
5 A 2014 4 36 14 1.322282 0.7175926 3.540984 0.7380952
6 A 2015 4 45 14 1.343094 0.7308642 3.715596 0.7474747
7 B 2010 4 45 14 1.371850 0.7427160 3.886756 0.7595960
8 B 2011 4 38 14 1.296892 0.7091413 3.438095 0.7283073
9 B 2012 4 36 11 1.363289 0.7391975 3.834320 0.7603175
10 B 2013 4 39 11 1.379867 0.7468771 3.950649 0.7665317
11 B 2014 4 27 9 1.362721 0.7379973 3.816754 0.7663818
12 B 2015 4 42 13 1.366865 0.7403628 3.851528 0.7584204
13 C 2010 4 42 15 1.322869 0.7210884 3.585366 0.7386760
14 C 2011 4 37 15 1.267203 0.6968590 3.298795 0.7162162
15 C 2012 4 38 15 1.308673 0.7105263 3.454545 0.7297297
16 C 2013 4 32 12 1.328497 0.7207031 3.580420 0.7439516
17 C 2014 4 44 14 1.372269 0.7427686 3.887550 0.7600423
18 C 2015 4 41 14 1.320563 0.7198096 3.569002 0.7378049
19 D 2010 4 37 12 1.340163 0.7289993 3.690027 0.7492492
20 D 2011 4 48 19 1.315262 0.7135417 3.490909 0.7287234
21 D 2012 4 41 14 1.362762 0.7376562 3.811791 0.7560976
22 D 2013 4 36 13 1.340682 0.7268519 3.661017 0.7476190
23 D 2014 4 30 9 1.360577 0.7377778 3.813559 0.7632184
24 D 2015 4 25 7 1.383954 0.7488000 3.980892 0.7800000
25 E 2010 4 30 8 1.379292 0.7466667 3.947368 0.7724138
26 E 2011 4 34 14 1.283173 0.6989619 3.321839 0.7201426
27 E 2012 4 45 21 1.274065 0.6864198 3.188976 0.7020202
28 E 2013 4 40 14 1.349366 0.7312500 3.720930 0.7500000
29 E 2014 4 37 12 1.351950 0.7333820 3.750685 0.7537538
30 E 2015 4 37 12 1.364928 0.7392257 3.834734 0.7597598
31 F 2010 4 51 17 1.358035 0.7358708 3.786026 0.7505882
32 F 2011 4 59 18 1.367156 0.7405918 3.854928 0.7533606
33 F 2012 4 34 9 1.384563 0.7491349 3.986207 0.7718360
34 F 2013 4 32 9 1.373982 0.7441406 3.908397 0.7681452
35 F 2014 4 38 13 1.345289 0.7299169 3.702564 0.7496444
36 F 2015 4 41 11 1.382973 0.7483641 3.973995 0.7670732
37 G 2010 4 32 10 1.366586 0.7402344 3.849624 0.7641129
38 G 2011 4 36 11 1.363289 0.7391975 3.834320 0.7603175
39 G 2012 4 42 15 1.347336 0.7301587 3.705882 0.7479675
40 G 2013 4 32 12 1.336893 0.7246094 3.631206 0.7479839
41 G 2014 4 38 12 1.374311 0.7437673 3.902703 0.7638691
42 G 2015 4 35 12 1.355920 0.7346939 3.769231 0.7563025
43 H 2010 4 30 10 1.362447 0.7377778 3.813559 0.7632184
44 H 2011 4 38 15 1.296355 0.7077562 3.421801 0.7268848
45 H 2012 4 40 11 1.378502 0.7462500 3.940887 0.7653846
46 H 2013 4 44 13 1.371108 0.7427686 3.887550 0.7600423
47 H 2014 4 42 12 1.375572 0.7448980 3.920000 0.7630662
48 H 2015 4 48 15 1.363525 0.7387153 3.827243 0.7544326
DomMc expShannon
1 0.6470588 3.736031
2 0.6000000 3.834639
3 0.6000000 3.880328
4 0.6470588 3.736031
5 0.6388889 3.751972
6 0.6000000 3.830878
7 0.5777778 3.942638
8 0.6842105 3.657909
9 0.5833333 3.909029
10 0.5384615 3.974374
11 0.5925926 3.906808
12 0.5952381 3.923034
13 0.6190476 3.754176
14 0.6756757 3.550906
15 0.6842105 3.701257
16 0.6562500 3.775364
17 0.5681818 3.944289
18 0.6585366 3.745531
19 0.6216216 3.819665
20 0.6666667 3.725727
21 0.5853659 3.906970
22 0.6388889 3.821650
23 0.6000000 3.898443
24 0.5200000 3.990650
25 0.5333333 3.972089
26 0.7058824 3.608069
27 0.6666667 3.575356
28 0.6250000 3.854979
29 0.6216216 3.864954
30 0.5945946 3.915440
31 0.6078431 3.888547
32 0.5932203 3.924174
33 0.5294118 3.993082
34 0.5625000 3.951052
35 0.6315789 3.839297
36 0.5365854 3.986736
37 0.5937500 3.921938
38 0.5833333 3.909029
39 0.6190476 3.847165
40 0.6250000 3.807196
41 0.5526316 3.952353
42 0.6000000 3.880328
43 0.6000000 3.905741
44 0.6578947 3.655945
45 0.5500000 3.968954
46 0.5681818 3.939713
47 0.5476190 3.957339
48 0.6041667 3.909953
getAlphaMetrics works correctly for Biomass
Code
getAlphaMetrics(x = dataMetrics, measure = "BIOMASS")
Output
assemblageID YEAR S N maxN Shannon Simpson invSimpson PIE
1 A 2010 4 4051 1034 1.386206 0.7499555 3.999288 0.7501406
2 A 2011 4 4064 1049 1.385816 0.7497608 3.996177 0.7499454
3 A 2012 4 4107 1076 1.385474 0.7495905 3.993459 0.7497731
4 A 2013 4 3964 1014 1.386140 0.7499230 3.998768 0.7501122
5 A 2014 4 4048 1044 1.385972 0.7498395 3.997434 0.7500248
6 A 2015 4 3935 991 1.386227 0.7499664 3.999462 0.7501570
7 B 2010 4 3935 1007 1.386155 0.7499301 3.998881 0.7501207
8 B 2011 4 4002 1044 1.385871 0.7497876 3.996605 0.7499750
9 B 2012 4 3887 1009 1.385983 0.7498439 3.997504 0.7500368
10 B 2013 4 3863 1008 1.385833 0.7497689 3.996306 0.7499630
11 B 2014 4 3847 1014 1.385609 0.7496567 3.994515 0.7498516
12 B 2015 4 3954 1028 1.385803 0.7497551 3.996085 0.7499448
13 C 2010 4 3933 1014 1.386011 0.7498586 3.997739 0.7500493
14 C 2011 4 3932 1014 1.385825 0.7497674 3.996282 0.7499581
15 C 2012 4 4020 1025 1.386051 0.7498792 3.998068 0.7500658
16 C 2013 4 3991 1030 1.386114 0.7499094 3.998551 0.7500974
17 C 2014 4 4030 1023 1.386213 0.7499594 3.999351 0.7501456
18 C 2015 4 4034 1042 1.385888 0.7497978 3.996767 0.7499837
19 D 2010 4 4035 1066 1.385637 0.7496695 3.994719 0.7498553
20 D 2011 4 4021 1041 1.385371 0.7495455 3.992741 0.7497319
21 D 2012 4 3863 1001 1.385787 0.7497473 3.995961 0.7499415
22 D 2013 4 4033 1026 1.386179 0.7499424 3.999079 0.7501284
23 D 2014 4 4053 1040 1.385972 0.7498396 3.997435 0.7500247
24 D 2015 4 3986 1017 1.386145 0.7499257 3.998811 0.7501139
25 E 2010 4 3976 1025 1.386112 0.7499085 3.998537 0.7500972
26 E 2011 4 3978 1058 1.385497 0.7495975 3.993571 0.7497860
27 E 2012 4 3958 1005 1.386178 0.7499417 3.999068 0.7501312
28 E 2013 4 3919 989 1.386231 0.7499683 3.999493 0.7501597
29 E 2014 4 4082 1070 1.385042 0.7493789 3.990087 0.7495625
30 E 2015 4 3928 1010 1.386088 0.7498969 3.998352 0.7500879
31 F 2010 4 4121 1102 1.385123 0.7494143 3.990651 0.7495962
32 F 2011 4 3964 1016 1.386096 0.7499010 3.998416 0.7500902
33 F 2012 4 3994 1014 1.386206 0.7499558 3.999293 0.7501436
34 F 2013 4 3893 1018 1.385713 0.7497090 3.995349 0.7499016
35 F 2014 4 4063 1043 1.386040 0.7498735 3.997977 0.7500581
36 F 2015 4 3886 1027 1.385755 0.7497268 3.995634 0.7499198
37 G 2010 4 4030 1047 1.385674 0.7496924 3.995085 0.7498785
38 G 2011 4 4094 1041 1.386061 0.7498838 3.998142 0.7500670
39 G 2012 4 3892 1020 1.385449 0.7495783 3.993264 0.7497709
40 G 2013 4 4049 1050 1.385988 0.7498462 3.997541 0.7500315
41 G 2014 4 3895 1000 1.385836 0.7497728 3.996368 0.7499654
42 G 2015 4 3929 997 1.386236 0.7499707 3.999531 0.7501616
43 H 2010 4 3929 1035 1.385340 0.7495233 3.992387 0.7497141
44 H 2011 4 4020 1018 1.386264 0.7499850 3.999760 0.7501716
45 H 2012 4 4009 1040 1.385847 0.7497770 3.996435 0.7499640
46 H 2013 4 3970 1031 1.385565 0.7496389 3.994231 0.7498278
47 H 2014 4 4060 1065 1.385746 0.7497245 3.995596 0.7499092
48 H 2015 4 4011 1032 1.386086 0.7498954 3.998327 0.7500824
DomMc expShannon
1 0.5055542 3.999645
2 0.5152559 3.998086
3 0.5191137 3.996718
4 0.5063068 3.999383
5 0.5101285 3.998712
6 0.5034307 3.999730
7 0.5077510 3.999441
8 0.5129935 3.998308
9 0.5109339 3.998756
10 0.5135905 3.998156
11 0.5144268 3.997259
12 0.5131512 3.998035
13 0.5105517 3.998868
14 0.5116989 3.998124
15 0.5089552 3.999028
16 0.5063894 3.999280
17 0.5057072 3.999675
18 0.5116510 3.998374
19 0.5142503 3.997372
20 0.5138025 3.996308
21 0.5146259 3.997973
22 0.5058269 3.999538
23 0.5102393 3.998709
24 0.5075263 3.999404
25 0.5077968 3.999272
26 0.5170940 3.996810
27 0.5075796 3.999534
28 0.5039551 3.999745
29 0.5227829 3.994995
30 0.5089104 3.999176
31 0.5171075 3.995319
32 0.5090817 3.999207
33 0.5055083 3.999646
34 0.5163113 3.997677
35 0.5087374 3.998984
36 0.5102934 3.997842
37 0.5136476 3.997521
38 0.5085491 3.999065
39 0.5195272 3.996620
40 0.5102494 3.998773
41 0.5116816 3.998166
42 0.5047086 3.999765
43 0.5209977 3.996186
44 0.5029851 3.999880
45 0.5125967 3.998210
46 0.5148615 3.997082
47 0.5150246 3.997806
48 0.5095986 3.999165
getBetaMetrics works correctly for Abundance
Code
getBetaMetrics(x = dataMetrics, measure = "ABUNDANCE")
Output
YEAR assemblageID JaccardDiss MorisitaHornDiss BrayCurtisDiss
1 2010 A 1 1 1
2 2011 A 1 1 1
3 2012 A 1 1 1
4 2013 A 1 1 1
5 2014 A 1 1 1
6 2015 A 1 1 1
7 2010 B 1 1 1
8 2011 B 1 1 1
9 2012 B 1 1 1
10 2013 B 1 1 1
11 2014 B 1 1 1
12 2015 B 1 1 1
13 2010 C 1 1 1
14 2011 C 1 1 1
15 2012 C 1 1 1
16 2013 C 1 1 1
17 2014 C 1 1 1
18 2015 C 1 1 1
19 2010 D 1 1 1
20 2011 D 1 1 1
21 2012 D 1 1 1
22 2013 D 1 1 1
23 2014 D 1 1 1
24 2015 D 1 1 1
25 2010 E 1 1 1
26 2011 E 1 1 1
27 2012 E 1 1 1
28 2013 E 1 1 1
29 2014 E 1 1 1
30 2015 E 1 1 1
31 2010 F 1 1 1
32 2011 F 1 1 1
33 2012 F 1 1 1
34 2013 F 1 1 1
35 2014 F 1 1 1
36 2015 F 1 1 1
37 2010 G 1 1 1
38 2011 G 1 1 1
39 2012 G 1 1 1
40 2013 G 1 1 1
41 2014 G 1 1 1
42 2015 G 1 1 1
43 2010 H 1 1 1
44 2011 H 1 1 1
45 2012 H 1 1 1
46 2013 H 1 1 1
47 2014 H 1 1 1
48 2015 H 1 1 1
getBetaMetrics works correctly for Biomass
Code
getBetaMetrics(x = dataMetrics, measure = "BIOMASS")
Output
YEAR assemblageID JaccardDiss MorisitaHornDiss BrayCurtisDiss
1 2010 A 1 1 1
2 2011 A 1 1 1
3 2012 A 1 1 1
4 2013 A 1 1 1
5 2014 A 1 1 1
6 2015 A 1 1 1
7 2010 B 1 1 1
8 2011 B 1 1 1
9 2012 B 1 1 1
10 2013 B 1 1 1
11 2014 B 1 1 1
12 2015 B 1 1 1
13 2010 C 1 1 1
14 2011 C 1 1 1
15 2012 C 1 1 1
16 2013 C 1 1 1
17 2014 C 1 1 1
18 2015 C 1 1 1
19 2010 D 1 1 1
20 2011 D 1 1 1
21 2012 D 1 1 1
22 2013 D 1 1 1
23 2014 D 1 1 1
24 2015 D 1 1 1
25 2010 E 1 1 1
26 2011 E 1 1 1
27 2012 E 1 1 1
28 2013 E 1 1 1
29 2014 E 1 1 1
30 2015 E 1 1 1
31 2010 F 1 1 1
32 2011 F 1 1 1
33 2012 F 1 1 1
34 2013 F 1 1 1
35 2014 F 1 1 1
36 2015 F 1 1 1
37 2010 G 1 1 1
38 2011 G 1 1 1
39 2012 G 1 1 1
40 2013 G 1 1 1
41 2014 G 1 1 1
42 2015 G 1 1 1
43 2010 H 1 1 1
44 2011 H 1 1 1
45 2012 H 1 1 1
46 2013 H 1 1 1
47 2014 H 1 1 1
48 2015 H 1 1 1
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