alltools: Apply the whole analysis to the dataset.
In BioFTF: Biodiversity Assessment Using Functional Tools
Description
Usage
Arguments
Author(s)
Source
Examples
Description
This function provides the derivatives, the curvature, the radius of curvature and the arc length of diversity profiles. Morever, it computes the surface area under the beta profile and ranks the communities.
Usage
1
alltools(x,n)
Arguments
x
A data matrix with the abundance of the species (the rows are the communities and the columns indicate the species living in a community). The user can freely choose to use the absolute or relative frequencies.
n
The number of points of the domain [-1,1] that the user wants to consider in computing the functional tools. It is suggested to choose a number in the interval [3,10000] because a value of less than 3 has little sense; indeed, the major indices of biodiversity are the richness index, the index of Shannon and the index of Simpson (that we get for beta equal to -1, 0, +1, respectively). On the other hand, a value greater than 10000 is not very interesting because with a value of approximately 100 we already have a good approximation. The examples provided in this package always divide the domain into 20 intervals. The default value is n=20.
Author(s)
Fabrizio Maturo, Francesca Fortuna, Tonio Di Battista
Source
ENVIRONMENTAL MONITORING THROUGH FUNCTIONAL BIODIVERSITY TOOLS - T. Di Battista, F. Fortuna, F. Maturo - Ecological Indicators (2016) 60, 237-247 - online (2015). DOI: 10.1016/j.ecolind.2015.05.056.
PARAMETRIC FUNCTIONAL ANALYSIS OF VARIANCE FOR FISH BIODIVERSITY ASSESSMENT - T. Di Battista, F. Fortuna, F. Maturo - Journal of Environmental Informatics. Special issue of Marine and Freshwater Environmental Engineering and Management, Journal of Environmental Informatics. In press.
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
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33
34
35
36
37
38
#example 1
x=matrix(c(3,5,5,2,1,2,6,8,5,1),2,5)
x
alltools(x,20)
#Some examples expressed by relative abundance:
#example 2
x=matrix(c(0.3,0.5,0.1,0.05,0.05,0.25,0.25,0.25,0.25,0,0.35,0.3,0.35,0,0),3,5)
x
alltools(x,20)
#example 3
x=matrix(runif(1000),10,100)
#let's consider some missing species
x[1,1:20]=0
x[2,1:40]=0
x[3,1:60]=0
x[4,1:19]=0
x
alltools(x,20)
#example 4
x=matrix(runif(100),20,5)
x[1,1:2]=0
x[2,1:3]=0
x
alltools(x,20)
#example 5
a=c(0.35,0.35,0.27,0.01,0.02)
b=c(0.54,0.20,0.17,0.06,0.03)
c=c(0.35,0.35,0.30,0,0)
d=c(0.51,0.31,0.07,0.10,0.01)
e=c(0.40,0.20,0.10,0.30,0)
x=matrix(rbind(a,b,c,d,e),5,5)
x
alltools(x,20)
Example output
Attaching package: 'BioFTF'
The following object is masked from 'package:base':
beta
[,1] [,2] [,3] [,4] [,5]
[1,] 3 5 1 6 5
[2,] 5 2 2 8 1
[1] "Communities Ranking"
Richness Shannon Simpson Arc Area
community n.1 4 1.553442 0.7600000 3.978451 3.521920
community n.2 4 1.427358 0.6975309 4.064566 3.324774
[,1] [,2] [,3] [,4] [,5]
[1,] 0.3 0.05 0.25 0.00 0.35
[2,] 0.5 0.05 0.25 0.35 0.00
[3,] 0.1 0.25 0.25 0.30 0.00
[1] "Communities Ranking"
Richness Shannon Simpson Arc Area
community n.3 3 1.371977 0.7222222 3.146391 2.984744
community n.1 3 1.284566 0.6925208 3.201093 2.844643
community n.2 3 1.237469 0.6691871 3.234599 2.768349
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.0000000 0.000000000 0.0000000 0.00000000 0.00000000 0.00000000
[2,] 0.0000000 0.000000000 0.0000000 0.00000000 0.00000000 0.00000000
[3,] 0.0000000 0.000000000 0.0000000 0.00000000 0.00000000 0.00000000
[4,] 0.0000000 0.000000000 0.0000000 0.00000000 0.00000000 0.00000000
[5,] 0.4011274 0.444286812 0.6412625 0.05378237 0.64197642 0.72095449
[6,] 0.1580888 0.006899007 0.2160551 0.34464721 0.02690836 0.27821310
[7,] 0.2188947 0.038450459 0.2085245 0.12633427 0.69464326 0.07177104
[8,] 0.5220810 0.453902619 0.7641914 0.75175104 0.23480086 0.17313173
[9,] 0.4788486 0.649822330 0.3930794 0.36176148 0.11945985 0.70192098
[10,] 0.5972911 0.540697424 0.2494894 0.06298330 0.82205493 0.72382945
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.000000000 0.00000000 0.00000000 0.0000000 0.0000000 0.000000000
[2,] 0.000000000 0.00000000 0.00000000 0.0000000 0.0000000 0.000000000
[3,] 0.000000000 0.00000000 0.00000000 0.0000000 0.0000000 0.000000000
[4,] 0.000000000 0.00000000 0.00000000 0.0000000 0.0000000 0.000000000
[5,] 0.586380504 0.99917617 0.49280508 0.9850789 0.1141627 0.002322183
[6,] 0.002151049 0.67895947 0.71464262 0.4316209 0.4062646 0.868615214
[7,] 0.361030118 0.78997016 0.08346749 0.2262645 0.5379090 0.494607270
[8,] 0.425684557 0.09376064 0.78392815 0.2090034 0.8573384 0.631312967
[9,] 0.971591785 0.88903136 0.97993473 0.6079589 0.8929140 0.300360410
[10,] 0.305509672 0.98806363 0.28155138 0.2430984 0.6281422 0.592050995
[,13] [,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000
[2,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000
[3,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000
[4,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000
[5,] 0.3984816 0.3728082 0.29724354 0.34052126 0.7255152 0.33444763 0.66746786
[6,] 0.2978539 0.9148603 0.49920821 0.79764428 0.8146300 0.36299587 0.04260419
[7,] 0.6959564 0.8542949 0.63867080 0.99915392 0.2816912 0.05153839 0.55762752
[8,] 0.3531682 0.8579008 0.58862621 0.60531117 0.1407264 0.47268905 0.07026824
[9,] 0.5239106 0.3570238 0.26449820 0.03952134 0.5768931 0.39172620 0.89774371
[10,] 0.5051049 0.6923080 0.04634502 0.18420632 0.3001498 0.48407132 0.54586136
[,20] [,21] [,22] [,23] [,24] [,25]
[1,] 0.000000000 0.24170424 0.82179936 0.16384550 0.4850207 0.8374714
[2,] 0.000000000 0.00000000 0.00000000 0.00000000 0.0000000 0.0000000
[3,] 0.000000000 0.00000000 0.00000000 0.00000000 0.0000000 0.0000000
[4,] 0.131511819 0.13868008 0.01327023 0.52664807 0.1874813 0.1011648
[5,] 0.259504844 0.66689868 0.10240508 0.27605438 0.4236928 0.4638461
[6,] 0.302167635 0.42901795 0.98912353 0.91592210 0.1866119 0.4890050
[7,] 0.005315822 0.03798883 0.44333146 0.04591396 0.7461944 0.3254439
[8,] 0.453582264 0.63074960 0.53650450 0.01273343 0.4686055 0.3831858
[9,] 0.506539000 0.52991628 0.86432275 0.72827604 0.6256645 0.6526949
[10,] 0.143451103 0.77761653 0.61704521 0.27742621 0.1749559 0.7659214
[,26] [,27] [,28] [,29] [,30] [,31] [,32]
[1,] 0.1126338 0.2158135 0.85645807 0.01533732 0.8596092 0.77664188 0.9061248
[2,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.0000000
[3,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.0000000
[4,] 0.3744407 0.6897089 0.04871110 0.14483584 0.1801114 0.03394456 0.1689593
[5,] 0.6964784 0.4659248 0.33550378 0.56967378 0.4333417 0.38839200 0.5218118
[6,] 0.5418400 0.5732958 0.52448025 0.01985319 0.9894339 0.35443529 0.9383096
[7,] 0.8265350 0.1113880 0.02945411 0.11113144 0.4986352 0.41896681 0.3894486
[8,] 0.9626939 0.3492040 0.50365560 0.31574302 0.2872874 0.60144985 0.0868817
[9,] 0.6570333 0.6543677 0.21880138 0.28015611 0.8899665 0.87359517 0.8044213
[10,] 0.6711370 0.6184624 0.98754319 0.13736638 0.2495793 0.93224663 0.6280954
[,33] [,34] [,35] [,36] [,37] [,38] [,39]
[1,] 0.02822358 0.3113779 0.4544429 0.33814827 0.02020423 0.08828651 0.2590625
[2,] 0.00000000 0.0000000 0.0000000 0.00000000 0.00000000 0.00000000 0.0000000
[3,] 0.00000000 0.0000000 0.0000000 0.00000000 0.00000000 0.00000000 0.0000000
[4,] 0.35277328 0.9348589 0.8589601 0.22932359 0.92295062 0.56989580 0.3972038
[5,] 0.72466869 0.2952053 0.5105460 0.63900561 0.21321593 0.89415997 0.4898247
[6,] 0.60238220 0.1502750 0.5248639 0.44749333 0.50342911 0.73506130 0.2210673
[7,] 0.44961754 0.4829678 0.6684513 0.31738068 0.10665120 0.37417668 0.4670996
[8,] 0.56146378 0.6110110 0.2958976 0.81454258 0.79573656 0.44303223 0.7549487
[9,] 0.77344399 0.5022963 0.4313210 0.09044614 0.42097423 0.29790691 0.3993855
[10,] 0.58194396 0.3663718 0.4442853 0.83694414 0.70107378 0.28217514 0.3742053
[,40] [,41] [,42] [,43] [,44] [,45] [,46]
[1,] 0.7396079 0.2384019 0.13646033 0.51312737 0.44340211 0.27835068 0.4613610
[2,] 0.0000000 0.2391838 0.24801854 0.60206006 0.83633837 0.96945445 0.1137962
[3,] 0.0000000 0.0000000 0.00000000 0.00000000 0.00000000 0.00000000 0.0000000
[4,] 0.9815152 0.7483495 0.17959479 0.64931892 0.31048623 0.78870957 0.3648271
[5,] 0.7334532 0.5457406 0.13533933 0.56807887 0.34170455 0.93419418 0.3720169
[6,] 0.9004650 0.3864311 0.68868979 0.44386705 0.07724666 0.71633638 0.1933426
[7,] 0.4714387 0.4636079 0.54865857 0.70435477 0.39963080 0.21179856 0.6359276
[8,] 0.3465991 0.1798396 0.13138892 0.13213044 0.64796986 0.04706328 0.1960204
[9,] 0.9242367 0.5917151 0.02378541 0.63761321 0.09365602 0.84864308 0.8971944
[10,] 0.4434414 0.8458603 0.82103272 0.03656731 0.62425406 0.29598428 0.1242887
[,47] [,48] [,49] [,50] [,51] [,52]
[1,] 0.58648031 0.6983419 0.3763730 0.89079984 0.15550742 0.7945785
[2,] 0.31323374 0.4685806 0.3820746 0.07001316 0.29717758 0.7375523
[3,] 0.00000000 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000
[4,] 0.57681526 0.2186073 0.7042773 0.61380501 0.63174156 0.6139515
[5,] 0.64194837 0.6362454 0.5407349 0.03492500 0.39447651 0.9008951
[6,] 0.15172982 0.1805488 0.4285790 0.36335512 0.82543362 0.7361469
[7,] 0.03810356 0.6062070 0.4373250 0.83137295 0.45799527 0.4365708
[8,] 0.41600845 0.6830345 0.6253351 0.07561277 0.04412295 0.1428324
[9,] 0.93421850 0.9084933 0.6144268 0.66041990 0.59721296 0.5010067
[10,] 0.50874909 0.7388225 0.1451301 0.47108633 0.59738623 0.0713963
[,53] [,54] [,55] [,56] [,57] [,58]
[1,] 0.030034070 0.3195775 0.352267543 0.2437145 0.74028777 0.58184249
[2,] 0.006287697 0.7187082 0.052355445 0.8404530 0.81093921 0.59069330
[3,] 0.000000000 0.0000000 0.000000000 0.0000000 0.00000000 0.00000000
[4,] 0.521870652 0.2318088 0.158194846 0.5795539 0.18570090 0.05769629
[5,] 0.513541458 0.2475222 0.399980148 0.5083738 0.81490362 0.12677343
[6,] 0.440514972 0.3564393 0.766065159 0.7302267 0.15470426 0.09692838
[7,] 0.200798688 0.6771694 0.555683492 0.8710032 0.04426182 0.17375717
[8,] 0.827251548 0.9063911 0.702521908 0.6022886 0.77343814 0.32497060
[9,] 0.119665985 0.1047887 0.008297865 0.8478838 0.74377799 0.34856481
[10,] 0.761707903 0.1189481 0.745417675 0.6892447 0.61018697 0.17676352
[,59] [,60] [,61] [,62] [,63] [,64]
[1,] 0.50630978 0.766600916 0.23127055 0.9572221 0.008512205 0.43385200
[2,] 0.70606886 0.565114213 0.35301819 0.9074817 0.317606268 0.07450328
[3,] 0.00000000 0.000000000 0.51714288 0.3845099 0.948621924 0.60365966
[4,] 0.13695148 0.145033563 0.09981155 0.6418801 0.727583071 0.41602213
[5,] 0.45110252 0.997225481 0.67716557 0.2567867 0.077020862 0.04390422
[6,] 0.05273374 0.691067220 0.21167530 0.2492073 0.317494274 0.33435709
[7,] 0.58820546 0.916417541 0.94219353 0.5657998 0.431868274 0.19497837
[8,] 0.33782895 0.003825191 0.67713622 0.4260021 0.105047232 0.99789663
[9,] 0.33079698 0.967024885 0.71592197 0.1778241 0.700811186 0.58715619
[10,] 0.06392221 0.757348123 0.12130644 0.3616753 0.329301818 0.55251066
[,65] [,66] [,67] [,68] [,69] [,70] [,71]
[1,] 0.39959684 0.9281167 0.08123837 0.2537033 0.39758437 0.60260351 0.9719670
[2,] 0.49308742 0.2487549 0.05138476 0.7763969 0.67477809 0.52355971 0.3825577
[3,] 0.65258710 0.6713577 0.65517223 0.9996588 0.99755977 0.07696736 0.7688453
[4,] 0.03071067 0.3677199 0.48289075 0.5324784 0.97986249 0.34584441 0.0752827
[5,] 0.08123094 0.5954433 0.47211892 0.5544786 0.90401887 0.06473625 0.6503186
[6,] 0.26128098 0.6624737 0.58320945 0.4022971 0.94696345 0.83260071 0.2236028
[7,] 0.86369121 0.8703999 0.61926783 0.3432352 0.47735608 0.37928572 0.8394698
[8,] 0.42883804 0.5597365 0.46303329 0.3644199 0.57753813 0.13583322 0.8904121
[9,] 0.93390562 0.7784873 0.67167189 0.5097221 0.09937025 0.80742259 0.1954620
[10,] 0.18906073 0.9975195 0.92571173 0.7845709 0.04001989 0.45418355 0.7648700
[,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.1058174 0.33813363 0.81784183 0.2755743 0.97377667 0.50879421
[2,] 0.5920409 0.79256430 0.04551546 0.5254094 0.50534576 0.49165645
[3,] 0.5820709 0.86001026 0.26290118 0.8611382 0.08069622 0.21742121
[4,] 0.5564073 0.02788545 0.48345659 0.7828772 0.26441755 0.61378708
[5,] 0.7107441 0.85575994 0.07697914 0.7763206 0.90763806 0.29404271
[6,] 0.8777000 0.61350456 0.67198794 0.8981556 0.80362107 0.79958875
[7,] 0.2819617 0.84004201 0.82590028 0.3038542 0.50210855 0.35355601
[8,] 0.8232772 0.71698270 0.47789367 0.5686160 0.22805622 0.55323668
[9,] 0.5805652 0.22681472 0.88342533 0.2448300 0.60963236 0.38508744
[10,] 0.7830102 0.87683979 0.09010592 0.9420445 0.15606574 0.01408223
[,78] [,79] [,80] [,81] [,82] [,83]
[1,] 0.56075555 0.09920138 0.073631856 0.7054768 0.90016647 0.3364281
[2,] 0.02291368 0.93615006 0.305429616 0.5431087 0.81110475 0.4946811
[3,] 0.82254593 0.75617814 0.594219660 0.9554137 0.39746805 0.7047236
[4,] 0.74843982 0.84389909 0.603717087 0.8635685 0.18428616 0.6628849
[5,] 0.99437972 0.64734523 0.731738105 0.8649782 0.08153723 0.3465239
[6,] 0.20285183 0.66633980 0.706540967 0.4393346 0.18025317 0.7325172
[7,] 0.37553955 0.81041787 0.001221441 0.7089089 0.84445713 0.2609762
[8,] 0.91361043 0.61000272 0.257671360 0.1437518 0.64432536 0.7332135
[9,] 0.70500736 0.43529327 0.655665676 0.2762848 0.57079880 0.8117243
[10,] 0.55281916 0.28821597 0.291008163 0.4762671 0.27969863 0.6093084
[,84] [,85] [,86] [,87] [,88] [,89]
[1,] 0.48270447 0.36622711 0.27871195 0.07411564 0.85137599 0.24918021
[2,] 0.10994287 0.22845209 0.87468894 0.12403113 0.40171006 0.04919956
[3,] 0.21737670 0.40409816 0.14681963 0.79909657 0.26966148 0.67129737
[4,] 0.64122510 0.11169747 0.07894842 0.92932158 0.28534025 0.09979915
[5,] 0.05392044 0.07211554 0.70467339 0.41867528 0.92227711 0.35231695
[6,] 0.63716696 0.84307149 0.93796935 0.02256935 0.03393054 0.82765228
[7,] 0.95599873 0.12022905 0.77063540 0.12879711 0.98867204 0.60636065
[8,] 0.88623370 0.78705756 0.80720935 0.19422882 0.26895735 0.78032133
[9,] 0.40086083 0.13028637 0.20288315 0.12921168 0.15656141 0.99600256
[10,] 0.52300397 0.69244896 0.91759458 0.22889323 0.72147457 0.80163269
[,90] [,91] [,92] [,93] [,94] [,95] [,96]
[1,] 0.1179521 0.30461632 0.3621254 0.5858575 0.04138162 0.9662174 0.57758559
[2,] 0.4029802 0.47679947 0.7796595 0.8727960 0.98158054 0.3497803 0.01605949
[3,] 0.8771168 0.76361104 0.2983134 0.9482123 0.87090843 0.7039441 0.06523895
[4,] 0.1372104 0.88845090 0.7655739 0.9799887 0.31142880 0.1197100 0.61393093
[5,] 0.3689028 0.20085005 0.2870878 0.3724052 0.70057103 0.4932027 0.53480494
[6,] 0.9639197 0.05585737 0.3387032 0.3333424 0.47793138 0.1723964 0.65344798
[7,] 0.6208215 0.91775776 0.5619711 0.3288627 0.46982875 0.5186106 0.53951776
[8,] 0.2371105 0.95994655 0.7968732 0.7674738 0.95947440 0.6977739 0.45401673
[9,] 0.4639680 0.64518665 0.9853205 0.6514436 0.03448595 0.3579197 0.83036471
[10,] 0.1636136 0.52189309 0.3356801 0.9471208 0.61408240 0.8876882 0.79766654
[,97] [,98] [,99] [,100]
[1,] 0.14513313 0.1094394 0.183533517 0.96801066
[2,] 0.10293576 0.8830619 0.059129311 0.34988832
[3,] 0.07832356 0.2507777 0.002526075 0.85661359
[4,] 0.58942382 0.6198791 0.961523045 0.01071654
[5,] 0.87234005 0.6060280 0.027521854 0.94858596
[6,] 0.33262180 0.7414468 0.302334704 0.57934958
[7,] 0.97975837 0.2859644 0.285902314 0.06038719
[8,] 0.18490230 0.2846517 0.543103829 0.59056203
[9,] 0.81482781 0.9903134 0.691136690 0.93358945
[10,] 0.19317895 0.1439867 0.668829781 0.20937286
[1] "Communities Ranking"
Richness Shannon Simpson Arc Area
community n.9 99 5.022618 0.9874119 98.23259 29.56242
community n.8 99 5.003496 0.9870682 98.23354 29.48049
community n.10 99 4.987112 0.9867821 98.23434 29.43776
community n.5 99 4.995679 0.9869733 98.23385 29.42678
community n.6 99 4.966632 0.9865682 98.23513 29.26433
community n.7 99 4.958938 0.9864543 98.23548 29.22711
community n.4 80 4.640925 0.9821281 79.25044 24.90735
community n.1 79 4.630031 0.9818376 78.25118 24.70645
community n.2 59 4.279539 0.9764398 58.27085 20.06306
community n.3 39 3.860553 0.9677110 38.30201 15.27880
[,1] [,2] [,3] [,4] [,5]
[1,] 0.000000000 0.00000000 0.73161595 0.62438279 0.6779418713
[2,] 0.000000000 0.00000000 0.00000000 0.31812174 0.7575915963
[3,] 0.713275049 0.36064807 0.45653981 0.42605403 0.1609782730
[4,] 0.704373126 0.39525808 0.09967635 0.57865424 0.1716597306
[5,] 0.921849380 0.17407597 0.51887056 0.77769694 0.8816115449
[6,] 0.790399990 0.85487914 0.78698284 0.79310564 0.8164990211
[7,] 0.002584195 0.52877029 0.30715265 0.94550969 0.0001606732
[8,] 0.210232373 0.88036897 0.21802798 0.99132558 0.4694073740
[9,] 0.203984601 0.01356285 0.43837957 0.33425014 0.4851714598
[10,] 0.604971938 0.21966779 0.08283790 0.84122727 0.5723661999
[11,] 0.405502280 0.43076080 0.68254624 0.49480125 0.8396368981
[12,] 0.978409593 0.41948138 0.08455748 0.91304543 0.2729048126
[13,] 0.588437438 0.30740713 0.28252257 0.68811762 0.4331816186
[14,] 0.997661179 0.40880822 0.02635892 0.78144762 0.1437381865
[15,] 0.180921219 0.28506022 0.81754868 0.70297438 0.8968860777
[16,] 0.050755903 0.27592838 0.32999052 0.05078456 0.2838735913
[17,] 0.735854028 0.84515400 0.02082818 0.07772496 0.3082542217
[18,] 0.549612237 0.76633848 0.50841482 0.90253356 0.4458824093
[19,] 0.215374438 0.22909761 0.23071763 0.16418753 0.3360536436
[20,] 0.126369594 0.90965279 0.90686934 0.18630873 0.0377915949
[1] "Communities Ranking"
Richness Shannon Simpson Arc Area
community n.6 4 1.6790634 0.7998015 3.907958 3.721844
community n.19 4 1.6515022 0.7886623 3.924312 3.678991
community n.18 4 1.6427022 0.7853074 3.929452 3.665332
community n.11 4 1.6376233 0.7831138 3.932577 3.657424
community n.13 4 1.6191223 0.7765460 3.943203 3.628519
community n.3 4 1.5841438 0.7647763 3.963295 3.572685
community n.5 4 1.5647476 0.7638579 3.971736 3.540116
community n.15 4 1.5316416 0.7497029 3.992682 3.489498
community n.8 4 1.4924726 0.7301142 4.019346 3.428674
community n.4 4 1.4804518 0.7299113 4.024902 3.407521
community n.10 4 1.4668598 0.7296690 4.031526 3.382331
community n.16 4 1.4448181 0.7244751 4.043867 3.348780
community n.12 4 1.4284813 0.7122995 4.057568 3.320898
community n.9 4 1.4360938 0.7330375 4.048482 3.307962
community n.14 4 1.3077966 0.6772674 4.136275 3.109140
community n.17 4 1.2454745 0.6565120 4.179192 3.005798
community n.20 4 1.2285139 0.6375551 4.193052 2.993614
community n.7 4 1.0441391 0.6016900 4.371507 2.518354
community n.1 2 1.1289004 0.6652769 2.447505 2.347388
community n.2 1 0.6212978 0.4165483 2.095950 1.280227
[,1] [,2] [,3] [,4] [,5]
[1,] 0.35 0.35 0.27 0.01 0.02
[2,] 0.54 0.20 0.17 0.06 0.03
[3,] 0.35 0.35 0.30 0.00 0.00
[4,] 0.51 0.31 0.07 0.10 0.01
[5,] 0.40 0.20 0.10 0.30 0.00
[1] "Communities Ranking"
Richness Shannon Simpson Arc Area
community n.2 4 1.287308 0.6350 4.161938 3.093113
community n.1 4 1.260532 0.6816 4.164246 3.018096
community n.4 4 1.220762 0.6288 4.202864 2.969033
community n.5 3 1.329085 0.7000 3.175405 2.917174
community n.3 2 1.128438 0.6650 2.447772 2.346659
BioFTF documentation built on May 1, 2019, 10:26 p.m.
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Description Usage Arguments Author(s) Source Examples
Description
This function provides the derivatives, the curvature, the radius of curvature and the arc length of diversity profiles. Morever, it computes the surface area under the beta profile and ranks the communities.
Usage
1 | alltools(x,n)
|
Arguments
x |
A data matrix with the abundance of the species (the rows are the communities and the columns indicate the species living in a community). The user can freely choose to use the absolute or relative frequencies. |
n |
The number of points of the domain [-1,1] that the user wants to consider in computing the functional tools. It is suggested to choose a number in the interval [3,10000] because a value of less than 3 has little sense; indeed, the major indices of biodiversity are the richness index, the index of Shannon and the index of Simpson (that we get for beta equal to -1, 0, +1, respectively). On the other hand, a value greater than 10000 is not very interesting because with a value of approximately 100 we already have a good approximation. The examples provided in this package always divide the domain into 20 intervals. The default value is n=20. |
Author(s)
Fabrizio Maturo, Francesca Fortuna, Tonio Di Battista
Source
ENVIRONMENTAL MONITORING THROUGH FUNCTIONAL BIODIVERSITY TOOLS - T. Di Battista, F. Fortuna, F. Maturo - Ecological Indicators (2016) 60, 237-247 - online (2015). DOI: 10.1016/j.ecolind.2015.05.056.
PARAMETRIC FUNCTIONAL ANALYSIS OF VARIANCE FOR FISH BIODIVERSITY ASSESSMENT - T. Di Battista, F. Fortuna, F. Maturo - Journal of Environmental Informatics. Special issue of Marine and Freshwater Environmental Engineering and Management, Journal of Environmental Informatics. In press.
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 | #example 1
x=matrix(c(3,5,5,2,1,2,6,8,5,1),2,5)
x
alltools(x,20)
#Some examples expressed by relative abundance:
#example 2
x=matrix(c(0.3,0.5,0.1,0.05,0.05,0.25,0.25,0.25,0.25,0,0.35,0.3,0.35,0,0),3,5)
x
alltools(x,20)
#example 3
x=matrix(runif(1000),10,100)
#let's consider some missing species
x[1,1:20]=0
x[2,1:40]=0
x[3,1:60]=0
x[4,1:19]=0
x
alltools(x,20)
#example 4
x=matrix(runif(100),20,5)
x[1,1:2]=0
x[2,1:3]=0
x
alltools(x,20)
#example 5
a=c(0.35,0.35,0.27,0.01,0.02)
b=c(0.54,0.20,0.17,0.06,0.03)
c=c(0.35,0.35,0.30,0,0)
d=c(0.51,0.31,0.07,0.10,0.01)
e=c(0.40,0.20,0.10,0.30,0)
x=matrix(rbind(a,b,c,d,e),5,5)
x
alltools(x,20)
|
Example output
Attaching package: 'BioFTF'
The following object is masked from 'package:base':
beta
[,1] [,2] [,3] [,4] [,5]
[1,] 3 5 1 6 5
[2,] 5 2 2 8 1
[1] "Communities Ranking"
Richness Shannon Simpson Arc Area
community n.1 4 1.553442 0.7600000 3.978451 3.521920
community n.2 4 1.427358 0.6975309 4.064566 3.324774
[,1] [,2] [,3] [,4] [,5]
[1,] 0.3 0.05 0.25 0.00 0.35
[2,] 0.5 0.05 0.25 0.35 0.00
[3,] 0.1 0.25 0.25 0.30 0.00
[1] "Communities Ranking"
Richness Shannon Simpson Arc Area
community n.3 3 1.371977 0.7222222 3.146391 2.984744
community n.1 3 1.284566 0.6925208 3.201093 2.844643
community n.2 3 1.237469 0.6691871 3.234599 2.768349
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.0000000 0.000000000 0.0000000 0.00000000 0.00000000 0.00000000
[2,] 0.0000000 0.000000000 0.0000000 0.00000000 0.00000000 0.00000000
[3,] 0.0000000 0.000000000 0.0000000 0.00000000 0.00000000 0.00000000
[4,] 0.0000000 0.000000000 0.0000000 0.00000000 0.00000000 0.00000000
[5,] 0.4011274 0.444286812 0.6412625 0.05378237 0.64197642 0.72095449
[6,] 0.1580888 0.006899007 0.2160551 0.34464721 0.02690836 0.27821310
[7,] 0.2188947 0.038450459 0.2085245 0.12633427 0.69464326 0.07177104
[8,] 0.5220810 0.453902619 0.7641914 0.75175104 0.23480086 0.17313173
[9,] 0.4788486 0.649822330 0.3930794 0.36176148 0.11945985 0.70192098
[10,] 0.5972911 0.540697424 0.2494894 0.06298330 0.82205493 0.72382945
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.000000000 0.00000000 0.00000000 0.0000000 0.0000000 0.000000000
[2,] 0.000000000 0.00000000 0.00000000 0.0000000 0.0000000 0.000000000
[3,] 0.000000000 0.00000000 0.00000000 0.0000000 0.0000000 0.000000000
[4,] 0.000000000 0.00000000 0.00000000 0.0000000 0.0000000 0.000000000
[5,] 0.586380504 0.99917617 0.49280508 0.9850789 0.1141627 0.002322183
[6,] 0.002151049 0.67895947 0.71464262 0.4316209 0.4062646 0.868615214
[7,] 0.361030118 0.78997016 0.08346749 0.2262645 0.5379090 0.494607270
[8,] 0.425684557 0.09376064 0.78392815 0.2090034 0.8573384 0.631312967
[9,] 0.971591785 0.88903136 0.97993473 0.6079589 0.8929140 0.300360410
[10,] 0.305509672 0.98806363 0.28155138 0.2430984 0.6281422 0.592050995
[,13] [,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000
[2,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000
[3,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000
[4,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.00000000
[5,] 0.3984816 0.3728082 0.29724354 0.34052126 0.7255152 0.33444763 0.66746786
[6,] 0.2978539 0.9148603 0.49920821 0.79764428 0.8146300 0.36299587 0.04260419
[7,] 0.6959564 0.8542949 0.63867080 0.99915392 0.2816912 0.05153839 0.55762752
[8,] 0.3531682 0.8579008 0.58862621 0.60531117 0.1407264 0.47268905 0.07026824
[9,] 0.5239106 0.3570238 0.26449820 0.03952134 0.5768931 0.39172620 0.89774371
[10,] 0.5051049 0.6923080 0.04634502 0.18420632 0.3001498 0.48407132 0.54586136
[,20] [,21] [,22] [,23] [,24] [,25]
[1,] 0.000000000 0.24170424 0.82179936 0.16384550 0.4850207 0.8374714
[2,] 0.000000000 0.00000000 0.00000000 0.00000000 0.0000000 0.0000000
[3,] 0.000000000 0.00000000 0.00000000 0.00000000 0.0000000 0.0000000
[4,] 0.131511819 0.13868008 0.01327023 0.52664807 0.1874813 0.1011648
[5,] 0.259504844 0.66689868 0.10240508 0.27605438 0.4236928 0.4638461
[6,] 0.302167635 0.42901795 0.98912353 0.91592210 0.1866119 0.4890050
[7,] 0.005315822 0.03798883 0.44333146 0.04591396 0.7461944 0.3254439
[8,] 0.453582264 0.63074960 0.53650450 0.01273343 0.4686055 0.3831858
[9,] 0.506539000 0.52991628 0.86432275 0.72827604 0.6256645 0.6526949
[10,] 0.143451103 0.77761653 0.61704521 0.27742621 0.1749559 0.7659214
[,26] [,27] [,28] [,29] [,30] [,31] [,32]
[1,] 0.1126338 0.2158135 0.85645807 0.01533732 0.8596092 0.77664188 0.9061248
[2,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.0000000
[3,] 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000 0.00000000 0.0000000
[4,] 0.3744407 0.6897089 0.04871110 0.14483584 0.1801114 0.03394456 0.1689593
[5,] 0.6964784 0.4659248 0.33550378 0.56967378 0.4333417 0.38839200 0.5218118
[6,] 0.5418400 0.5732958 0.52448025 0.01985319 0.9894339 0.35443529 0.9383096
[7,] 0.8265350 0.1113880 0.02945411 0.11113144 0.4986352 0.41896681 0.3894486
[8,] 0.9626939 0.3492040 0.50365560 0.31574302 0.2872874 0.60144985 0.0868817
[9,] 0.6570333 0.6543677 0.21880138 0.28015611 0.8899665 0.87359517 0.8044213
[10,] 0.6711370 0.6184624 0.98754319 0.13736638 0.2495793 0.93224663 0.6280954
[,33] [,34] [,35] [,36] [,37] [,38] [,39]
[1,] 0.02822358 0.3113779 0.4544429 0.33814827 0.02020423 0.08828651 0.2590625
[2,] 0.00000000 0.0000000 0.0000000 0.00000000 0.00000000 0.00000000 0.0000000
[3,] 0.00000000 0.0000000 0.0000000 0.00000000 0.00000000 0.00000000 0.0000000
[4,] 0.35277328 0.9348589 0.8589601 0.22932359 0.92295062 0.56989580 0.3972038
[5,] 0.72466869 0.2952053 0.5105460 0.63900561 0.21321593 0.89415997 0.4898247
[6,] 0.60238220 0.1502750 0.5248639 0.44749333 0.50342911 0.73506130 0.2210673
[7,] 0.44961754 0.4829678 0.6684513 0.31738068 0.10665120 0.37417668 0.4670996
[8,] 0.56146378 0.6110110 0.2958976 0.81454258 0.79573656 0.44303223 0.7549487
[9,] 0.77344399 0.5022963 0.4313210 0.09044614 0.42097423 0.29790691 0.3993855
[10,] 0.58194396 0.3663718 0.4442853 0.83694414 0.70107378 0.28217514 0.3742053
[,40] [,41] [,42] [,43] [,44] [,45] [,46]
[1,] 0.7396079 0.2384019 0.13646033 0.51312737 0.44340211 0.27835068 0.4613610
[2,] 0.0000000 0.2391838 0.24801854 0.60206006 0.83633837 0.96945445 0.1137962
[3,] 0.0000000 0.0000000 0.00000000 0.00000000 0.00000000 0.00000000 0.0000000
[4,] 0.9815152 0.7483495 0.17959479 0.64931892 0.31048623 0.78870957 0.3648271
[5,] 0.7334532 0.5457406 0.13533933 0.56807887 0.34170455 0.93419418 0.3720169
[6,] 0.9004650 0.3864311 0.68868979 0.44386705 0.07724666 0.71633638 0.1933426
[7,] 0.4714387 0.4636079 0.54865857 0.70435477 0.39963080 0.21179856 0.6359276
[8,] 0.3465991 0.1798396 0.13138892 0.13213044 0.64796986 0.04706328 0.1960204
[9,] 0.9242367 0.5917151 0.02378541 0.63761321 0.09365602 0.84864308 0.8971944
[10,] 0.4434414 0.8458603 0.82103272 0.03656731 0.62425406 0.29598428 0.1242887
[,47] [,48] [,49] [,50] [,51] [,52]
[1,] 0.58648031 0.6983419 0.3763730 0.89079984 0.15550742 0.7945785
[2,] 0.31323374 0.4685806 0.3820746 0.07001316 0.29717758 0.7375523
[3,] 0.00000000 0.0000000 0.0000000 0.00000000 0.00000000 0.0000000
[4,] 0.57681526 0.2186073 0.7042773 0.61380501 0.63174156 0.6139515
[5,] 0.64194837 0.6362454 0.5407349 0.03492500 0.39447651 0.9008951
[6,] 0.15172982 0.1805488 0.4285790 0.36335512 0.82543362 0.7361469
[7,] 0.03810356 0.6062070 0.4373250 0.83137295 0.45799527 0.4365708
[8,] 0.41600845 0.6830345 0.6253351 0.07561277 0.04412295 0.1428324
[9,] 0.93421850 0.9084933 0.6144268 0.66041990 0.59721296 0.5010067
[10,] 0.50874909 0.7388225 0.1451301 0.47108633 0.59738623 0.0713963
[,53] [,54] [,55] [,56] [,57] [,58]
[1,] 0.030034070 0.3195775 0.352267543 0.2437145 0.74028777 0.58184249
[2,] 0.006287697 0.7187082 0.052355445 0.8404530 0.81093921 0.59069330
[3,] 0.000000000 0.0000000 0.000000000 0.0000000 0.00000000 0.00000000
[4,] 0.521870652 0.2318088 0.158194846 0.5795539 0.18570090 0.05769629
[5,] 0.513541458 0.2475222 0.399980148 0.5083738 0.81490362 0.12677343
[6,] 0.440514972 0.3564393 0.766065159 0.7302267 0.15470426 0.09692838
[7,] 0.200798688 0.6771694 0.555683492 0.8710032 0.04426182 0.17375717
[8,] 0.827251548 0.9063911 0.702521908 0.6022886 0.77343814 0.32497060
[9,] 0.119665985 0.1047887 0.008297865 0.8478838 0.74377799 0.34856481
[10,] 0.761707903 0.1189481 0.745417675 0.6892447 0.61018697 0.17676352
[,59] [,60] [,61] [,62] [,63] [,64]
[1,] 0.50630978 0.766600916 0.23127055 0.9572221 0.008512205 0.43385200
[2,] 0.70606886 0.565114213 0.35301819 0.9074817 0.317606268 0.07450328
[3,] 0.00000000 0.000000000 0.51714288 0.3845099 0.948621924 0.60365966
[4,] 0.13695148 0.145033563 0.09981155 0.6418801 0.727583071 0.41602213
[5,] 0.45110252 0.997225481 0.67716557 0.2567867 0.077020862 0.04390422
[6,] 0.05273374 0.691067220 0.21167530 0.2492073 0.317494274 0.33435709
[7,] 0.58820546 0.916417541 0.94219353 0.5657998 0.431868274 0.19497837
[8,] 0.33782895 0.003825191 0.67713622 0.4260021 0.105047232 0.99789663
[9,] 0.33079698 0.967024885 0.71592197 0.1778241 0.700811186 0.58715619
[10,] 0.06392221 0.757348123 0.12130644 0.3616753 0.329301818 0.55251066
[,65] [,66] [,67] [,68] [,69] [,70] [,71]
[1,] 0.39959684 0.9281167 0.08123837 0.2537033 0.39758437 0.60260351 0.9719670
[2,] 0.49308742 0.2487549 0.05138476 0.7763969 0.67477809 0.52355971 0.3825577
[3,] 0.65258710 0.6713577 0.65517223 0.9996588 0.99755977 0.07696736 0.7688453
[4,] 0.03071067 0.3677199 0.48289075 0.5324784 0.97986249 0.34584441 0.0752827
[5,] 0.08123094 0.5954433 0.47211892 0.5544786 0.90401887 0.06473625 0.6503186
[6,] 0.26128098 0.6624737 0.58320945 0.4022971 0.94696345 0.83260071 0.2236028
[7,] 0.86369121 0.8703999 0.61926783 0.3432352 0.47735608 0.37928572 0.8394698
[8,] 0.42883804 0.5597365 0.46303329 0.3644199 0.57753813 0.13583322 0.8904121
[9,] 0.93390562 0.7784873 0.67167189 0.5097221 0.09937025 0.80742259 0.1954620
[10,] 0.18906073 0.9975195 0.92571173 0.7845709 0.04001989 0.45418355 0.7648700
[,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.1058174 0.33813363 0.81784183 0.2755743 0.97377667 0.50879421
[2,] 0.5920409 0.79256430 0.04551546 0.5254094 0.50534576 0.49165645
[3,] 0.5820709 0.86001026 0.26290118 0.8611382 0.08069622 0.21742121
[4,] 0.5564073 0.02788545 0.48345659 0.7828772 0.26441755 0.61378708
[5,] 0.7107441 0.85575994 0.07697914 0.7763206 0.90763806 0.29404271
[6,] 0.8777000 0.61350456 0.67198794 0.8981556 0.80362107 0.79958875
[7,] 0.2819617 0.84004201 0.82590028 0.3038542 0.50210855 0.35355601
[8,] 0.8232772 0.71698270 0.47789367 0.5686160 0.22805622 0.55323668
[9,] 0.5805652 0.22681472 0.88342533 0.2448300 0.60963236 0.38508744
[10,] 0.7830102 0.87683979 0.09010592 0.9420445 0.15606574 0.01408223
[,78] [,79] [,80] [,81] [,82] [,83]
[1,] 0.56075555 0.09920138 0.073631856 0.7054768 0.90016647 0.3364281
[2,] 0.02291368 0.93615006 0.305429616 0.5431087 0.81110475 0.4946811
[3,] 0.82254593 0.75617814 0.594219660 0.9554137 0.39746805 0.7047236
[4,] 0.74843982 0.84389909 0.603717087 0.8635685 0.18428616 0.6628849
[5,] 0.99437972 0.64734523 0.731738105 0.8649782 0.08153723 0.3465239
[6,] 0.20285183 0.66633980 0.706540967 0.4393346 0.18025317 0.7325172
[7,] 0.37553955 0.81041787 0.001221441 0.7089089 0.84445713 0.2609762
[8,] 0.91361043 0.61000272 0.257671360 0.1437518 0.64432536 0.7332135
[9,] 0.70500736 0.43529327 0.655665676 0.2762848 0.57079880 0.8117243
[10,] 0.55281916 0.28821597 0.291008163 0.4762671 0.27969863 0.6093084
[,84] [,85] [,86] [,87] [,88] [,89]
[1,] 0.48270447 0.36622711 0.27871195 0.07411564 0.85137599 0.24918021
[2,] 0.10994287 0.22845209 0.87468894 0.12403113 0.40171006 0.04919956
[3,] 0.21737670 0.40409816 0.14681963 0.79909657 0.26966148 0.67129737
[4,] 0.64122510 0.11169747 0.07894842 0.92932158 0.28534025 0.09979915
[5,] 0.05392044 0.07211554 0.70467339 0.41867528 0.92227711 0.35231695
[6,] 0.63716696 0.84307149 0.93796935 0.02256935 0.03393054 0.82765228
[7,] 0.95599873 0.12022905 0.77063540 0.12879711 0.98867204 0.60636065
[8,] 0.88623370 0.78705756 0.80720935 0.19422882 0.26895735 0.78032133
[9,] 0.40086083 0.13028637 0.20288315 0.12921168 0.15656141 0.99600256
[10,] 0.52300397 0.69244896 0.91759458 0.22889323 0.72147457 0.80163269
[,90] [,91] [,92] [,93] [,94] [,95] [,96]
[1,] 0.1179521 0.30461632 0.3621254 0.5858575 0.04138162 0.9662174 0.57758559
[2,] 0.4029802 0.47679947 0.7796595 0.8727960 0.98158054 0.3497803 0.01605949
[3,] 0.8771168 0.76361104 0.2983134 0.9482123 0.87090843 0.7039441 0.06523895
[4,] 0.1372104 0.88845090 0.7655739 0.9799887 0.31142880 0.1197100 0.61393093
[5,] 0.3689028 0.20085005 0.2870878 0.3724052 0.70057103 0.4932027 0.53480494
[6,] 0.9639197 0.05585737 0.3387032 0.3333424 0.47793138 0.1723964 0.65344798
[7,] 0.6208215 0.91775776 0.5619711 0.3288627 0.46982875 0.5186106 0.53951776
[8,] 0.2371105 0.95994655 0.7968732 0.7674738 0.95947440 0.6977739 0.45401673
[9,] 0.4639680 0.64518665 0.9853205 0.6514436 0.03448595 0.3579197 0.83036471
[10,] 0.1636136 0.52189309 0.3356801 0.9471208 0.61408240 0.8876882 0.79766654
[,97] [,98] [,99] [,100]
[1,] 0.14513313 0.1094394 0.183533517 0.96801066
[2,] 0.10293576 0.8830619 0.059129311 0.34988832
[3,] 0.07832356 0.2507777 0.002526075 0.85661359
[4,] 0.58942382 0.6198791 0.961523045 0.01071654
[5,] 0.87234005 0.6060280 0.027521854 0.94858596
[6,] 0.33262180 0.7414468 0.302334704 0.57934958
[7,] 0.97975837 0.2859644 0.285902314 0.06038719
[8,] 0.18490230 0.2846517 0.543103829 0.59056203
[9,] 0.81482781 0.9903134 0.691136690 0.93358945
[10,] 0.19317895 0.1439867 0.668829781 0.20937286
[1] "Communities Ranking"
Richness Shannon Simpson Arc Area
community n.9 99 5.022618 0.9874119 98.23259 29.56242
community n.8 99 5.003496 0.9870682 98.23354 29.48049
community n.10 99 4.987112 0.9867821 98.23434 29.43776
community n.5 99 4.995679 0.9869733 98.23385 29.42678
community n.6 99 4.966632 0.9865682 98.23513 29.26433
community n.7 99 4.958938 0.9864543 98.23548 29.22711
community n.4 80 4.640925 0.9821281 79.25044 24.90735
community n.1 79 4.630031 0.9818376 78.25118 24.70645
community n.2 59 4.279539 0.9764398 58.27085 20.06306
community n.3 39 3.860553 0.9677110 38.30201 15.27880
[,1] [,2] [,3] [,4] [,5]
[1,] 0.000000000 0.00000000 0.73161595 0.62438279 0.6779418713
[2,] 0.000000000 0.00000000 0.00000000 0.31812174 0.7575915963
[3,] 0.713275049 0.36064807 0.45653981 0.42605403 0.1609782730
[4,] 0.704373126 0.39525808 0.09967635 0.57865424 0.1716597306
[5,] 0.921849380 0.17407597 0.51887056 0.77769694 0.8816115449
[6,] 0.790399990 0.85487914 0.78698284 0.79310564 0.8164990211
[7,] 0.002584195 0.52877029 0.30715265 0.94550969 0.0001606732
[8,] 0.210232373 0.88036897 0.21802798 0.99132558 0.4694073740
[9,] 0.203984601 0.01356285 0.43837957 0.33425014 0.4851714598
[10,] 0.604971938 0.21966779 0.08283790 0.84122727 0.5723661999
[11,] 0.405502280 0.43076080 0.68254624 0.49480125 0.8396368981
[12,] 0.978409593 0.41948138 0.08455748 0.91304543 0.2729048126
[13,] 0.588437438 0.30740713 0.28252257 0.68811762 0.4331816186
[14,] 0.997661179 0.40880822 0.02635892 0.78144762 0.1437381865
[15,] 0.180921219 0.28506022 0.81754868 0.70297438 0.8968860777
[16,] 0.050755903 0.27592838 0.32999052 0.05078456 0.2838735913
[17,] 0.735854028 0.84515400 0.02082818 0.07772496 0.3082542217
[18,] 0.549612237 0.76633848 0.50841482 0.90253356 0.4458824093
[19,] 0.215374438 0.22909761 0.23071763 0.16418753 0.3360536436
[20,] 0.126369594 0.90965279 0.90686934 0.18630873 0.0377915949
[1] "Communities Ranking"
Richness Shannon Simpson Arc Area
community n.6 4 1.6790634 0.7998015 3.907958 3.721844
community n.19 4 1.6515022 0.7886623 3.924312 3.678991
community n.18 4 1.6427022 0.7853074 3.929452 3.665332
community n.11 4 1.6376233 0.7831138 3.932577 3.657424
community n.13 4 1.6191223 0.7765460 3.943203 3.628519
community n.3 4 1.5841438 0.7647763 3.963295 3.572685
community n.5 4 1.5647476 0.7638579 3.971736 3.540116
community n.15 4 1.5316416 0.7497029 3.992682 3.489498
community n.8 4 1.4924726 0.7301142 4.019346 3.428674
community n.4 4 1.4804518 0.7299113 4.024902 3.407521
community n.10 4 1.4668598 0.7296690 4.031526 3.382331
community n.16 4 1.4448181 0.7244751 4.043867 3.348780
community n.12 4 1.4284813 0.7122995 4.057568 3.320898
community n.9 4 1.4360938 0.7330375 4.048482 3.307962
community n.14 4 1.3077966 0.6772674 4.136275 3.109140
community n.17 4 1.2454745 0.6565120 4.179192 3.005798
community n.20 4 1.2285139 0.6375551 4.193052 2.993614
community n.7 4 1.0441391 0.6016900 4.371507 2.518354
community n.1 2 1.1289004 0.6652769 2.447505 2.347388
community n.2 1 0.6212978 0.4165483 2.095950 1.280227
[,1] [,2] [,3] [,4] [,5]
[1,] 0.35 0.35 0.27 0.01 0.02
[2,] 0.54 0.20 0.17 0.06 0.03
[3,] 0.35 0.35 0.30 0.00 0.00
[4,] 0.51 0.31 0.07 0.10 0.01
[5,] 0.40 0.20 0.10 0.30 0.00
[1] "Communities Ranking"
Richness Shannon Simpson Arc Area
community n.2 4 1.287308 0.6350 4.161938 3.093113
community n.1 4 1.260532 0.6816 4.164246 3.018096
community n.4 4 1.220762 0.6288 4.202864 2.969033
community n.5 3 1.329085 0.7000 3.175405 2.917174
community n.3 2 1.128438 0.6650 2.447772 2.346659
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