Calculate topological indices for ecological networks. The mean trophic level and Omnivory and the Level of omnivory are calculated with the function NetIndices::TrophInd()
Source: R/calcTopologicalIndices.r
calc_topological_indices.RdCalculate topological indices for ecological networks. The mean trophic level
and Omnivory and the Level of omnivory are calculated with the function NetIndices::TrophInd()
Value
a data.frame with the following fields:
Network: Name of the network if the list have names
Size: Number of species
Top: Number of top predator species
Basal: Number of basal especies
Omnivory: Proportion of omnivorous species
Links: number of interactions
LD: linkage density
Connectance: directed Connectance
PathLength: average path length
Clustering: clustering coeficient
Cannib: number of cannibalistic species
TLmean: mean trophic level
TLmax: maximum trophic level
LOmnivory: Level of omnivory, quantifies mean of the variety in trophic levels of the preys of a consumer
Components: number of weakly connected components
Vulnerability: mean of number of consumers per prey
VulSD: the standard deviation of normalized Vulnerability
Generality: mean number of prey per consumer
GenSD: the standard deviation of normalized Generality
Examples
calc_topological_indices(netData)
#> Network Size Top Basal Omnivory Links LD Connectance
#> 1 Angola 28 4 2 0.7500000 127 4.535714 0.161989796
#> 2 Baltic Sea 33 4 4 0.4848485 191 5.787879 0.175390266
#> 3 Barents Sea Arctic 159 43 7 0.5911950 848 5.333333 0.033542977
#> 4 Barents Sea Boreal 180 22 6 0.6722222 1546 8.588889 0.047716049
#> 5 Beach Peru 46 20 5 0.3043478 88 1.913043 0.041587902
#> 6 Beagle Channel 145 11 36 0.5517241 1115 7.689655 0.053032105
#> 7 Benguela 29 0 2 0.8620690 212 7.310345 0.252080856
#> 8 Caribbean Reef 250 5 1 0.9760000 3382 13.528000 0.054112000
#> 9 Cayman Is 242 10 11 0.7727273 3766 15.561983 0.064305717
#> 10 Celtic Sea 48 19 17 0.4583333 169 3.520833 0.073350694
#> 11 Chilean rocky 106 8 48 0.3679245 1362 12.849057 0.121217515
#> 12 Cuba 240 10 11 0.8291667 3874 16.141667 0.067256944
#> 13 Florida 48 9 6 0.7083333 221 4.604167 0.095920139
#> 14 Gulf Alaska 405 14 373 0.0345679 1057 2.609877 0.006444140
#> 15 Gulf Cadiz 42 6 2 0.8333333 410 9.761905 0.232426304
#> 16 Gulf Lions 39 9 6 0.8461538 189 4.846154 0.124260355
#> 17 Gulf Tortugas 256 23 204 0.0546875 647 2.527344 0.009872437
#> 18 Jamaica 249 11 9 0.8273092 4105 16.485944 0.066208610
#> 19 Kerguelen Plateau 28 4 4 0.8214286 173 6.178571 0.220663265
#> 20 La Guajira 27 3 4 0.8518519 198 7.333333 0.271604938
#> 21 Monterey Bay 37 12 5 0.3513514 79 2.135135 0.057706355
#> 22 NE US Shelf 81 4 2 0.9506173 1490 18.395062 0.227099528
#> 23 Potter Cove 110 6 30 0.4636364 649 5.900000 0.053636364
#> 24 Sanak intertidal 235 19 41 0.6042553 1804 7.676596 0.032666365
#> 25 Sanak nearshore 513 41 56 0.7270955 6774 13.204678 0.025740114
#> 26 Simon Bay 26 5 10 0.1923077 70 2.692308 0.103550296
#> 27 Southern Brazil 143 9 66 0.4895105 840 5.874126 0.041077803
#> 28 SW Pacific Ocean 108 78 27 0.1574074 202 1.870370 0.017318244
#> 29 Weddell Sea 435 252 14 0.4689655 1978 4.547126 0.010453164
#> PathLength Clustering Cannib TLmean TLmax LOmnivory Components
#> 1 1.608333 0.35763293 3 2.897171 4.039211 0.210661151 1
#> 2 1.413115 0.30550459 7 2.393618 3.678314 0.127265400 1
#> 3 2.056762 0.16540420 10 2.843582 5.190582 0.159415794 1
#> 4 2.280036 0.24859772 23 3.002873 4.796090 0.227145018 1
#> 5 1.733032 0.09312639 0 2.633627 4.162698 0.073120694 1
#> 6 2.121089 0.22267298 0 2.376811 4.120973 0.220455060 1
#> 7 1.503012 0.57603518 7 3.426052 4.666712 0.300625568 1
#> 8 1.893206 0.15505307 10 3.944124 5.874534 0.469036276 1
#> 9 1.854293 0.11295708 2 3.195069 4.954891 0.419532533 1
#> 10 1.419118 0.28825623 6 1.814819 2.944444 0.123462555 1
#> 11 1.339971 0.11196400 2 1.714422 3.233646 0.043858545 1
#> 12 1.860959 0.11358725 2 3.312343 5.010049 0.416505669 1
#> 13 1.765112 0.31518010 3 2.738179 4.650676 0.261322309 1
#> 14 2.310446 0.04313612 4 1.087722 3.025025 0.003162364 1
#> 15 1.992410 0.55996358 14 3.320370 4.672548 0.369765638 1
#> 16 1.771552 0.34351145 9 2.785397 4.316024 0.242857024 1
#> 17 1.650193 0.02872340 0 1.218783 2.828880 0.009791776 1
#> 18 1.840726 0.11603916 2 3.279659 4.959277 0.390369432 1
#> 19 1.561905 0.58473421 5 3.115334 4.796731 0.340087506 1
#> 20 1.532578 0.66183206 10 2.820707 4.237618 0.471580050 1
#> 21 1.396694 0.08674699 0 2.248430 3.388889 0.069381710 1
#> 22 2.006478 0.57322245 25 4.740175 6.500256 0.695680643 1
#> 23 2.336854 0.18495684 0 2.221820 4.419660 0.226861551 1
#> 24 3.064434 0.15531988 47 2.555023 4.304591 0.211130071 1
#> 25 3.412703 0.17897753 94 3.096074 5.270032 0.296344995 1
#> 26 1.707006 0.14457831 0 1.975078 4.214286 0.038418487 1
#> 27 3.370396 0.17738952 12 1.917638 3.661938 0.229439952 1
#> 28 1.198413 0.01675042 0 1.892855 3.000000 0.030252434 1
#> 29 2.173006 0.05561247 7 2.790835 5.146343 0.191524063 1
#> Vulnerability VulSD Generality GenSD
#> 1 5.291667 0.9515706 4.884615 0.5954786
#> 2 6.586207 0.7377881 6.586207 0.9311804
#> 3 7.310345 1.6540281 5.578947 1.0462268
#> 4 9.784810 1.2292073 8.885057 1.3645655
#> 5 3.384615 1.3800444 2.146341 0.8452183
#> 6 8.320896 1.2057445 10.229358 1.2296630
#> 7 7.310345 0.7652203 7.851852 0.9059806
#> 8 13.804082 1.9035733 13.582329 1.2104641
#> 9 16.232759 1.0535105 16.303030 1.2135240
#> 10 5.827586 1.3411641 5.451613 1.3257180
#> 11 13.897959 0.7838649 23.482759 1.3479895
#> 12 16.843478 1.0330555 16.917031 1.1701145
#> 13 5.666667 0.9491005 5.261905 0.7453336
#> 14 2.703325 1.2310513 33.031250 6.0630973
#> 15 11.388889 0.8138112 10.250000 0.7203884
#> 16 6.300000 0.9650096 5.727273 0.5998126
#> 17 2.776824 1.1689865 12.442308 2.6285446
#> 18 17.247899 1.0461240 17.104167 1.1989725
#> 19 7.208333 0.8530838 7.208333 0.6666741
#> 20 8.250000 0.7815213 8.608696 0.6807684
#> 21 3.160000 1.2738808 2.468750 1.1846588
#> 22 19.350649 0.9186556 18.860759 0.7305467
#> 23 6.240385 1.1878726 8.112500 1.5936057
#> 24 8.351852 1.2690317 9.298969 1.2754158
#> 25 14.351695 1.4059570 14.822757 1.2438225
#> 26 3.333333 0.7984884 4.375000 1.0387748
#> 27 6.268657 1.0900308 10.909091 1.2942680
#> 28 6.733333 2.4211246 2.493827 1.5644876
#> 29 10.808743 3.1827981 4.698337 1.0908340
# Generate a test network
g <- graph_from_literal( 1 -+ 4 -+ 7,2 -+ 5 -+7, 3-+6-+7, 7-+7, 4+-3, simplify = FALSE)
calc_topological_indices(g)
#> Size Top Basal Omnivory Links LD Connectance PathLength Clustering
#> 1 7 1 3 0.1428571 8 1.142857 0.1632653 1.3 0
#> Cannib TLmean TLmax LOmnivory Components Vulnerability VulSD Generality
#> 1 1 1.642857 2.5 0.0625 1 1.333333 0.3307189 2
#> GenSD
#> 1 1.280869