Description Usage Arguments Details Value Author(s) References Examples
Discriminating species between two groups using Bray-Curtis dissimilarities
1 2 3 4 5 |
comm |
Community data matrix. |
group |
Factor describing the group structure. Must have at least 2 levels. |
permutations |
a list of control values for the permutations
as returned by the function |
trace |
Trace permutations. |
object |
an object returned by |
ordered |
Logical; Should the species be ordered by their average contribution? |
digits |
Number of digits in output. |
parallel |
Number of parallel processes or a predefined socket
cluster. With |
... |
Parameters passed to other functions. In |
Similarity percentage, simper
(Clarke 1993) is based
on the decomposition of Bray-Curtis dissimilarity index (see
vegdist
, designdist
). The contribution
of individual species i to the overall Bray-Curtis dissimilarity
d[jk] is given by
d[ijk] = abs(x[ij]-x[ik])/sum(x[ij]+x[ik])
where x is the abundance of species i in sampling units j and k. The overall index is the sum of the individual contributions over all S species d[jk] = sum(i=1..S) d[ijk].
The simper
functions performs pairwise comparisons of groups
of sampling units and finds the average contributions
of each species to the average overall Bray-Curtis dissimilarity.
The function displays most important species for each pair of
groups
. These species contribute at least to 70 % of the
differences between groups. The function returns much more
extensive results which can be accessed directly from the result
object (see section Value). Function summary
transforms the
result to a list of data frames. With argument ordered = TRUE
the data frames also include the cumulative contributions and
are ordered by species contribution.
The results of simper
can be very difficult to interpret. The
method very badly confounds the mean between group differences and
within group variation, and seems to single out variable species
instead of distinctive species (Warton et al. 2012). Even if you make
groups that are copies of each other, the method will single out
species with high contribution, but these are not contributions
to non-existing between-group differences but to within-group
variation in species abundance.
A list of class "simper"
with following items:
species |
The species names. |
average |
Average contribution to overall dissimilarity. |
overall |
The overall between-group dissimilarity. |
sd |
Standard deviation of contribution. |
ratio |
Average to sd ratio. |
ava, avb |
Average abundances per group. |
ord |
An index vector to order vectors by their contribution or
order |
cusum |
Ordered cumulative contribution. |
p |
Permutation p-value. Probability of getting a larger or equal average contribution in random permutation of the group factor. |
Eduard Szöcs eduardszoecs@gmail.com
Clarke, K.R. 1993. Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology, 18, 117–143.
Warton, D.I., Wright, T.W., Wang, Y. 2012. Distance-based multivariate analyses confound location and dispersion effects. Methods in Ecology and Evolution, 3, 89–101.
1 2 3 4 |
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3
cumulative contributions of most influential species:
$SF_BF
Agrostol Alopgeni Lolipere Trifrepe Poatriv Scorautu Bromhord
0.09824271 0.18254830 0.25956958 0.33367870 0.40734444 0.47729205 0.53120026
Achimill Planlanc Elymrepe Bracruta
0.57946526 0.62522255 0.67016196 0.71098133
$SF_HF
Agrostol Alopgeni Lolipere Planlanc Rumeacet Elymrepe Poatriv
0.08350879 0.16534834 0.23934930 0.30843624 0.37716139 0.43334492 0.48351753
Bracruta Eleopalu Poaprat Anthodor Sagiproc Trifprat
0.52804045 0.57205850 0.61423981 0.65549838 0.69628951 0.73696831
$SF_NM
Poatriv Alopgeni Agrostol Lolipere Eleopalu Poaprat Bracruta Elymrepe
0.1013601 0.1935731 0.2667383 0.3377578 0.3999419 0.4526707 0.5044725 0.5505643
Scorautu Trifrepe Sagiproc Salirepe
0.5926117 0.6320111 0.6712478 0.7091528
$BF_HF
Rumeacet Poatriv Planlanc Bromhord Lolipere Elymrepe Trifrepe
0.08163219 0.15193797 0.21918333 0.27967181 0.33969561 0.39843338 0.45298204
Anthodor Achimill Bracruta Alopgeni Trifprat Juncarti
0.50276849 0.55222648 0.60021994 0.64584333 0.69126471 0.73366621
$BF_NM
Lolipere Poatriv Poaprat Trifrepe Bromhord Bracruta Eleopalu Agrostol
0.1242718 0.1992126 0.2711756 0.3414609 0.3958520 0.4448077 0.4910724 0.5369083
Achimill Scorautu Anthodor Planlanc
0.5823926 0.6253645 0.6638182 0.7012577
$HF_NM
Poatriv Lolipere Rumeacet Poaprat Planlanc Bracruta Eleopalu
0.09913221 0.17468460 0.23917190 0.29701331 0.35469313 0.40365488 0.44804851
Agrostol Trifrepe Elymrepe Anthodor Juncarti Trifprat Salirepe
0.49226546 0.53434466 0.57564661 0.61543243 0.65341300 0.68921695 0.72432408
Contrast: SF_BF
average sd ratio ava avb cumsum
Agrostol 0.061374 0.034193 1.7949 4.6667 0.0000 0.09824
Alopgeni 0.052667 0.036476 1.4439 4.3333 0.6667 0.18255
Lolipere 0.048116 0.039445 1.2198 3.0000 6.0000 0.25957
Trifrepe 0.046297 0.025525 1.8138 1.3333 4.6667 0.33368
Poatriv 0.046020 0.033801 1.3615 4.6667 3.6667 0.40734
Scorautu 0.043697 0.024922 1.7534 1.3333 4.3333 0.47729
Bromhord 0.033677 0.025860 1.3023 0.5000 2.6667 0.53120
Achimill 0.030152 0.020821 1.4482 0.1667 2.3333 0.57947
Planlanc 0.028585 0.021549 1.3265 0.0000 2.0000 0.62522
Elymrepe 0.028074 0.029778 0.9428 2.0000 1.3333 0.67016
Bracruta 0.025501 0.023902 1.0669 2.0000 2.0000 0.71098
Poaprat 0.025129 0.023967 1.0485 2.5000 4.0000 0.75121
Sagiproc 0.024326 0.022149 1.0983 1.8333 0.6667 0.79014
Bellpere 0.019859 0.017088 1.1622 0.6667 1.6667 0.82193
Eleopalu 0.018611 0.042958 0.4333 1.3333 0.0000 0.85172
Anthodor 0.017543 0.025804 0.6798 0.0000 1.3333 0.87981
Juncbufo 0.016031 0.023708 0.6762 1.1667 0.0000 0.90547
Vicilath 0.014671 0.013306 1.1026 0.0000 1.0000 0.92895
Hyporadi 0.010286 0.015198 0.6768 0.0000 0.6667 0.94542
Ranuflam 0.009306 0.013595 0.6845 0.6667 0.0000 0.96031
Juncarti 0.006979 0.016109 0.4333 0.5000 0.0000 0.97148
Callcusp 0.006979 0.016109 0.4333 0.5000 0.0000 0.98266
Rumeacet 0.004526 0.010444 0.4333 0.3333 0.0000 0.98990
Cirsarve 0.003983 0.009185 0.4336 0.3333 0.0000 0.99628
Chenalbu 0.002326 0.005370 0.4333 0.1667 0.0000 1.00000
Airaprae 0.000000 0.000000 NaN 0.0000 0.0000 1.00000
Comapalu 0.000000 0.000000 NaN 0.0000 0.0000 1.00000
Empenigr 0.000000 0.000000 NaN 0.0000 0.0000 1.00000
Salirepe 0.000000 0.000000 NaN 0.0000 0.0000 1.00000
Trifprat 0.000000 0.000000 NaN 0.0000 0.0000 1.00000
Contrast: SF_HF
average sd ratio ava avb cumsum
Agrostol 0.047380 0.031273 1.5151 4.6667 1.4 0.08351
Alopgeni 0.046433 0.032897 1.4115 4.3333 1.6 0.16535
Lolipere 0.041986 0.027007 1.5546 3.0000 4.0 0.23935
Planlanc 0.039198 0.033208 1.1804 0.0000 3.0 0.30844
Rumeacet 0.038992 0.027369 1.4247 0.3333 3.2 0.37716
Elymrepe 0.031877 0.029550 1.0787 2.0000 2.0 0.43334
Poatriv 0.028466 0.021522 1.3227 4.6667 4.8 0.48352
Bracruta 0.025261 0.021044 1.2004 2.0000 2.8 0.52804
Eleopalu 0.024974 0.038877 0.6424 1.3333 0.8 0.57206
Poaprat 0.023932 0.019180 1.2478 2.5000 3.4 0.61424
Anthodor 0.023409 0.021430 1.0923 0.0000 1.8 0.65550
Sagiproc 0.023144 0.020479 1.1301 1.8333 0.8 0.69629
Trifprat 0.023080 0.023432 0.9850 0.0000 1.8 0.73697
Juncarti 0.022850 0.025677 0.8899 0.5000 1.6 0.77724
Trifrepe 0.022383 0.019487 1.1486 1.3333 2.8 0.81669
Juncbufo 0.021643 0.022237 0.9733 1.1667 1.2 0.85484
Scorautu 0.020509 0.016422 1.2489 1.3333 2.8 0.89099
Achimill 0.015183 0.011393 1.3326 0.1667 1.2 0.91775
Bromhord 0.013375 0.014504 0.9222 0.5000 0.8 0.94132
Ranuflam 0.010661 0.013387 0.7964 0.6667 0.4 0.96011
Bellpere 0.009991 0.012571 0.7948 0.6667 0.4 0.97772
Callcusp 0.006623 0.015076 0.4393 0.5000 0.0 0.98939
Cirsarve 0.003809 0.008669 0.4394 0.3333 0.0 0.99611
Chenalbu 0.002208 0.005025 0.4393 0.1667 0.0 1.00000
Airaprae 0.000000 0.000000 NaN 0.0000 0.0 1.00000
Comapalu 0.000000 0.000000 NaN 0.0000 0.0 1.00000
Empenigr 0.000000 0.000000 NaN 0.0000 0.0 1.00000
Hyporadi 0.000000 0.000000 NaN 0.0000 0.0 1.00000
Salirepe 0.000000 0.000000 NaN 0.0000 0.0 1.00000
Vicilath 0.000000 0.000000 NaN 0.0000 0.0 1.00000
Contrast: SF_NM
average sd ratio ava avb cumsum
Poatriv 0.078284 0.040947 1.9118 4.6667 0.0000 0.1014
Alopgeni 0.071219 0.046958 1.5167 4.3333 0.0000 0.1936
Agrostol 0.056508 0.044176 1.2792 4.6667 2.1667 0.2667
Lolipere 0.054851 0.059914 0.9155 3.0000 0.3333 0.3378
Eleopalu 0.048027 0.047168 1.0182 1.3333 2.1667 0.3999
Poaprat 0.040724 0.031790 1.2810 2.5000 0.6667 0.4527
Bracruta 0.040008 0.034398 1.1631 2.0000 2.8333 0.5045
Elymrepe 0.035598 0.038515 0.9243 2.0000 0.0000 0.5506
Scorautu 0.032475 0.034813 0.9328 1.3333 3.1667 0.5926
Trifrepe 0.030430 0.031634 0.9619 1.3333 1.8333 0.6320
Sagiproc 0.030304 0.030477 0.9943 1.8333 0.5000 0.6712
Salirepe 0.029275 0.032014 0.9144 0.0000 1.8333 0.7092
Anthodor 0.024541 0.036694 0.6688 0.0000 1.3333 0.7409
Callcusp 0.022763 0.029443 0.7731 0.5000 1.1667 0.7704
Ranuflam 0.022566 0.022819 0.9889 0.6667 1.3333 0.7996
Juncarti 0.022543 0.028598 0.7883 0.5000 1.1667 0.8288
Hyporadi 0.020108 0.031291 0.6426 0.0000 1.1667 0.8548
Juncbufo 0.019860 0.029034 0.6840 1.1667 0.0000 0.8806
Planlanc 0.015420 0.022769 0.6772 0.0000 0.8333 0.9005
Airaprae 0.014883 0.021881 0.6802 0.0000 0.8333 0.9198
Bellpere 0.012317 0.015921 0.7737 0.6667 0.3333 0.9357
Comapalu 0.011883 0.017407 0.6826 0.0000 0.6667 0.9511
Achimill 0.009294 0.014931 0.6224 0.1667 0.3333 0.9632
Bromhord 0.007172 0.016333 0.4391 0.5000 0.0000 0.9724
Rumeacet 0.005590 0.012751 0.4384 0.3333 0.0000 0.9797
Empenigr 0.005225 0.012001 0.4354 0.0000 0.3333 0.9864
Cirsarve 0.004782 0.010889 0.4391 0.3333 0.0000 0.9926
Chenalbu 0.002893 0.006602 0.4382 0.1667 0.0000 0.9964
Vicilath 0.002792 0.006425 0.4345 0.0000 0.1667 1.0000
Trifprat 0.000000 0.000000 NaN 0.0000 0.0000 1.0000
Contrast: BF_HF
average sd ratio ava avb cumsum
Rumeacet 0.038666 0.02606 1.4838 0.0000 3.2 0.08163
Poatriv 0.033301 0.02579 1.2911 3.6667 4.8 0.15194
Planlanc 0.031852 0.01830 1.7401 2.0000 3.0 0.21918
Bromhord 0.028651 0.01799 1.5926 2.6667 0.8 0.27967
Lolipere 0.028431 0.02215 1.2834 6.0000 4.0 0.33970
Elymrepe 0.027822 0.02959 0.9404 1.3333 2.0 0.39843
Trifrepe 0.025838 0.01656 1.5603 4.6667 2.8 0.45298
Anthodor 0.023582 0.02042 1.1547 1.3333 1.8 0.50277
Achimill 0.023426 0.01474 1.5893 2.3333 1.2 0.55223
Bracruta 0.022733 0.01802 1.2617 2.0000 2.8 0.60022
Alopgeni 0.021610 0.02308 0.9363 0.6667 1.6 0.64584
Trifprat 0.021514 0.02207 0.9747 0.0000 1.8 0.69126
Juncarti 0.020084 0.02555 0.7860 0.0000 1.6 0.73367
Scorautu 0.019318 0.01356 1.4241 4.3333 2.8 0.77445
Bellpere 0.018290 0.01486 1.2305 1.6667 0.4 0.81306
Agrostol 0.017605 0.02284 0.7708 0.0000 1.4 0.85023
Juncbufo 0.015000 0.02066 0.7260 0.0000 1.2 0.88190
Vicilath 0.012848 0.01140 1.1274 1.0000 0.0 0.90903
Sagiproc 0.011685 0.01297 0.9008 0.6667 0.8 0.93369
Eleopalu 0.010169 0.02111 0.4817 0.0000 0.8 0.95516
Hyporadi 0.008950 0.01312 0.6824 0.6667 0.0 0.97406
Poaprat 0.007203 0.01010 0.7133 4.0000 3.4 0.98927
Ranuflam 0.005084 0.01055 0.4817 0.0000 0.4 1.00000
Airaprae 0.000000 0.00000 NaN 0.0000 0.0 1.00000
Chenalbu 0.000000 0.00000 NaN 0.0000 0.0 1.00000
Cirsarve 0.000000 0.00000 NaN 0.0000 0.0 1.00000
Comapalu 0.000000 0.00000 NaN 0.0000 0.0 1.00000
Empenigr 0.000000 0.00000 NaN 0.0000 0.0 1.00000
Salirepe 0.000000 0.00000 NaN 0.0000 0.0 1.00000
Callcusp 0.000000 0.00000 NaN 0.0000 0.0 1.00000
Contrast: BF_NM
average sd ratio ava avb cumsum
Lolipere 0.090681 0.02644 3.4292 6.0000 0.3333 0.1243
Poatriv 0.054684 0.04465 1.2248 3.6667 0.0000 0.1992
Poaprat 0.052511 0.01813 2.8966 4.0000 0.6667 0.2712
Trifrepe 0.051287 0.02756 1.8611 4.6667 1.8333 0.3415
Bromhord 0.039689 0.02920 1.3590 2.6667 0.0000 0.3959
Bracruta 0.035723 0.02869 1.2452 2.0000 2.8333 0.4448
Eleopalu 0.033759 0.03573 0.9449 0.0000 2.1667 0.4911
Agrostol 0.033446 0.03473 0.9630 0.0000 2.1667 0.5369
Achimill 0.033190 0.02338 1.4198 2.3333 0.3333 0.5824
Scorautu 0.031356 0.02026 1.5480 4.3333 3.1667 0.6254
Anthodor 0.028060 0.03295 0.8517 1.3333 1.3333 0.6638
Planlanc 0.027319 0.02193 1.2458 2.0000 0.8333 0.7013
Salirepe 0.026770 0.02927 0.9145 0.0000 1.8333 0.7379
Bellpere 0.023529 0.01909 1.2322 1.6667 0.3333 0.7702
Hyporadi 0.021721 0.02450 0.8864 0.6667 1.1667 0.8000
Ranuflam 0.020314 0.02275 0.8928 0.0000 1.3333 0.8278
Elymrepe 0.019993 0.02926 0.6833 1.3333 0.0000 0.8552
Callcusp 0.017833 0.02681 0.6653 0.0000 1.1667 0.8796
Juncarti 0.017694 0.02600 0.6806 0.0000 1.1667 0.9039
Vicilath 0.015773 0.01447 1.0902 1.0000 0.1667 0.9255
Sagiproc 0.015432 0.01857 0.8310 0.6667 0.5000 0.9466
Airaprae 0.013410 0.01969 0.6809 0.0000 0.8333 0.9650
Comapalu 0.010739 0.01571 0.6835 0.0000 0.6667 0.9797
Alopgeni 0.009997 0.01463 0.6833 0.6667 0.0000 0.9934
Empenigr 0.004787 0.01105 0.4332 0.0000 0.3333 1.0000
Chenalbu 0.000000 0.00000 NaN 0.0000 0.0000 1.0000
Cirsarve 0.000000 0.00000 NaN 0.0000 0.0000 1.0000
Juncbufo 0.000000 0.00000 NaN 0.0000 0.0000 1.0000
Rumeacet 0.000000 0.00000 NaN 0.0000 0.0000 1.0000
Trifprat 0.000000 0.00000 NaN 0.0000 0.0000 1.0000
Contrast: HF_NM
average sd ratio ava avb cumsum
Poatriv 0.071553 0.013681 5.2302 4.8 0.0000 0.09913
Lolipere 0.054533 0.029625 1.8408 4.0 0.3333 0.17468
Rumeacet 0.046546 0.030806 1.5109 3.2 0.0000 0.23917
Poaprat 0.041750 0.018852 2.2146 3.4 0.6667 0.29701
Planlanc 0.041633 0.029560 1.4084 3.0 0.8333 0.35469
Bracruta 0.035340 0.020104 1.7579 2.8 2.8333 0.40365
Eleopalu 0.032043 0.032315 0.9916 0.8 2.1667 0.44805
Agrostol 0.031915 0.028887 1.1048 1.4 2.1667 0.49227
Trifrepe 0.030372 0.022871 1.3280 2.8 1.8333 0.53434
Elymrepe 0.029811 0.038676 0.7708 2.0 0.0000 0.57565
Anthodor 0.028717 0.024799 1.1580 1.8 1.3333 0.61543
Juncarti 0.027414 0.028537 0.9607 1.6 1.1667 0.65341
Trifprat 0.025843 0.025972 0.9951 1.8 0.0000 0.68922
Salirepe 0.025340 0.027291 0.9285 0.0 1.8333 0.72432
Alopgeni 0.024459 0.032399 0.7549 1.6 0.0000 0.75821
Scorautu 0.020703 0.014125 1.4658 2.8 3.1667 0.78689
Ranuflam 0.019285 0.019939 0.9672 0.4 1.3333 0.81361
Juncbufo 0.018181 0.024648 0.7376 1.2 0.0000 0.83880
Hyporadi 0.017141 0.026548 0.6457 0.0 1.1667 0.86255
Callcusp 0.016833 0.024901 0.6760 0.0 1.1667 0.88587
Achimill 0.016555 0.014900 1.1111 1.2 0.3333 0.90881
Sagiproc 0.015282 0.016535 0.9243 0.8 0.5000 0.92998
Airaprae 0.012605 0.018243 0.6910 0.0 0.8333 0.94744
Bromhord 0.012094 0.015169 0.7973 0.8 0.0000 0.96420
Comapalu 0.010105 0.014556 0.6942 0.0 0.6667 0.97820
Bellpere 0.008801 0.013732 0.6409 0.4 0.3333 0.99039
Empenigr 0.004536 0.010325 0.4393 0.0 0.3333 0.99668
Vicilath 0.002399 0.005461 0.4393 0.0 0.1667 1.00000
Chenalbu 0.000000 0.000000 NaN 0.0 0.0000 1.00000
Cirsarve 0.000000 0.000000 NaN 0.0 0.0000 1.00000
Permutation: free
Number of permutations: 0
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