simper: Similarity Percentages

Description Usage Arguments Details Value Author(s) References Examples

Description

Discriminating species between two groups using Bray-Curtis dissimilarities

Usage

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simper(comm, group, permutations = 0, trace = FALSE, 
    parallel = getOption("mc.cores"), ...)
## S3 method for class 'simper'
summary(object, ordered = TRUE,
    digits = max(3,getOption("digits") - 3), ...)

Arguments

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 how, or the number of permutations required, or a permutation matrix where each row gives the permuted indices.

trace

Trace permutations.

object

an object returned by simper.

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 parallel = 1 uses ordinary, non-parallel processing.

...

Parameters passed to other functions. In simper the extra parameters are passed to shuffleSet if permutations are used.

Details

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.

Value

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 back to the original data 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.

Author(s)

Eduard Szöcs eduardszoecs@gmail.com

References

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.

Examples

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data(dune)
data(dune.env)
(sim <- with(dune.env, simper(dune, Management)))
summary(sim)

Example output

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

vegan documentation built on Aug. 24, 2017, 5:21 p.m.