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To undertake this test, you must first have defined the group membership of the individual samples (see Allocating samples to groups).
This analysis breaks down the contribution of each species (or other variable) to the observed similarity (or dissimilarity) between samples. It will allow you to identify the species that are most important in creating the observed pattern of similarity. The method uses the Bray-Curtis measure of similarity, comparing in turn, each sample in Group 1 with each sample in Group 2. The Bray-Curtis method operates at the species level, and therefore the mean similarity between Groups 1 & 2 can be obtained for each species.
In the following example, using the Romano British pottery.csv data file, the data have been divided into 3 location groups.
cumulative contributions of most influential species:
$Llanederyn_Caldicot
Al Fe Mg
0.3475663 0.6402357 0.9222869 - These values are the cumulative proportion of the dissimilarity from each element between the 2 groups
$`Llanederyn_Ashley Rails`
Al Fe Mg
0.3600725 0.6869017 0.9749251
$`Caldicot_Ashley Rails`
Al Fe
0.4515666 0.7374816
Contrast: Llanederyn_Caldicot
average sd ratio ava avb cumsum
Al 0.029000 0.018356 1.580 12.5643 11.700 0.3476 - Average abundance Al in Llanederyn = 12.56, in Caldicot = 11.7
Fe 0.024419 0.010210 2.392 6.3721 5.415 0.6402 - The contribution of Al and Fe to dissimilarity = 0.6402 = 64%
Mg 0.023533 0.019578 1.202 4.8264 3.855 0.9223
Na 0.004391 0.002558 1.716 0.2507 0.050 0.9749
Ca 0.002093 0.001169 1.790 0.2021 0.295 1.0000
Contrast: Llanederyn_Ashley Rails
average sd ratio ava avb cumsum
Al 0.117845 0.049056 2.402 12.5643 17.750 0.3601
Fe 0.106965 0.018641 5.738 6.3721 1.612 0.6869
Mg 0.094265 0.021610 4.362 4.8264 0.640 0.9749
Na 0.004501 0.002631 1.711 0.2507 0.051 0.9887
Ca 0.003706 0.001470 2.521 0.2021 0.039 1.0000
Contrast: Caldicot_Ashley Rails
average sd ratio ava avb cumsum
Al 0.1450682 0.0347999 4.169 11.700 17.750 0.4516
Fe 0.0918517 0.0137446 6.683 5.415 1.612 0.7375
Mg 0.0777523 0.0040412 19.240 3.855 0.640 0.9795
Ca 0.0062040 0.0008860 7.002 0.295 0.039 0.9988
Na 0.0003792 0.0003395 1.117 0.050 0.051 1.0000
Permutation: free
Number of permutations: 0
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