anosim: Analysis of Similarities

In vegan: Community Ecology Package

Description

Analysis of similarities (ANOSIM) provides a way to test statistically whether there is a significant difference between two or more groups of sampling units.

Usage

anosim(dat, grouping, permutations = 999, distance = "bray", strata = NULL,
    parallel = getOption("mc.cores"))

Arguments

dat	Data matrix or data frame in which rows are samples and columns are response variable(s), or a dissimilarity object or a symmetric square matrix of dissimilarities.
grouping	Factor for grouping observations.
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.
distance	Choice of distance metric that measures the dissimilarity between two observations. See vegdist for options. This will be used if dat was not a dissimilarity structure or a symmetric square matrix.
strata	An integer vector or factor specifying the strata for permutation. If supplied, observations are permuted only within the specified strata.
parallel	Number of parallel processes or a predefined socket cluster. With parallel = 1 uses ordinary, non-parallel processing. The parallel processing is done with parallel package.

Details

Analysis of similarities (ANOSIM) provides a way to test statistically whether there is a significant difference between two or more groups of sampling units. Function anosim operates directly on a dissimilarity matrix. A suitable dissimilarity matrix is produced by functions dist or vegdist. The method is philosophically allied with NMDS ordination (monoMDS), in that it uses only the rank order of dissimilarity values.

If two groups of sampling units are really different in their species composition, then compositional dissimilarities between the groups ought to be greater than those within the groups. The anosim statistic R is based on the difference of mean ranks between groups (r_B) and within groups (r_W):

R = (r_B - r_W)/(N (N-1) / 4)

The divisor is chosen so that R will be in the interval -1 … +1, value 0 indicating completely random grouping.

The statistical significance of observed R is assessed by permuting the grouping vector to obtain the empirical distribution of R under null-model. See permutations for additional details on permutation tests in Vegan. The distribution of simulated values can be inspected with the permustats function.

The function has summary and plot methods. These both show valuable information to assess the validity of the method: The function assumes that all ranked dissimilarities within groups have about equal median and range. The plot method uses boxplot with options notch=TRUE and varwidth=TRUE.

Value

The function returns a list of class "anosim" with following items:

call	Function call.
statistic	The value of ANOSIM statistic R
signif	Significance from permutation.
perm	Permutation values of R. The distribution of permutation values can be inspected with function permustats.
class.vec	Factor with value Between for dissimilarities between classes and class name for corresponding dissimilarity within class.
dis.rank	Rank of dissimilarity entry.
dissimilarity	The name of the dissimilarity index: the "method" entry of the dist object.
control	A list of control values for the permutations as returned by the function how.

Note

The anosim function can confound the differences between groups and dispersion within groups and the results can be difficult to interpret (cf. Warton et al. 2012). The function returns a lot of information to ease studying its performance. Most anosim models could be analysed with adonis which seems to be a more robust alternative.

Author(s)

Jari Oksanen, with a help from Peter R. Minchin.

References

Clarke, K. R. (1993). Non-parametric multivariate analysis 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

See Also

mrpp for a similar function using original dissimilarities instead of their ranks. dist and vegdist for obtaining dissimilarities, and rank for ranking real values. For comparing dissimilarities against continuous variables, see mantel. Function adonis is a more robust alternative that should preferred.

Examples

data(dune)
data(dune.env)
dune.dist <- vegdist(dune)
attach(dune.env)
dune.ano <- anosim(dune.dist, Management)
summary(dune.ano)
plot(dune.ano)

Example output

Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3

Call:
anosim(dat = dune.dist, grouping = Management) 
Dissimilarity: bray 

ANOSIM statistic R: 0.2579 
      Significance: 0.009 

Permutation: free
Number of permutations: 999

Upper quantiles of permutations (null model):
  90%   95% 97.5%   99% 
0.112 0.156 0.194 0.245 

Dissimilarity ranks between and within classes:
        0%   25%    50%     75%  100%   N
Between  4 58.50 104.00 145.500 188.0 147
BF       5 15.25  25.50  41.250  57.0   3
HF       1  7.25  46.25  68.125  89.5  10
NM       6 64.75 124.50 156.250 181.0  15
SF       3 32.75  53.50  99.250 184.0  15

Warning message:
In bxp(list(stats = c(4, 58.5, 104, 145.5, 188, 5, 15.25, 25.5,  :
  some notches went outside hinges ('box'): maybe set notch=FALSE

vegan documentation built on May 2, 2019, 5:51 p.m.