Description Usage Arguments Details Value Examples
Data input cm is community matrix
defined in ComMA.
Rows are OTUs or individual species, and columns are sites or samples.
It is a transposed matrix of vegdist
input.
1 2 3 4 5 6 7 8 | getDissimilarity(cm, tree = NA, is.transposed = FALSE, progressBar = TRUE,
method = c("beta1-1", "jaccard", "horn.morisita", "bray.curtis",
"unwt.unif", "wt.unif"))
beta1minus1(cm, is.transposed = FALSE, progressBar = TRUE,
return.dist = TRUE)
TurnoverDist(t.community.matrix)
|
cm |
The community matrix. |
tree |
The ape tree object required
to caculate |
is.transposed |
If TRUE, then the community matrix is already
transposed to be the valid input of |
progressBar |
Whether to print progress bar
only when method="beta1-1" calculated by |
method |
The method to calculate similarity/dissimilarity distance.
The options are jaccard, horn.morisita,
bray.curtis, beta1-1, and unwt.unif, wt.unif.
The last two are unweighted or weighted |
return.dist |
If TRUE, as default,
return a |
getDissimilarity
calculates various
multivariate distance metrics among samples.
beta1minus1
calculates beta1-1.
TurnoverDist
returns a dist
composed of pair-wise turnovers.
getDissimilarity
returns a dist
object of
similarity/dissimilarity, whose rows and columns are
sample names from the community matrix.
1 2 3 4 5 | dist.jaccard <- getDissimilarity(cm, method="jaccard")
turnover.dist <- beta1minus1(cm)
turnover.dist <- TurnoverDist(t.community.matrix)
|
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