Description Usage Arguments Details Value Examples
Data input t.community.matrix is
a transposed matrix of community matrix we defined in ComMA.
Community matrix from file is a matrix where rows are OTUs or individual species
and columns are sites or samples. See ComMA
.
1 2 3 4 | diversityTable(t.community.matrix, named.vector = FALSE)
summaryCMPerSample(t.community.matrix, hasTotal = TRUE, digits = 2,
sort = "descending", comma.in.number = TRUE)
|
t.community.matrix |
is abundances argument
in vegetarian |
named.vector |
Logical, if TRUE, then return a named vector instead of data.frame. |
hasTotal |
If TRUE, then display the Total. Default to TRUE. |
sort |
Sort abundance column by "descending", "ascending", or do nothing for any other string. |
comma.in.number |
If TRUE, then add comma to bug numbers. Default to TRUE. |
digit |
The digits of Shannon index. Default to 2. |
diversityTable
creates a data frame
or named vector of Jost diversity measurement.
summaryCMPerSample
creates a brief summary table of diversities per sample.
diversityTable
returns a 3x3 data frame:
columns are levels of diversity c("gamma", "alpha", "beta"),
rows are orders of the diversity measure c(0, 1, 2). For example,
$q=0$ | $q=1$ | $q=1$ | |
$D_\gamma(q)$ | 13922.000000 | 2501.693162 | 601.509610 |
$D_\alpha(q)$ | 2238.392857 | 880.944977 | 251.127187 |
$D_\beta(q)$ | 6.219641 | 2.839784 | 2.395239 |
summaryCMPerSample
returns a summary data frame:
columns are types of diversity c("abundance", "richness", "shannon"),
rows are samples. For example,
$q=0$ | $q=1$ | $q=1$ | |
Total | 688,733 | 16,860 | NA |
sample1 | 32,837 | 508 | 23.02 |
sample2 | 25,023 | 181 | 7.9 |
1 2 3 | diversity.table <- diversityTable(t.community.matrix)
summary.t.cm <- summaryCMPerSample(t.community.matrix)
|
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