DiversityTest-class: S4 class defining diversity significance

Description Usage Arguments Slots

Description

DiversityTest defines the signifance of diversity (D) differences at a fixed diversity order (q).

Usage

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## S4 method for signature 'DiversityTest'
print(x)

## S4 method for signature 'DiversityTest,missing'
plot(x, y, ...)

Arguments

x

DiversityTest object.

y

ignored.

...

arguments to pass to plotDiversityTest.

Slots

tests

data.frame describing the significance test results with columns:

  • TEST: string listing the two groups tested.

  • DELTA_MEAN: mean of the D bootstrap delta distribution for the test.

  • DELTA_SD: standard deviation of the D bootstrap delta distribution for the test.

  • PVALUE: p-value for the test.

summary

data.frame containing summary statistics for the diversity index bootstrap distributions, at the given value of q, with columns:

  • GROUP: the name of the group.

  • MEAN: mean of the D bootstrap distribution.

  • SD: standard deviation of the D bootstrap distribution.

groups

character vector of groups retained in diversity calculation.

q

diversity order tested (q).

n

numeric vector indication the number of sequences sampled from each group.

nboot

number of bootstrap realizations.


alakazam documentation built on Sept. 21, 2018, 6:26 p.m.