R: S4 class defining a diversity curve

DiversityCurve-class {alakazam} | R Documentation

## S4 class defining a diversity curve

### Description

`DiversityCurve` defines diversity (D) scores over multiple diversity orders (Q).

### Usage

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

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

    ## S4 method for signature 'DiversityCurve,numeric'
    plot(x, y, ...)

### Arguments

`x` | DiversityCurve object
`y` | diversity order to plot (q).
`...` | arguments to pass to plotDiversityCurve or plotDiversityTest.

### Slots

`diversity`

  data.frame defining the diversity curve with the following columns:

  - `GROUP`: group label.

  - `Q`: diversity order.

  - `D`: mean diversity index over all bootstrap realizations.

  - `D_SD`: standard deviation of the diversity index over all bootstrap realizations.

  - `D_LOWER`: diversity lower confidence inverval bound.

  - `D_UPPER`: diversity upper confidence interval bound.

  - `E`: evenness index calculated as `D` divided by `D` at `Q=0`.

  - `E_LOWER`: evenness lower confidence inverval bound.

  - `E_UPPER`: eveness upper confidence interval bound.

`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.

`group_by`

  string specifying the name of the grouping column in diversity calculation.

`groups`

  vector specifying the names of unique groups in group column in diversity calculation.

`method`

  string specifying the type of diversity calculated.

`q`

  vector of diversity hill diversity indices used for computing diversity.

`n`

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

`ci`

  confidence interval defining the upper and lower bounds (a value between 0 and 1).

[Package alakazam version 0.3.0 Index]