areaCAT {benchdamic} | R Documentation

## areaCAT

### Description

Compute the area between the bisector and the concordance curve.

### Usage

    areaCAT(concordance, plotIt = FALSE)

### Arguments

`concordance` | A long format `data.frame` produced by createConcordance function.
`plotIt` | Plot the concordance (default `plotIt = FALSE`).

### Value

A long format `data.frame` object with several columns:

- `comparison` which indicates the comparison number;

- `n_features` which indicates the total number of taxa in the comparison dataset;

- `method1` which contains the first method name;

- `method2` which contains the first method name;

- `rank`;

- `concordance` which is defined as the cardinality of the intersection of the top rank elements of each list, divided by rank, i.e. , (L_{1:rank} \bigcap M_{1:rank})/(rank), where L and M represent the lists of the extracted statistics of method1 and method2 respectively;

- `heightOver` which is the distance between the bisector and the concordance value;

- `areaOver` which is the cumulative sum of the `heightOver` value.

### See Also

`createConcordance` and `plotConcordance`

### Examples

    data(ps_plaque_16S)

    # Balanced design for independent samples
    my_splits <- createSplits(
        object = ps_plaque_16S, varName =
        "HMP_BODY_SUBSITE", balanced = TRUE, N = 10 # N = 100 suggested
    )

    # Initialize some limma based methods
    my_limma <- set_limma(design = ~ HMP_BODY_SUBSITE, coef = 2,
        norm = c("TMM", "CSSmedian"))

    # Set the normalization methods according to the DA methods
    my_norm <- setNormalizations(fun = c("norm_edgeR", "norm_CSS"),
        method = c("TMM", "median"))

    # Run methods on split datasets
    results <- runSplits(split_list = my_splits, method_list = my_limma,
        normalization_list = my_norm, object = ps_plaque_16S)

    # Concordance for p-values
    concordance_pvalues <- createConcordance(
        object = results, slot = "pValMat", colName = "rawP", type = "pvalue"
    )

    # Add area over the concordance curve
    concordance_area <- areaCAT(concordance = concordance_pvalues)

[Package benchdamic version 1.0.0 Index]