HSDEM {structToolbox} | R Documentation

## Tukey's Honest Significant Difference using estimated marginal means

### Description

Tukey's HSD post hoc test is a modified t-test applied for all features to all pairs of levels in a factor. It is used to determine which groups are different (if any). A multiple test corrected p-value is computed to indicate which groups are significantly different to the others for each feature. For mixed effects models estimated marginal means are used.

### Usage

    HSDEM(alpha = 0.05, mtc = "fdr", formula, ...)

### Arguments

`alpha` | (numeric) The p-value cutoff for determining significance. The default is `0.05`.
`mtc` | (character) Multiple test correction method. Allowed values are limited to the following: `"bonferroni"`: Bonferroni correction in which the p-values are multiplied by the number of comparisons. `"fdr"`: Benjamini and Hochberg False Discovery Rate correction. `"none"`: No correction. The default is `"fdr"`.
`formula` | (formula) A symbolic description of the model to be fitted.
`...` | Additional slots and values passed to `struct_class`.

### Details

This object makes use of functionality from the following packages:

- `emmeans`

- `nlme`

### Value

A `HSDEM` object with the following `output` slots:

`p_value` | (data.frame) The probability of observing the calculated statistic if the null hypothesis is true.
`significant` | (data.frame) True/False indicating whether the p-value computed for each variable is less than the threshold.

### References

Lenth R (2021). emmeans: Estimated Marginal Means, aka Least-Squares Means. R package version 1.6.3, https://CRAN.R-project.org/package=emmeans.

Pinheiro J, Bates D, DebRoy S, Sarkar D, R Core Team (2021). nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-153, https://CRAN.R-project.org/package=nlme.

### Examples

    D = iris_DatasetExperiment()
    D$sample_meta$id=rownames(D) # dummy id column
    M = HSDEM(formula = y~Species+ Error(id/Species))
    M = model_apply(M,D)

[Package structToolbox version 1.6.1 Index]