HSDEM: Tukey's Honest Significant Difference using estimated...

View source: R/HSDEM_class.R

HSDEMR Documentation

Tukey's Honest Significant Difference using estimated marginal means


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.


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



(numeric) The p-value cutoff for determining significance. The default is 0.05.


(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) A symbolic description of the model to be fitted.


Additional slots and values passed to struct_class.


This object makes use of functionality from the following packages:

  • emmeans

  • nlme


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.


Lenth R (2023). emmeans: Estimated Marginal Means, aka Least-Squares Means. R package version 1.8.4-1, https://CRAN.R-project.org/package=emmeans.

Pinheiro J, Bates D, R Core Team (2022). nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-161, https://CRAN.R-project.org/package=nlme.

Pinheiro JC, Bates DM (2000). Mixed-Effects Models in S and S-PLUS. Springer, New York. \Rhrefhttps://doi.org/10.1007/b98882doi:10.1007\slashb98882.


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)

computational-metabolomics/structToolbox documentation built on Feb. 6, 2023, 2:43 p.m.