mixed_effect: Mixed effects model

In computational-metabolomics/structToolbox: Data processing & analysis tools for Metabolomics and other omics

Mixed effects model

Description

A mixed effects model is an extension of ANOVA where there are both fixed and random effects.

Usage

mixed_effect(alpha = 0.05, mtc = "fdr", formula, ss_type = "marginal", ...)

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.
ss_type	(character) Sum of squares type. Allowed values are limited to the following: "marginal": Type III sum of squares. "sequential": Type II sum of squares. The default is "marginal".
...	Additional slots and values passed to struct_class.

Details

This object makes use of functionality from the following packages:

• nlme

• emmeans

Value

A mixed_effect object with the following output slots:

f_statistic	(data.frame) The value of the calculated statistic.
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.

Inheritance

A mixed_effect object inherits the following struct classes:

⁠[mixed_effect]⁠ >> ⁠[ANOVA]⁠ >> ⁠[model]⁠ >> ⁠[stato]⁠ >> ⁠[struct_class]⁠

References

Pinheiro J, Bates D, R Core Team (2023). nlme: Linear and Nonlinear Mixed Effects Models. R package version 3.1-164, https://CRAN.R-project.org/package=nlme.

Pinheiro JC, Bates DM (2000). Mixed-Effects Models in S and S-PLUS. Springer, New York. doi:10.1007/b98882 https://doi.org/10.1007/b98882.

Lenth R (2023). emmeans: Estimated Marginal Means, aka Least-Squares Means. R package version 1.9.0, https://CRAN.R-project.org/package=emmeans.

Fox J, Weisberg S (2019). An R Companion to Applied Regression, Third edition. Sage, Thousand Oaks CA. https://socialsciences.mcmaster.ca/jfox/Books/Companion/.

Examples

M = mixed_effect(
      alpha = 0.05,
      mtc = "fdr",
      formula = y ~ x,
      ss_type = "marginal")

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

computational-metabolomics/structToolbox documentation built on Feb. 12, 2024, 2:15 a.m.