Statistics
REGRESSION
Alpha diversity estimates and cytokine concentrations were log-transformed prior to model fitting. For parameter estimation, error estimation, and model validation, the dataset was randomly and evenly partitioned into training and validation subsets. Statistical models were fit against the training subset and prediction accuracy (mean absolute error) was evaluated against the validation subset. Effect sizes were estimated from logistic regression models implemented as generalized linear models in R. Statistical tests used include permutational MANOVA (permanova) for comparisons among multiple (>2) groups in the beta-diversity analysis, ANCOVA models were used to evaluate the effect of contraceptive option on alpha diversity and Nugent scores while controlling for enrollment values, and Student’s t tests or Wilcoxon Rank Sum tests for comparisons among two groups. McNemar’s and chi-squared tests were used for assessing data in contingency tables. Regardless of the test used, significance was evaluated using an α value cutoff of 0.05. 