areaPermutation |
Calculate Area Ratio (AR) of each feature's time interval for all permutations |
curveFitting |
Fit longitudinal data |
findSigInterval |
Find significant time intervals |
intervalArea |
Calculate Area Ratio (AR) of each feature's time interval |
metalonda |
Metagenomic Longitudinal Differential Abundance Analysis for one feature |
metalondaAll |
Metagenomic Longitudinal Differential Abundance Analysis for all Features |
metalonda_test_data |
Simulated data of OTU abundance for 2 phenotypes each has 5 subjects at 10 time-points |
normalize |
Normalize count matrix |
permutation |
Permute group labels |
visualizeArea |
Visualize significant time interval |
visualizeARHistogram |
Visualize Area Ratio (AR) empirical distribution |
visualizeFeature |
Visualize Longitudinal Feature |
visualizeFeatureSpline |
Visualize the feature trajectory with the fitted Splines |
visualizeTimeIntervals |
Visualize all significant time intervals for all tested features |
visualizeVolcanoPlot |
Visualize log2 fold-change and significance of each interval as volcano plot |