borenstein-lab / longitudinal_interpolation

longitudinal_interpolation

This repository contains the analysis code for: "Interpolation of Microbiome Composition in Longitudinal Datasets" (Peleg & Borenstein).

Scripts and files overview

• "Interpolation - Analysis.ipynb": Includes all the analysis and figures that appear in the paper.
• "all interpolation results.zip" - results of interpolation results for each individual and interpolation method. Also include a folder for the results of the interpolationin the Monte-Carlo analysis

Code:

• MethodAnalysis.py, ToolsForTemporalAnalysis.py - utility functions for interpolation resut analysis
• PlotTemporalFiguresAnalysis.py - code for basic figures based on the interpolation results
• gLV_interpolation.py - code for interpolation using the gLV based methods.
• interpolation_methods.py - code for interpolation using non-gLV methods
• parsing_data.py - code for reading and parsing datasets