PySurvey 0.1.1

UNKNOWN

survey is a Python package designed to perform interactive analysis of survey data, composed of counts of occurrence of different categories in a collection of samples. Specifically, survey is developed in the context of genomic surveys, such as 16S surveys, where one studies the occurrence of OTUs across samples. Though much of survey’s functionality is not unique to survey data, and equivalent features are implemented in many other packages, survey is intended to serve as a ‘one-stop-shop’, and thus attempts to includes all the methods that are commonly used in the analysis of survey data (often by wrapping around other packages), with a sensible choice of default parameters (e.g. distance metrics, etc’).

Working with survey

• Documentation - Includes code examples!

• Wiki - A place to put your own tips, tricks and recipes.

• Issue Tracker - For reporting bugs, requesting new features, and getting help.

Key Features

• General utility:

  • All the features of the extremely useful pandas package, which supports fast operations on labeled arrays (and much more).

  • Filtering of samples/components.

  • ML and Bayesian estimation of component fractions.

• Exploratory analysis:

  • Dimension reduction: PCoA, PCA.

  • Clustering: hierarchical, c-means, GMM.

  • Compositional correlations via SparCC.

  • Plotting: sorted heatmaps, stacked plots, grouped bar plots, …

• Ecological theory:

  • Compute various measures of sample diversity (alpha diversity).

  • Rarefaction.

  • Rank abundance plots.

  • Relative Species abundance plots.