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HIV polymerase sequences derived from patients included in the MSM HIV transmission cluster ( Patiño-Galindo et al., 2017) were retrieved from supplementary material made public on GenBank.
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We give the details on their sources and preliminary data processing procedures below. (2017) were obtained from public sources. The respective virus datasets in Monod et al.
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For tips on how to avoid errors dealing with "-lgfortran" or "-lquadmath", please visit here. For extra tips on how to run C++ on macOS, please visit here.
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Instructions on how to install Xcode may be found here. macOS users may use this collection by installing the Homebrew package manager and then typing the following into the terminal:įor macOS users, the Xcode Command Line Tools include a GCC compiler. If not, certain versions of Tropix functions may not work properly. The code in this repository assumes that basic C++ functions and applications are already set up on the running personal computer or cluster. For more on licensing options, please visit here. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages. MATLAB is a multi-paradigm numerical computing environment and a proprietary programming language developed by MathWorks. (2017) is available in the directory entitled "Datasets". The preprocessed data used in Monod et al. We suggest using the C++ or Matlab versions, if possible. Tropix is implemented in three different language environments: (1) Matlab, (2) Python, and (3) C++. In this repository, we use Tropix to conceptually demonstrate sufficiency and illustrate its utility in persistent homology dimensions 0 and 1 with concrete parametric applications to HIV and avian influenza data.
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In particular, this work shows that exponential family distributions may be assumed, and that likelihoods for persistent homology may be constructed. This in turn makes a variety of parametric inference methods amenable to barcodes, all while maintaining their initial interpretations. (2017) and allows for the assumption of classical probability distributions on Euclidean representations of barcodes. This statistical sufficiency result was derived in Monod et al. In this repository, we present code that uses an embedding in Euclidean space based on tropical geometry to generate stable sufficient statistics for barcodes - multiscale summaries of topological characteristics that capture the “shape” of data, but have complex structures and are therefore difficult to use in statistical settings. Tropical Sufficient Statistics for Persistent Homology (Tropix)