TDAstats - Pipeline for Topological Data Analysis
A comprehensive toolset for any useR conducting topological data analysis, specifically via the calculation of persistent homology in a Vietoris-Rips complex. The tools this package currently provides can be conveniently split into three main sections: (1) calculating persistent homology; (2) conducting statistical inference on persistent homology calculations; (3) visualizing persistent homology and statistical inference. The published form of TDAstats can be found in Wadhwa et al. (2018) <doi:10.21105/joss.00860>. For a general background on computing persistent homology for topological data analysis, see Otter et al. (2017) <doi:10.1140/epjds/s13688-017-0109-5>. To learn more about how the permutation test is used for nonparametric statistical inference in topological data analysis, read Robinson & Turner (2017) <doi:10.1007/s41468-017-0008-7>. To learn more about how TDAstats calculates persistent homology, you can visit the GitHub repository for Ripser, the software that works behind the scenes at <https://github.com/Ripser/ripser>. This package has been published as Wadhwa et al. (2018) <doi:10.21105/joss.00860>.
Last updated 3 years ago
data-scienceggplot2homologyhomology-calculationshomology-computationjosspersistent-homologypipelineripsertdatopological-data-analysistopologytopology-visualizationvisualizationcpp
8.29 score 39 stars 4 dependents 46 scripts 261 downloadsripserr - Calculate Persistent Homology with Ripser-Based Engines
Ports the Ripser <arXiv:1908.02518> and Cubical Ripser <arXiv:2005.12692> persistent homology calculation engines from C++. Can be used as a rapid calculation tool in topological data analysis pipelines.
Last updated 4 months ago
algebraic-topologycohomologycppcubical-complexpersistent-homologypixelpoint-cloudr-languager-programmingrcpprips-complexripsersimplicial-complexsimplicial-homologytopological-data-analysistopologyvietoris-complexvoxelcpp
5.50 score 7 stars 6 scripts 223 downloadspatentr - Access USPTO Bulk Data in Tidy Rectangular Format
Converts TXT and XML data curated by the United States Patent and Trademark Office (USPTO). Allows conversion of bulk data after downloading directly from the USPTO bulk data website, eliminating need for users to wrangle multiple data formats to get large patent databases in tidy, rectangular format. Data details can be found on the USPTO website <https://bulkdata.uspto.gov/>. Currently, all 3 formats: 1. TXT data (1976-2001); 2. XML format 1 data (2002-2004); and 3. XML format 2 data (2005-current) can be converted to rectangular, CSV format. Relevant literature that uses data from USPTO includes Wada (2020) <doi:10.1007/s11192-020-03674-4> and Plaza & Albert (2008) <doi:10.1007/s11192-007-1763-3>.
Last updated 3 years ago
patentpatent-datapatentsr-programmingusptocpp
4.70 score 10 stars 5 scripts 179 downloadshelixvis - Visualize Alpha-Helical Peptide Sequences
Create publication-quality, 2-dimensional visualizations of alpha-helical peptide sequences. Specifically, allows the user to programmatically generate helical wheels and wenxiang diagrams to provide a bird's eye, top-down view of alpha-helical oligopeptides. See Wadhwa RR, et al. (2018) <doi:10.21105/joss.01008> for more information.
Last updated 6 years ago
biochemistryhelical-wheelspeptide-sequencesvisualizationwenxiang-diagrams
4.00 score 2 stars 3 scripts 232 downloadsfitscape - Classes for Fitness Landscapes and Seascapes
Convenient classes to model fitness landscapes and fitness seascapes. A low-level package with which most users will not interact but upon which other packages modeling fitness landscapes and fitness seascapes will depend.
Last updated 3 years ago
3.18 score 1 dependents 2 scripts 217 downloadshealthfinance - Financial Projections and Planning for Health Care Practices
Provides a shiny interface for a free, open-source managerial accounting-like system for health care practices. This package allows health care administrators to project revenue with monthly adjustments and procedure-specific boosts up to a 3-year period. Granular data (patient-level) to aggregated data (department- or hospital-level) can all be used as valid inputs provided historical volume and revenue data is available. For more details on managerial accounting techniques, see Brewer et al. (2015, ISBN:9780078025792).
Last updated 4 years ago
3.18 score 3 stars 1 scripts 252 downloadsdragonking - Statistical Tools to Identify Dragon Kings
Statistical tests and test statistics to identify events in a dataset that are dragon kings (DKs). The statistical methods in this package were reviewed in Wheatley & Sornette (2015) <doi:10.2139/ssrn.2645709>.
Last updated 6 years ago
3.00 score 2 stars 6 scripts 130 downloads