software.html

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<h1 style="margin-top:0;">Software</h1>

<p class="lead"><small>
  All publicly available software that I maintain is available on 
  <a href = "https://github.com/bryandmartin">my GitHub</a>. I try to actively respond to feature requests and bug reports submitted via GitHub issues. </small>
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<h4> corncob: Count Regression for Correlated Observations with the Beta-binomial </h4>
<p class="content" style="padding:0px;margin:0px 20px 0px;"> An R software package 
  an individual taxon regression model that uses abundance tables and sample data.
  corncob uses a beta-binomial model that permits hypothesis testing for changes in relative abundance and overdispersion.
  It addresses different sequencing depths, excessive zeros, overdispersion, and within-taxon correlation. <br/> 
                  <strong>Availablility:</strong>  <a href = "https://github.com/bryandmartin/corncob">GitHub</a>
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  <strong>Reference:</strong> <a href = "https://projecteuclid.org/euclid.aoas/1587002666">Available here</a>.</p>
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<h4>DivNet: Diversity Estimation in Networked Communities</h4>
<p class="content" style="padding:0px;margin:0px 20px 0px;"> An R software package for estimating common diversity indices such as the Shannon, Simpson, Bray-Curtis, and Euclidean indices.
  DivNet utilizes covariate information (sample data) to model taxa in the ecosystem as interacting and co-occuring. <br/> 
                  <strong>Availablility:</strong>  <a href = "https://github.com/adw96/DivNet">GitHub</a>
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  <strong>Reference:</strong> <a href = "https://www.biorxiv.org/content/early/2018/04/21/305045">Available here</a>, to appear in <i>Biostatistics</i>, 2020+.</p>
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<h4>mRkov: a statistical tool to scrape and imitate Twitter activity</h4>
<p class="content" style="padding:0px;margin:0px 20px 0px;"> An R software package and Shiny web app that takes a Twitter handle as input and generates tweets that mimic the speech patterns of the handle. Developed as part of the <a href = "https://spa-drp.github.io/">Directed Reading Program</a> (DRP) at the University of Washington Department of Statistics. The DRP is an undergraduate research program managed by PhD students with the goal to build community, develop research skills for mentors and mentees, and provide an opportunity for students from traditionally underrepresented backgrounds to explore statistics.
  It's very fun to play with, give it a try! <br/> 
                  <strong>Availablility:</strong>  
                  <a href = "https://serrat839.shinyapps.io/mRkov_shiny/">Shiny web app</a> and 
                  <a href = "https://github.com/serrat839/mRkov_shiny">GitHub</a>
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<h4>breakaway</h4>
<p class="content" style="padding:0px;margin:0px 20px 0px;"> An R software package 
 that provides a suite of methods for modeling microbial communities, along with hypothesis testing for alpha-diversity.<br/> 
                  <strong>Availablility:</strong>  <a href = "https://github.com/adw96/breakaway">GitHub</a>
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  <strong>Reference:</strong> <a href = "https://onlinelibrary.wiley.com/doi/pdf/10.1111/biom.12332">Available here</a>.</p>
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<h4>SUMMER: Spatio-temporal Under-five Mortality Model Estimation in R</h4>
<p class="content" style="padding:0px;margin:0px 20px 0px;"> An R software package providing a user-friendly implementation of methods for estimating, projecting,
  and plotting spatio-temporal under-five mortality rates. <br/> 
                  <strong>Availablility:</strong> <a href = "https://CRAN.R-project.org/package=SUMMER">CRAN</a> and <a href = "https://github.com/bryandmartin/SUMMER">GitHub</a>
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  <strong>Reference:</strong> <a href = "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210645">Available here</a>.</p>
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<h4>WSC</h4>
<p class="content" style="padding:0px;margin:0px 20px 0px;"> An R software package intended for personal use by myself and friends. 
  You may find it useful if you play DnD, want to split checks fairly, or want to be guided 
  through the process of updating R in OSX without losing your packages. <br/> 
  <strong>Availablility:</strong> <a href = "https://github.com/bryandmartin/WSC">GitHub</a>
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