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24 25 26 27</head> 28 29 30 <body> 31 32 <div class="navbar navbar-default navbar-fixed-top" role="navigation"> 33 <div class="container-fluid"> 34 <div class="navbar-header"> 35 <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar-collapse-1" aria-expanded="false"> 36 <span class="sr-only">Toggle navigation</span> 37 <span class="icon-bar"></span> 38 <span class="icon-bar"></span> 39 <span class="icon-bar"></span> 40 </button> 41 42 <a class="navbar-brand" href="/">Pearse Lab | biodiversity - health - AI</a> 43 </div> 44 <div class="collapse navbar-collapse" id="navbar-collapse-1"> 45 <ul class="nav navbar-nav navbar-right"> 46 <li><a href="/">Home</a></li> 47 <li><a href="/research">Research</a></li> 48 <li><a href="/fieldsites">Fieldsites</a></li> 49 <li><a href="/software">Software</a></li> 50 <li><a href="/team">Team</a></li> 51 <li><a href="/join">Join</a></li> 52 <li><a href="https://ecofracnetwork.github.io/">EFN</a></li> 53 <li><a href="https://scholar.google.com/citations?hl=en&user=6jtxReMAAAAJ&view_op=list_works&sortby=pubdate">Publications</a></li> 54 55 </ul> 56 </div> 57 </div> 58</div> 59 60 61 <div class="container-fluid"> 62 <div class="row"> 63 <div id="gridid" class="col-sm-12"> 64 <h1 id="software">Software</h1> 65 66<div class="row"> 67 68 <div class="col-sm-6 clearfix"> 69 <div class="well"> 70 <pubtit>AREAData: automatically updating epidemiological data pipeline</pubtit> 71 <p><img src="/images/AREAData.png" class="img-responsive" width="33%" style="float: left" /></p> 72 <p>Daily climate and human data, automatically updated and released in a format to support epidemiological forecasting.</p> 73 <p><em>TP Smith, M Stemkovski, A Koontz, WD Pearse</em></p> 74 <p><strong><a href="https://pearselab.github.io/areadata/">Data in Brief 43: 108438</a></strong></p> 75 <p class="text-danger"><strong> </strong></p> 76 <p> </p> 77 </div> 78 </div> 79 80 <div class="col-sm-6 clearfix"> 81 <div class="well"> 82 <pubtit>Tyrell: COVID-19 toolkit</pubtit> 83 <p><img src="/images/tyrell-building.jpg" class="img-responsive" width="33%" style="float: left" /></p> 84 <p>Internal reproducible data cleaning and analysis pipeline to support our funded COVID-19 work</p> 85 <p><em>TP Smith, WD Pearse</em></p> 86 <p><strong><a href="https://github.com/pearselab/">https://github.com/pearselab/</a></strong></p> 87 <p class="text-danger"><strong> </strong></p> 88 <p> </p> 89 </div> 90 </div> 91 92</div> 93 94<div class="row"> 95 96 <div class="col-sm-6 clearfix"> 97 <div class="well"> 98 <pubtit>SymbiotaR2: Symbiota2 R interface</pubtit> 99 <p><img src="/images/ropensci.png" class="img-responsive" width="33%" style="float: left" /></p> 100 <p>R Package for searching and downloading data stored in a Symbiota2 portal</p> 101 <p><em>Koontz A, Brandt B, Dyreson C, and Pearse WD</em></p> 102 <p><strong><a href="https://github.com/ropensci/SymbiotaR2">Journal of Open Source Software 5(56): 2917</a></strong></p> 103 <p class="text-danger"><strong> </strong></p> 104 <p> </p> 105 </div> 106 </div> 107 108 <div class="col-sm-6 clearfix"> 109 <div class="well"> 110 <pubtit>pez: phylogenetics for the environmental s(z)ciences</pubtit> 111 <p><img src="/images/pearse-2014-review.png" class="img-responsive" width="33%" style="float: left" /></p> 112 <p>R package to calculate phylogenetic diversity metrics, Phylogenetic Generalized Linear Mixed Models, and more.</p> 113 <p><em>Pearse WD, Cadotte MW, Cavender-Bares J, Ives AR, Tucker CM, Walker SC, Helmus MR</em></p> 114 <p><strong><a href="https://academic.oup.com/bioinformatics/article/31/17/2888/183404">Bioinformatics 31(17): 2888-2890</a></strong></p> 115 <p class="text-danger"><strong> </strong></p> 116 <p> </p> 117 </div> 118 </div> 119 120</div> 121 122<div class="row"> 123 124 <div class="col-sm-6 clearfix"> 125 <div class="well"> 126 <pubtit>phyloGenerator: an automated phylogeny generation tool for ecologists</pubtit> 127 <p><img src="/images/phyloGenerator.png" class="img-responsive" width="33%" style="float: left" /></p> 128 <p>Python (version 1) and Ruby (version 2) program that automates phylogeny construction. Awarded the Robert May Prize by the British Ecological Society.</p> 129 <p><em>Pearse WD, Purvis A</em></p> 130 <p><strong><a href="https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12055">Methods in Ecology and Evolution 4(7): 692-698</a></strong></p> 131 <p class="text-danger"><strong> </strong></p> 132 <p> </p> 133 </div> 134 </div> 135 136 <div class="col-sm-6 clearfix"> 137 <div class="well"> 138 <pubtit>Suppdata: downloading supplementary data from published manuscripts</pubtit> 139 <p><img src="/images/ropensci.png" class="img-responsive" width="33%" style="float: left" /></p> 140 <p>R package to download the supplementary data from papers using only their DOI</p> 141 <p><em>Pearse WD, Chamberlain SA, with vital contributions from <a href="https://nuest.staff.ifgi.de">
141Daniel Nüst</a></em></p> 142 <p><strong><a href="https://www.theoj.org/joss-papers/joss.00721/10.21105.joss.00721.pdf">Journal of Open Source Software 3(25): 721</a></strong></p> 143 <p class="text-danger"><strong> </strong></p> 144 <p> </p> 145 </div> 146 </div> 147 148</div> 149 150<div class="row"> 151 152 <div class="col-sm-6 clearfix"> 153 <div class="well"> 154 <pubtit>phest: phenology estimation</pubtit> 155 <p><img src="/images/pearse-2017-pullout.png" class="img-responsive" width="33%" style="float: left" /></p> 156 <p>R package that calculates phenology estimators</p> 157 <p><em>Pearse WD, Stemkovski M</em></p> 158 <p><strong><a href="https://github.com/willpearse/phest">https://github.com/willpearse/phest</a></strong></p> 159 <p class="text-danger"><strong> </strong></p> 160 <p> </p> 161 </div> 162 </div> 163 164 <div class="col-sm-6 clearfix"> 165 <div class="well"> 166 <pubtit>MADtraits: Make A Database of traits</pubtit> 167 <p><img src="/images/natdb-coverage.png" class="img-responsive" width="33%" style="float: left" /></p> 168 <p>R package that automates the download of over 4 million pieces of trait data</p> 169 <p><em><a href="https://usubionerdherd.github.io">The Bio Nerd Herd (run by the Pearse Lab)</a></em></p> 170 <p><strong><a href="https://github.com/willpearse/MADtraits">https://github.com/willpearse/MADtraits</a></strong></p> 171 <p class="text-danger"><strong> </strong></p> 172 <p> </p> 173 </div> 174 </div> 175 176</div> 177 178<div class="row"> 179 180 <div class="col-sm-6 clearfix"> 181 <div class="well"> 182 <pubtit>MADcomm: Make A Database of community data</pubtit> 183 <p><img src="/images/nacdb-coverage.png" class="img-responsive" width="33%" style="float: left" /></p> 184 <p>R package that automates the download of over 16 million pieces of ecological community data</p> 185 <p><em><a href="https://usubionerdherd.github.io">The Bio Nerd Herd (run by the Pearse Lab)</a></em></p> 186 <p><strong><a href="https://github.com/willpearse/MADcomm">https://github.com/willpearse/MADcomm</a></strong></p> 187 <p class="text-danger"><strong> </strong></p> 188 <p> </p> 189 </div> 190 </div> 191 192 <div class="col-sm-6 clearfix"> 193 <div class="well"> 194 <pubtit>Austin: MCMCMC for the brave</pubtit> 195 <p><img src="/images/austin-city.jpg" class="img-responsive" width="33%" style="float: left" /></p> 196 <p>C++ Multiple Chain Monte Carlo Markov Chain. Really more of a toy, but useful for classwork</p> 197 <p><em>Pearse WD</em></p> 198 <p><strong><a href="https://github.com/willpearse/astin">https://github.com/willpearse/astin</a></strong></p> 199 <p class="text-danger"><strong> </strong></p> 200 <p> </p> 201 </div> 202 </div> 203 204</div> 205 206 207</div> 208 209 </div> 210 </div> 211 212 <div id="footer" class="panel"> 213 <div class="panel-footer"> 214 <div class="container-fluid"> 215 <div class="row"> 216 <div class="col-sm-4"> 217 <p>© 2024 Pearse Lab. Site made with <a href="https://jekyllrb.com">Jekyll</a> from the <a href="https://www.allanlab.org"all>Allan Lab</a> template</p> 218 <p>Part of <a href="https://www.imperial.ac.uk/">ICL</a>'s <a href="https://www.imperial.ac.uk/life-sciences/">Department of Life Sciences</a> and <a href="https://www.turing.ac.uk/">the Alan Turing Institute</a>.</p> 219 </div> 220 <div class="col-sm-4"> 221 <p>We use species evolutionary history to understand and predict their ecology.</p> 222 <p>Grateful for funding from <a href="https://www.ukri.org/councils/nerc/">UKRI/NERC</a>, <a href="https://www.ukri.org/councils/bbsrc/">UKRI/BBSRC</a>, and others.</p> 223 <p> 224 </div> 225 <div class="col-sm-4"> 226 Silwood Park, Imperial College London<br /> 227 Buckhurst Rd, Berkshire, SL5 7PY, UK<br /> 228 (+44) (0)20 7594 2322<br /> 229 <a href="mailto:[email protected]">[email protected]</a> <br /> 230 </div> 231 </div> 232 </div> 233 </div> 234</div> 235
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