{"Package":"TransPhylo","Version":"1.4.5","Date":"2021-04-20","Title":"Inference of Transmission Tree from a Dated Phylogeny","Authors@R":"c(person(\"Xavier\",\"Didelot\",\nemail=\"xavier.didelot@gmail.com\",\ncomment = c(ORCID = \"0000-0003-1885-500X\"),\nrole=c(\"aut\", \"cre\")),\nperson(\"Yuanwei\", \"Xu\",\nemail = \"y.xu@bham.ac.uk\",\nrole = c(\"ctb\")))","Maintainer":"Xavier Didelot ","Description":"Inference of transmission tree from a dated phylogeny.\nIncludes methods to simulate and analyse outbreaks.\nThe methodology is described in\nDidelot et al. (2014) ,\nDidelot et al. (2017) .","License":"GPL (>= 2)","Depends":"R (>= 3.0.0)","Imports":"Rcpp (>= 0.12.8), stats, graphics, ape","Suggests":"knitr, testthat, purrr, coda, grDevices, lattice, rmarkdown","LinkingTo":"Rcpp","Encoding":"UTF-8","RoxygenNote":"7.1.1","SystemRequirements":"C++11","VignetteBuilder":"knitr","NeedsCompilation":"yes","Packaged":"2021-04-20 12:19:58 UTC; Xavier","Author":"Xavier Didelot [aut, cre] (),\nYuanwei Xu [ctb]","Repository":"CRAN","Date/Publication":"2021-04-20 13:30:03 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/TransPhylo_1.4.5.tar.gz","jsonAuthors":[{"name":"Xavier Didelot","email":"xavier.didelot@gmail.com","maintainer":true},{"name":"Yuanwei Xu","email":"y.xu@bham.ac.uk","maintainer":false}],"readme":"\n\n\n# TransPhylo\n\n[![Travis-CI Build\nStatus](https://travis-ci.com/xavierdidelot/TransPhylo.svg?branch=master)](https://travis-ci.com/xavierdidelot/TransPhylo)\n[![codecov](https://codecov.io/gh/xavierdidelot/TransPhylo/branch/master/graph/badge.svg)](https://codecov.io/gh/xavierdidelot/TransPhylo)\n![GitHub](https://img.shields.io/github/license/xavierdidelot/TransPhylo)\n\n# Introduction\n\nThis is the homepage of TransPhylo, a software package that can\nreconstruct infectious disease transmission using genomic data. The\ninput is a dated phylogeny, where leaves correspond to pathogens sampled\nfrom the known infected hosts. The main output is a transmission tree\nwhich indicates who infected whom, including the potential existence of\nunsampled individuals who may have acted as missing transmission links.\nTransPhylo works by colouring the branches of the phylogeny using a\nseparate colour for each host, sampled or not. Each section of the tree\ncoloured in a unique colour represents the pathogen evolution happening\nwithin a distinct host. Changes of colours on branches therefore\ncorrespond to transmission events from one host to another.\n\nFor example, in the tree below, the outbreak started with the unsampled\nhost 8, who transmitted to sampled host 4, who transmitted to unsampled\nhost 3, who transmitted to both sampled hosts 1 and 2. Host 8 also\ntransmitted to unsampled host 7 who transmitted to both sampled hosts 5\nand 6\n.\n\n

\n\nFor a more formal description of TransPhylo, see the following paper:\n\nDidelot, Fraser, Gardy and Colijn (2017) Genomic infectious disease\nepidemiology in partially sampled and ongoing outbreaks Molecular\nBiology and Evolution, 34:997-1007\n\n\n# Installation\n\nYou can install TransPhylo in R using the following command:\n\n`devtools::install_github('xavierdidelot/TransPhylo')`\n\n# Documentation\n\nSee the TransPhylo tutorial at\n.\nThis tutorial is also available within the R package as a vignette. The\nTransPhylo reference manual is available at\n.\n\n# Getting help\n\nIf you need assistance using TransPhylo, you can get in touch by\nemailing `xavier.didelot@gmail.com`\n\n# TransPhyloMatlab\n\nIf you are looking for the older Matlab version of TransPhylo described\nin Didelot et al (2014) Molecular Biology and Evolution 31:1869-1879,\nplease note that this has now been moved to the repository\nTransPhyloMatlab, available at\n","jobInfo":{"package":"TransPhylo","version":"1.4.5","parsingStatus":"success","parserVersion":1,"parsedAt":"2021-04-20T16:30:58+0000"}}

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