OutbreakTools

Package: OutbreakTools
Version: 0.1-14
Date: 2015-12-25
Title: Basic Tools for the Analysis of Disease Outbreaks
Author: The Hackout team (In alphabetic order: David Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames, Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues, Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Suggests: EpiEstim
Depends: R (>= 3.0.0), methods, ggplot2, network, knitr
Imports: utils, RColorBrewer, ape, reshape2, sna, plyr, ggmap, scales,
rjson, networkDynamic, RCurl
Description: Implements basic tools for storing, handling and visualizing disease outbreak data, as well as simple analysis tools. OutbreakTools defines the new formal class obkData which can be used to store any case-base outbreak data, and provides summaries for these objects, alongside a range of functions for subsetting and data manipulation. It implements a range of graphics for visualising timelines, maps, contact networks and genetic analyses. It also includes a simple case-base outbreak simulation tool.
License: GPL (>= 2)
LazyLoad: yes
VignetteBuilder: knitr
URL: http://sites.google.com/site/therepiproject/r-pac/about
Encoding: UTF-8
Collate: 'auxClasses.R' 'generics.R' 'obkContacts.R' 'obkSequences.R'
'obkData.R' 'obkData_Accessors.R' 'subset.R' 'obkData_basics.R'
'uniqSequences.R' 'dna2uniqSequences.R' 'make.phylo.R'
'make.attributes.R' 'get.incidence.R' 'phylo2ggphy.R'
'plotggMST.R' 'plotggphy.R' 'plot.R' 'plotIndividualTimeline.R'
'simuEpi.R' 'utils.R' 'plotGeo.R' 'annotatedTreeReader.R'
'importFromJSON.R' 'zzz.R' 'OutbreakTools.R'
NeedsCompilation: no
Packaged: 2015-12-25 12:02:42 UTC; thibaut
Repository: CRAN
Date/Publication: 2015-12-26 00:40:07

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'OutbreakTools' ...
** package 'OutbreakTools' successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'OutbreakTools'
Creating a generic function for 'as.matrix' from package 'base' in package 'OutbreakTools'
Creating a generic function for 'as.data.frame' from package 'base' in package 'OutbreakTools'
Creating a generic function for 'summary' from package 'base' in package 'OutbreakTools'
Creating a generic function for 'head' from package 'utils' in package 'OutbreakTools'
Creating a generic function for 'tail' from package 'utils' in package 'OutbreakTools'
** help
*** installing help indices
  converting help for package 'OutbreakTools'
    finding HTML links ... done
    FluH1N1pdm2009                          html  
    finding level-2 HTML links ... done

    HorseFlu                                html  
    HorseFluRaw                             html  
    OutbreakTools.package                   html  
    ToyOutbreak                             html  
    ToyOutbreakRaw                          html  
    annotatedTreeReader                     html  
    auxClasses                              html  
    dna2uniqSequences                       html  
    get.data                                html  
    get.dates                               html  
    get.incidence                           html  
    get.individuals                         html  
    importFromJSON                          html  
    make.attributes                         html  
    make.phylo                              html  
Rd warning: /tmp/RtmpVYxX5H/R.INSTALL3e331b257f56/OutbreakTools/man/make.phylo.Rd:39: missing file link 'fastme.bal'
Rd warning: /tmp/RtmpVYxX5H/R.INSTALL3e331b257f56/OutbreakTools/man/make.phylo.Rd:40: missing file link 'fastme.ols'
    obkContacts                             html  
    obkData                                 html  
    obkDataPlot                             html  
    obkSequences                            html  
    phylo2ggphy                             html  
    phylofromtranstree                      html  
    plotEpi                                 html  
    plotGeo                                 html  
    plotIndividualTimeline                  html  
    plotggMST                               html  
    plotggphy                               html  
    simuEpi                                 html  
    subset                                  html  
    uniqSequences                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OutbreakTools)
Making 'packages.html' ... done