Man pages for thibautjombart/OutbreakTools
Basic Tools for the Analysis of Disease Outbreaks
| annotatedTreeReader | Read annotated tree files in Newick or NEXUS format |
| auxClasses | Auxiliary classes for OutbreakTools |
| dna2uniqSequences | Convert a DNAbin with duplicated sequences to the class... |
| FluH1N1pdm2009 | Dataset from the 2009 influenza A/H1N1 pandemic |
| get.data | Access data in "obkData" objects |
| get.dates | Retrieve dates data |
| get.incidence | Compute incidence |
| get.individuals | Retrieve individual identifiers |
| HorseFlu | Dataset from the Newmarket 2003 equine influenza outbreak |
| HorseFluRaw | Raw dataset from the Newmarket 2003 equine influenza outbreak |
| importFromJSON | Import data from JSON file into OutbreakTools |
| make.attributes | Obtain meta data for items in 'obkData' objects |
| make.phylo | Obtain phylogenies from outbreak data |
| obkContacts | Formal class "obkContacts" |
| obkData | Formal class "obkData" |
| obkDataPlot | Plot outbreak data |
| obkSequences | Formal class "obkSequences" |
| OutbreakTools.package | The OutbreakTools package |
| phylo2ggphy | Convert phylogenies from the class 'phylo' to the class... |
| phylofromtranstree | Create phylogenetic tree from transmission tree |
| plotEpi | Plot the number of susceptible, infected and recovered as a... |
| plotGeo | Function to plot cases on a map |
| plotggMST | Function to plot a minimum spanning tree of the class... |
| plotggphy | Function to plot phylogenies using 'ggplot2' |
| plotIndividualTimeline | Plot a timeline of recorded data |
| simuEpi | Simulate an epidemic following a SIR model |
| subset | Subset data in "obkData" objects |
| ToyOutbreak | Simulated outbreak dataset |
| ToyOutbreakRaw | Raw simulated outbreak dataset |
| uniqSequences | Formal class "uniqSequences" |
