The function make.phylo is used to obtain phylogenies for each of the genes sequenced in an obkData object. Phylogenetic trees can optionally be plotted before being returned. Colors are used to distinguish samples, individuals, dates, or any other requested information. make.phylo is a wrapper for functions from the ape package: dist.dna for computing genetic distances, and specific methods for getting trees such as nj.
get.incidence is a generic function with a method for Date, obkData, obkSequences and obkContacts objects. In obkSequences and obkContacts objects, it uses collection/occurence dates to derive incidence data. In obkData, more options are available as different types of information can be used. The procedure looks for a time-stamped data with a given named field, and as an option allows for selecting specific dates based on the values of that field, provided as a range (numeric data), a list of retained values, or a regular expression. This allows for defining 'positives' in a flexible way.
get.data is a generic function with a method for obkData objects. It can be used to retrieve various information, known only by the name of the field looked for.
The class uniqSequences is a formal (S4) class for storing unique sequences in the form of a DNAbin and an associated list of vectors containing the original sequenceID.
This function plots a timeline of recorded data per individual, using an obkData object. Colors can be used to display meta-information on individuals, while different types of records are indicated using different symbols.
get.dates is a generic function with a method for obkData, obkSequences and obkContacts objects. It can be used to retrieve dates stored in the object.
OutbreakTools (previously known as 'epibase') is a package providing basic tools for the analysis of disease outbreaks. Its main features lie in handling possibly very different types of data within a coherent framework, represented by the class obkData (for "outbreak data"). This class allows to store and manipulate data on samples, individuals, records interventions, genetic sequences, phylogenetic trees and contact networks, most of this information being time-stamped and possibly geo-referenced.
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