make.attributes: Obtain meta data for items in 'obkData' objects

In OutbreakTools: Basic Tools for the Analysis of Disease Outbreaks

Description

Thes functions derive all available data relating to genetic sequences, tips of a tree, or individuals, based on matching individuals identifiers and collection dates. Note that for individuals, repeated measures will result in a 'wide' format for a data.frame, with possibly many missing entries resulting from uneven sampling.

Usage

make.sequence.attributes(x)

make.tip.attributes(x, which.tree=1)

make.individual.attributes(x)

Arguments

x	an obkData object.
which.tree	an integer indicating which tree to use.

Value

A data.frame named after the sequences, the tips, or the individuals, with various meta-information.

Author(s)

Thibaut Jombart [e-mail]

Examples

data(ToyOutbreak)
data(HorseFlu)

head(make.tip.attributes(ToyOutbreak))

head(make.sequence.attributes(HorseFlu))

## no repeated measures
head(make.individual.attributes(ToyOutbreak))

## note wide format when there are repeated measures
head(make.individual.attributes(HorseFlu))

OutbreakTools documentation built on Oct. 6, 2017, 1:03 a.m.