sampleYearsFromLabels: Compute a vector of numeric sample times from labels in a...

In emvolz-phylodynamics/treedater-dev: Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation

Description

Compute a vector of numeric sample times from labels in a sequence aligment or phylogeny

Usage

sampleYearsFromLabels(tips, dateFormat = "%Y-%m-%d",
  delimiter = NULL, index = NULL, regex = NULL)

Arguments

tips	A character vector supplying the name of each sample
dateFormat	The format of the sample date. See ?Date for more information
delimiter	Character(s) which separate data in each label
index	Integer position of the date string in each label with respect to *delimiter*
regex	A regular expression for finding the date substring. Should not be used with *delimiter* or *index*

Value

Numeric vector with sample time in decimal format.

Examples

## A couple of labels for Ebola virus sequences: 
sampleYearsFromLabels( c('EBOV|AA000000|EM104|SierraLeone_EM|2014-06-02'
                       , 'EBOV|AA000000|G3713|SierraLeone_G|2014-06-09')
, delimiter='|' )
## Equivalently: 
sampleYearsFromLabels( c('EBOV|AA000000|EM104|SierraLeone_EM|2014-06-02'
                       , 'EBOV|AA000000|G3713|SierraLeone_G|2014-06-09')
 , regex='[0-9]+-[0-9]+-[0-9]+')

emvolz-phylodynamics/treedater-dev documentation built on Jan. 28, 2020, 6:05 p.m.