sampleYearsFromLabels function

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

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

Returns

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]+')