prep_tip_labels_phydyn: Change the name of sequences to recognize numeric time of...

In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses

Description

Change the name of sequences to recognize numeric time of sampling and deme

Usage

prep_tip_labels_phydyn(
  path_to_align,
  path_to_save = NULL,
  regexprs = c(".*/Netherlands/.*", ".*/Netherlands/.*"),
  invert_regexpr = c(FALSE, TRUE),
  demes = c("Il", "exog")
)

Arguments

regexprs	A vector of regular expressions that can be used to match tip labels and categorize in to demes. These must include *all* sequcence IDs, and each ID should match at most one regular expression
invert_regexpr	A logical vector specifying if the i'th regular expression should be an inverse match
demes	A character vector of deme names to be appended to corresponding sequence IDs
path_to_algn	A DNAbin alignment *or* a system path (type character) where original alignment can be found
deme	The name of the deme to add to the end of each label

emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.