AuditionBarcodes: AuditionBarcodes

In Ulises-Rosas/boldminer: Wrapper for BOLD API and DNA barcode auditing

Description

Despite AuditionBarcodes function is coupled with auditOnID function, it can also work with just a list of names. It is pending, when using records mined from NCBI database, assess whether these sequences used to assess barcode's quality come from either a published article or direct submission. Please notice that grades are obtained with accepted names of species according to WoRMS Rest API by using its taxamatch algorithm. Hence, since currently accepted names within 'species' vector has not been figured out, unevenness between the column 'BIN_structure' and 'species' could pop up.

Usage

AuditionBarcodes(species, matches = NULL, validate_name = FALSE,
  exclude_ncbi = TRUE, quiet = FALSE)

Arguments

species	species name vector
matches	This is only filled when this function is coupled with auditOnID function
validate_name	if TRUE, validation of species name is performed. This validation of name is performed by using taxamatch algorithm from WoRMS Rest API
exclude_ncbi	exclude barcodes obtained from NCBI database
quiet	let to use running messages while auditing

Value

DNA barcode auditing

Examples

## Not run: 
species <- c( "Caranx ruber", "Bathygobius lineatus", "Diodon hystrix")
boldminer::AuditionBarcodes(species, exclude_ncbi = FALSE, validate_name = TRUE)

## End(Not run)

Ulises-Rosas/boldminer documentation built on Dec. 18, 2019, 2:53 a.m.