Title Check the curation of per-participant metadata against a template.

checkCuration(
  curated,
  template = read.csv(system.file("extdata/template.csv", package =
    "curatedMetagenomicDataCuration"), as.is = TRUE)
)

Arguments

curated: a data.frame containing the curated per-participant metadata to be checked
template: a data.frame defining valid syntax

Value

a list with two elements, [["colnames"]] and [["values]]

Details

See Examples for the template used for curatedMetagenomicData. The template has five columns:

1. "col.name" specifies the name of the column in the curated data.frame. 2. "multiplevalues": multiple semicolon-separated values are allowed 3. "uniqueness": unique means each value must be unique, non-unique means repeated values are allowed 4. "requiredness": if "required", there must be no missing (NA) values. If "optional", missing values are allowed. 5. "allowedvalues": a regex defining allowable values for the column 6. "description": a free-form description of the variable