Check ids

Source: R/check-ids-match.R

Compare IDs (such as individual IDs or specimen IDs) between two data frames.

Ensure that all individual IDs in two data frames match.

Ensure that all specimen IDS in two data frames match

check_ids_match(
  x,
  y,
  idcol = c("individualID", "specimenID"),
  xname = NULL,
  yname = NULL,
  bidirectional = TRUE
)

check_indiv_ids_match(x, y, xname = NULL, yname = NULL, bidirectional = TRUE)

check_specimen_ids_match(
  x,
  y,
  xname = NULL,
  yname = NULL,
  bidirectional = TRUE
)

Arguments

x, y

Data frames to compare
idcol

Name of column containing ids to compare
xname, yname

Names of x and y (to be used in resulting messages)
bidirectional

Should mismatches from both x and y be reported? Defaults to TRUE; if FALSE, will return only IDs in y that are not present in x (IDs in x but not y will be ignored).

Value

A condition object indicating whether IDs match ("check_pass") or not ("check_fail"). Mismatched IDs are included as data within the object.

Examples

a <- data.frame(individualID = LETTERS[1:3])
b <- data.frame(individualID = LETTERS[1:4])
check_ids_match(a, b, idcol = "individualID", xname = "a", yname = "b")

#> <error/check_fail>
#> individualID values are mismatched between a and b
a <- data.frame(individualID = LETTERS[1:3])
b <- data.frame(individualID = LETTERS[1:4])
check_specimen_ids_match(a, b, "individual", "biospecimen")

#> <error/check_fail>
#> Missing column specimenID in individual or biospecimen metadata
a <- data.frame(specimenID = LETTERS[1:3])
b <- data.frame(specimenID = LETTERS[1:4])
check_specimen_ids_match(a, b, "biospecimen", "assay")

#> <error/check_fail>
#> specimenID values are mismatched between biospecimen and assay