Filter BOLD specimen + sequence data (output of bold_seqspec)

Picks either shortest or longest sequences, for a given grouping variable (e.g., species name)

Usage

bold_filter(x, by, how = "max", returnTibble = TRUE)

Arguments

x

(data.frame) a data.frame, as returned from bold_seqspec. Note that some combinations of parameters in bold_seqspec don't return a data.frame. Stops with error message if this is not a data.frame. Required.

by

(character) the column by which to group. For example, if you want the longest sequence for each unique species name, then pass species_name. If the column doesn't exist, error with message saying so. Required.

how

(character) one of "max" or "min", which get used as which.max or which.min to get the longest or shortest sequence, respectively. Note that we remove gap/alignment characters (-)

returnTibble

Whether the output should be a tibble or a data.frame. Default is TRUE, but verifies that the tibble package is installed, if it's not, it will be returned as data.frame. Since this package is only used in this function, doing this so it can be moved to suggested instead of dependency without breaking old scripts.

Value

a data.frame

Examples

if (FALSE) { # \dontrun{
res <- bold_seqspec(taxon = 'Osmia')
maxx <- bold_filter(res, by = "species_name")
minn <- bold_filter(res, by = "species_name", how = "min")

vapply(maxx$nucleotides, nchar, 1, USE.NAMES = FALSE)
vapply(minn$nucleotides, nchar, 1, USE.NAMES = FALSE)
} # }