bold_filter {bold}R Documentation

Filter BOLD specimen + sequence data (output of bold_seqspec)

Description

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

Usage

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

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 (-)

Value

a tibble/data.frame

Examples

## Not run: 
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)

## End(Not run)

[Package bold version 1.2.0 Index]