| format_check {fossilbrush} | R Documentation |
format_check
Description
Function to perform a series of basic formatting checks geared towards taxonomic name data. The function very simply checks for non letter characters in the taxonomic names, that species-level names contain two words, and genus-level and above names contain one word.
Usage
format_check(x, ranks, species = FALSE, species_sep = " ", verbose = TRUE)
Arguments
x |
A dataframe with hierarchically organised, taxonomic information. If x only comprises the taxonomic information, |
ranks |
does not need to be specified, but the columns must be in order of decreasing taxonomic rank @param ranks The column names of the taxonomic data fields in x. These must be provided in order of decreasing taxonomic rank |
species |
A logical indicating if x contains a species column. As the data must be supplied in hierarchical order, this column will naturally be the last column in x and species-specific spell checks will be performed on this column. |
species_sep |
A character vector of length one specifying the genus name and specific epithet in the species column, if present |
verbose |
A logical determining if any flagged errors should be reported to the console |
Value
A list of two lists. The first list flags the row indexes of columns whose elements contains non-letter characters. The second list flags the row indexes of columns whose elements do not contain the correct numbers of words
Examples
# load dataset
data("brachios")
# define ranks
b_ranks <- c("phylum", "class", "order", "family", "genus")
# run function
flag <- format_check(brachios, ranks = b_ranks)