occurrences {pTITAN2}

Occurrence

Description

Generate a taxonomic data set with codes which have at least n occurrences.

Usage

occurrences(data, n = 5L)

Arguments

data

A data.frame wit

n

the minimum number of occurrences.

Details

Of the codes with at least n occurrences, the code with the most taxonomic detail needs to be selected for the titan run. This means if the macroinvertebrate count has at least n occurrences in a genus code, the family, order, and class codes associated with these counts should be removed. Or, for another example, if there are too few counts at the genus level, but at least n counts at the family level- the family code would be retained and the order and class codes would be removed.

Coding: All of the macroinvertebrates were coded so the first two letters indicate the class, the second two letters indicate the order, the third two letters indicate the family, and the last two numbers indicate the genus. "00" indicates that there is no information at that level. For example: A code that is 'Bi000000' is the Bivalvia class, while BiVe0000 is the Bivalvia class, Veneroida order. BiVeSh00 is the Bivalvia class, Veneroida order, Spheriridae family. BiVeSh01 is a genus within that family.

NOTE: The example script that inspired the development of this function required the data set to have the column names in alpha order. This function relaxes that requirement by using the arrange call.

Value

a data.frame with six columns: taxon, Class, Order, Family, Genus, and count.

See Also

vignette(topic = "pTITAN2", package = "pTITAN2")

Examples

# Report the tax with minimum of five (default) occurrences.
occurrences(CN_06_Mall_wID[, -1])

# Report the tax with at least six occurrences
occurrences(CN_06_Mall_wID[, -1], n = 6)