get_compound_info: get_compound_info

Description Usage Arguments Value

View source: R/get_compound_info.R

Description

Merges user PAH data with compound-specific metadata, including whether the compound is: one of the 16 EPA priority compounds, low or high molecular weight, a parent or alkylated PAH, and whether the compound is in the source profiles.

Usage

1
2
get_compound_info(pah_dat, merge_type = "name",
  merge_col = "parameter_nm", compound_info = pah_compounds)

Arguments

pah_dat

data frame of user PAH data, either retrieved using the get_pah data, or the user's own PAH concentration data. Data frame must include a PAH identifier column, which can be either the USGS parameter code, casrn, or compound name. Not all compounds have casrn numbers. This function requires that pah_dat be in long format; that is, there is a parameter column and site column, where site or sample id is repeated for each compound.

merge_type

whether the merge should being done by USGS parameter codes ('pcode'), Chemical Abstracts Service Registry Number ('casrn'), or compound name ('name'). Note that alkylated PAHs (e.g., C2-alkylated naphthalene) do not have casrn numbers, and metadata on these compounds will not be merged if merge_type = "casrn".

merge_col

column name that contains the PAH identifier by which to merge

compound_info

table with compound metadata. A built-in table is the default but may not contain all compounds in user-supplied dataset. See documentation for the pah_compounds table to see if it fits your needs.

Value

A data frame with all of the columns from the user-supplied pah_dat, as well as columns from the built in data frame pah_compounds. These included...


limnoliver/pah documentation built on April 30, 2020, 2:45 p.m.