calc_tox_thresholds: calc_tox_thresholds
In limnoliver/pah: Common Analyses for Polycyclic Aromatic Hydrocarbons (PAH) Data

Summarizes PAH concentrations relative to toxicity thresholds including 1) the concentration above which adverse outcomes to aquatic biota are expected (probable effect concentration or PEC), 2) the concentration below which adverse outcomes to aquatic biota are unlikely (threshold effect concentration or TEC), and 3) a threshold that accounts for the bioavailability of PAHs based on the organic carbon content of the sediment (sum equilibrium-partitioning sediment benchmark toxicity unit or ESBTU).

1 2	calc_tox_thresholds(compound_info, sample_column, conc_column, compound_column, conc_unit = "ppb")

`compound_info`	The output dataframe from 'get_compound_info', which contains sample concentrations as well as compound-specific information, including whether the compound is one of 16 EPA priority compounds and compound-specific toxicity.
`sample_column`	string, column that contains unique sample identifier
`conc_column`	string, column that contains sample concentrations
`compound_column`	string, column that contains compound names. For this function to work properly, there must be a compound named "TOC" for total organic carbon (for TOC normalization in ESBTU calculation), with units of percent TOC.
`conc_unit`	string, the units of PAH concentrations, either "ppb" (ug/kg) or "ppm" (mg/kg).

a list of two dataframes. 'results_bysite' reports sample-specific thresholds and percent TOC, while 'results_summary' reports summary statistics of thresholds and TOC across all samples.

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