get_concentration_summary: Create concentration summary

In toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

Create concentration summary

Description

Use this function to create a chemical_summary, but instead of using any benchmarks, the EAR column is simply the concentration. The output of this function can be used in any of the plotting or table functions in the same way that the output of get_chemical_summary.

Usage

get_concentration_summary(
  tox_list,
  chem_data = NULL,
  chem_site = NULL,
  chem_info = NULL,
  tox_names = TRUE
)

Arguments

tox_list	List with data frames for chem_data, chem_info, and chem_site. Created with create_toxEval.
chem_data	Optional data frame with (at least) columns: CAS, SiteID, and Value. Default is NULL. The argument will over-ride what is in tox_list.
chem_site	Optional data frame with (at least) columns: SiteID, and Short Name. Default is NULL. The argument will over-ride what is in tox_list.
chem_info	Optional data frame with (at least) columns: CAS, and class. Default is NULL. The argument will over-ride what is in tox_list.
tox_names	Logical whether to use the provided chemical names from the ToxCast or not. If there is not a match by CAS, the function will look for a column "Chemical" in the "Chemical" tab. If that column doesn't exist, it will create a (not good!) name.

Value

a data frame with the columns: CAS, chnm (chemical name as a factor), site, date, EAR (which is just concentration), Bio_category, shortName (of site), Class. The output of this function is where you find EAR values for every chemical/endpoint combination.

Examples

path_to_tox <- system.file("extdata", package = "toxEval")
file_name <- "OWC_data_fromSup.xlsx"
full_path <- file.path(path_to_tox, file_name)

tox_list <- create_toxEval(full_path)

chemical_summary_conc <- get_concentration_summary(tox_list)
head(chemical_summary_conc)
plot_tox_boxplots(chemical_summary_conc,
  category = "Chemical",
  x_label = "Concentration [ug/L]"
)

toxEval documentation built on April 15, 2023, 1:13 a.m.