endpoint_hits_DT: Rank endpoints by category

In toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

Rank endpoints by category

Description

The endpoint_hits_DT (data.table (DT) option) and endpoint_hits (data frame option) functions create tables with one row per endPoint, and one column per category("Biological", "Chemical", or "Chemical Class"). The values in the table are the number of sites where the EAR exceeded the user-defined EAR hit_threshold in that endpoint/category combination. If the category "Chemical" is chosen, an "info" link is provided to the chemical information available in the "Comptox Dashboard" https://comptox.epa.gov/dashboard/.

Usage

endpoint_hits_DT(
  chemical_summary,
  category = "Biological",
  mean_logic = FALSE,
  sum_logic = TRUE,
  hit_threshold = 0.1,
  include_links = TRUE
)

endpoint_hits(
  chemical_summary,
  category = "Biological",
  mean_logic = FALSE,
  sum_logic = TRUE,
  hit_threshold = 0.1
)

Arguments

chemical_summary	Data frame from get_chemical_summary
category	Character. Either "Biological", "Chemical Class", or "Chemical".
mean_logic	Logical. TRUE displays the mean sample from each site, FALSE displays the maximum sample from each site.
sum_logic	Logical. TRUE sums the EARs in a specified grouping, FALSE does not. FALSE indicates that EAR values are not considered to be additive and often will be a more appropriate choice for traditional benchmarks as opposed to ToxCast benchmarks.
hit_threshold	Numeric. EAR threshold defining a "hit".
include_links	Logical. whether or not to include a link to the ToxCast dashboard. Only needed for the "Chemical" category.

Details

The tables show slightly different results when choosing to explore data from a single site rather than all sites. The value displayed in this instance is the number of samples with hits rather than the number of sites with hits.

Value

data frame with one row per endpoint that had a hit (based on the hit_threshold). The columns are based on the category.

Examples

# This is the example workflow:
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)

ACC <- get_ACC(tox_list$chem_info$CAS)
ACC <- remove_flags(ACC)

cleaned_ep <- clean_endPoint_info(end_point_info)
filtered_ep <- filter_groups(cleaned_ep)
chemical_summary <- get_chemical_summary(tox_list, ACC, filtered_ep)

hits_df <- endpoint_hits(chemical_summary, category = "Biological")
endpoint_hits_DT(chemical_summary, category = "Biological")
endpoint_hits_DT(chemical_summary, category = "Chemical Class")
endpoint_hits_DT(chemical_summary, category = "Chemical")

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