Rank sites by EAR — rank_sites

The rank_sites_DT (DT option) and rank_sites (data frame option) functions create tables with one row per site. Columns represent the maximum or mean EAR (depending on the mean_logic argument) for each category ("Chemical Class", "Chemical", or "Biological") and the frequency of the maximum or mean EAR exceeding a user specified hit_threshold.

Usage

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

rank_sites(
  chemical_summary,
  category,
  hit_threshold = 0.1,
  mean_logic = FALSE,
  sum_logic = TRUE
)

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 may be better for traditional benchmarks as opposed to ToxCast benchmarks.
hit_threshold: Numeric threshold defining a "hit".

Value

data frame with one row per site, and the mas or mean EAR and frequency of hits based on the category.

Details

The tables show slightly different results for a single site. Rather than multiple columns for categories, there is now 1 row per category (since the site is known).

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)

stats_df <- rank_sites(chemical_summary, "Biological")

rank_sites_DT(chemical_summary, category = "Biological")

rank_sites_DT(chemical_summary, category = "Chemical Class")

rank_sites_DT(chemical_summary, category = "Chemical")