rank_sites_DT: Rank sites by EAR

In toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

Rank sites by EAR

Description

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".

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).

Value

data frame with one row per site, and the mas or mean EAR and frequency of hits 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)

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")

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