Create an interactive map of the data — make_tox

The function make_tox_map creates a leaflet map of the sites. This function places symbols at the location of each site in the data file that represent the magnitude of EAR (color) and the number of samples in the data set (size). This is the only function that requires "dec_lon" and "dec_lat" (decimal longitude and decimal latitude) in the data frame specified for the chem_site argument.

Usage

make_tox_map(
  chemical_summary,
  chem_site,
  category = "Biological",
  mean_logic = FALSE,
  sum_logic = TRUE
)

map_tox_data(
  chemical_summary,
  chem_site,
  category = "Biological",
  mean_logic = FALSE,
  sum_logic = TRUE
)

Arguments

chemical_summary: Data frame from get_chemical_summary.
chem_site: Data frame containing the columns SiteID, site_grouping, Short Name, dec_lon, and dec_lat.
category: Character. Either "Biological", "Chemical Class", or "Chemical".
mean_logic: Logical. TRUE displays the mean EAR from each site, FALSE displays the maximum EAR 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.

Details

The function map_tox_data calculates the statistics for the map. It my be useful on it's own.

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)

make_tox_map(chemical_summary, tox_list$chem_site, "Biological")

make_tox_map(chemical_summary, tox_list$chem_site, "Chemical Class")

make_tox_map(chemical_summary, tox_list$chem_site, "Chemical")