make_tox_map: Create an interactive map of the data

In toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

Create an interactive map of the data

Description

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")

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