View source: R/endpoint_hits.R
endpoint_hits_DT | R Documentation |
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/.
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
)
chemical_summary |
Data frame from |
category |
Character. Either "Biological", "Chemical Class", or "Chemical". |
mean_logic |
Logical. |
sum_logic |
Logical. |
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. |
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.
data frame with one row per endpoint that had a hit (based on the hit_threshold). The columns are based on the category.
# 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")
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