Up until version 1.3.1, toxEval only required “CAS” and
“Class” in the Chemicals tab of the data (see
vignette("PrepareData", package = "toxEval"). In those
previous versions of toxEval, the chemical names were taken
from the Substance_Name in the included data frame . The
information in that table (including substance name) come from the
ToxCast database.
Many users are using toxEval for user-curated benchmarks
workflows, and the auto-generated chemical names became difficult to
work with. So going forward from version 1.3.1, the chemical names seen
in tables and figures come from the “Chemical” tab.
To get the pre-1.3.1 names, use a join. We’ll open the example data,
delete the pre-defined column of chemical names, and show how to do a
join using tox_chemicals.
library(toxEval)
library(dplyr)
path_to_tox <- system.file("extdata", package = "toxEval")
file_name <- "OWC_data_fromSup.xlsx"
full_path <- file.path(path_to_tox, file_name)
chem_info <- readxl::read_xlsx(full_path, sheet = "Chemicals")
#remove Chemical column for demonstration:
chem_info <- chem_info[, c("CAS", "Class")]
tox_chemicals <- tox_chemicals
chem_info_with_names <- chem_info %>%
left_join(select(tox_chemicals,
CAS = casn,
Chemical = chnm),
by = "CAS")
head(chem_info_with_names)## # A tibble: 6 × 3
## CAS Class Chemical
## <chr> <chr> <chr>
## 1 121-00-6 Antioxidants 2-tert-Butyl-4-methoxyphenol
## 2 136-85-6 Antioxidants 5-Methyl-1H-benzotriazole
## 3 80-05-7 Antioxidants Bisphenol A
## 4 84-65-1 Dyes/Pigments Anthraquinone
## 5 5436-43-1 Fire Retardants 2,2',4,4'-Tetrabromodiphenyl ether
## 6 126-73-8 Fire Retardants Tributyl phosphateUsers need to supply their own names for chemicals that are not in
the tox_chemicals data frame.