extr_comptox, extr_iris,
extr_pprtv) now automatically handle connection issues that
can occur on systems with modern libcurl and
OpenSSL. The functions detect problematic configurations
and use the {condathis} package to perform requests with a
compatible version of curl in an isolated environment. This
ensures reliability without requiring manual user intervention.extr_chem_info now accepts the argument
domain to specify the PubChem domain
(substance or compound).extr_tox now accepts a delay parameter to
control the delay between requests, helping to avoid rate-limiting
errors.delay parameter to
PubChem functions to allow for a pause between requests, helping to
avoid rate-limiting errors.verbose option has been added to
several functions for more detailed output during execution.Testing: Corrected various tests, including a fix for an incorrect row count expectation in the PubChem test.
Fixed extr_chem_info duplicated name in outout
columns (#47).
Function Cleanup: Refined the extr_comptox function,
removing unnecessary requirements and cleaning up the code.
extr_iris extracting the correct number of
chemicals without repetition (#15).extr_comtox working when a single
download_items different from DTXCID is
selected (#17).extr_casrn_from_cid failure when no results are
found.extr_ice_assay_names to retrieve ICE assay names
(#16).extr_monograph to check if a substance is listed
in WHO IARC monograph and return its details (#19).extr_pprtv to extract information from the EPA
Provisional Peer-Reviewed Toxicity Values database (#20). Introduced
save_to_cache and load_from_cache functions to
avoid re-downloading the file each time. See force
argument.cancer_types argument from
extr_iris. Database returns a dataframe with different
columns based on request arguments.stop_at_warning argument from
extr_casrn_from_cid. Now warns and returns a dataframe with
NA if no IDs are found.extr_tox now returns a longer list of dataframes,
including the outputs of extr_monograph and
extr_pprtv.verbose argument to all extr_
functions (#18).extr_ functions when
chemicals are not found (#30-#35):
extr_comptox, a
query column reports the IDs searched. In
extr_comptox, this info is in the main_sheet
element. For extr_ice, query values contain
all IDs found.query).extr_pprtv and extr_monograph use
save_and_match to output results with NA for missing
IDs.extr_comptox now outputs a list of dataframes with
clean names.extr_ctd column names: pub_med_ids
or pub_med_i_ds are now pubmed_ids.extr_pubchem_section_ internal function to
fetch FEMA and GHS info, avoiding repeated code.check_na_warn internal function to generate
warnings for missing IDs.with_extr_sandbox to handle cache for CRAN
examples.