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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.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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