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.