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extractox 1.0.0

Bug Fixes

• Fixed extr_iris extracting the correct number of chemicals without repetition (#15).
• Fixed extr_comtox working when a single download_items different from DTXCID is selected (#17).
• Fixed extr_casrn_from_cid failure when no results are found.

New Features

• Added extr_ice_assay_names to retrieve ICE assay names (#16).
• Added extr_monograph to check if a substance is listed in WHO IARC monograph and return its details (#19).
• Added 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.

Other Breaking Changes

• Removed cancer_types argument from extr_iris. Database returns a dataframe with different columns based on request arguments.
• Removed 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.

Enhancements and Fixes

• Added verbose argument to all extr_ functions (#18).
• Unified behavior across all extr_ functions when chemicals are not found (#30-#35):
  • For all functions except 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.
  • Results now contain rows with NA values for all columns (except query).
  • extr_pprtv and extr_monograph use save_and_match to output results with NA for missing IDs.
• Improved and extended all unit tests.
• extr_comptox now outputs a list of dataframes with clean names.
• Fixed extr_ctd column names: pub_med_ids or pub_med_i_ds are now pubmed_ids.
• Introduced extr_pubchem_section_ internal function to fetch FEMA and GHS info, avoiding repeated code.
• Introduced check_na_warn internal function to generate warnings for missing IDs.
• Created with_extr_sandbox to handle cache for CRAN examples.

extractox 0.1.0

• Initial CRAN submission.

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.