NEWS.md

In hugheylab/pmparser: Create and Maintain a Relational Database of Data from PubMed/MEDLINE

pmparser 1.0.21

• Updated test standards based on Jan 2025 update to PubMed XML files.

pmparser 1.0.20

• Updated readme table in test standards.

pmparser 1.0.19

• Updated test standards based on the annual update to PubMed XML files.

pmparser 1.0.18

• Fixed parsing of CitedMedium within Journal.

pmparser 1.0.17

• Updated parsing of empty investigator fields.

pmparser 1.0.16

• Updated readme table in test standards.

pmparser 1.0.15

• Changed ftp URLs to https.
• Updated test standards based on new PubMed XML files.

pmparser 1.0.14

• Added columns for language and vernacular_title to the article table.

pmparser 1.0.13

• Added tables from the OtherAbstract and OtherID sections.

pmparser 1.0.12

• Fixed issues found by lintr.

pmparser 1.0.11

• Updated test standards based on PubMed's updated README.txt.

pmparser 1.0.10

• Added import for curl::curl() to circumvent check NOTE.

pmparser 1.0.9

• Clarified error message when downloading PubMed files.
• Skip testing of file downloads on CRAN.

pmparser 1.0.8

• Increased timeout for downloading citation file.
• Reordered steps to check citation table even if other tables are up-to-date.
• Update to match lab style standard.

pmparser 1.0.7

• Explicitly added curl to Imports, since it's used by utils::download.file().
• Set "HUGE" option for xml2::read_xml() to avoid occasional error.

pmparser 1.0.6

• Updated styling based on linter.

pmparser 1.0.5

• Added abstract_pos column to abstract table.
• If pub_year in journal table is empty, now extracts pub_year from medline_date.

pmparser 1.0.4

• Updated test standards for latest PubMed XML files.
• Returned to doParallel in scripts for simplicity.

pmparser 1.0.3

• Simplified xml2 dependency, since new version is now on CRAN.

pmparser 1.0.2

• Fixed windows compatibility.

pmparser 1.0.1

• Revised code to not need globalVariables() in order to pass R CMD check without notes.

pmparser 1.0.0

• Updated tests.

pmparser 0.0.0.9036

• Added data dictionary as a vignette and a table in the database.

pmparser 0.0.0.9035

• Remove rare, obnoxious unicode character from keyword name.

pmparser 0.0.0.9034

• Explicitly set doFuture chunking for all dopar loops.

pmparser 0.0.0.9033

• Suppress irrelevant warnings from future.

pmparser 0.0.0.9032

• %dopar% loops in other places now work with doFuture.

pmparser 0.0.0.9031

• %dopar% loops in getPubmedFiles() now work with doFuture.
• Use updated version of withr on CRAN.

pmparser 0.0.0.9030

• Renamed internal functions for consistency and clarity.

pmparser 0.0.0.9029

• getCitation() now uses data.table::fread() to write table in chunks, ~3.3x faster.
• Switched from dbAppendTable() to dbWriteTable(..., append = TRUE) for inexplicable speed increase.

pmparser 0.0.0.9028

• getCitation() now uses vroom for arkdb::unark().
• Moved DBI driver packages to Suggests to reduce dependencies.

pmparser 0.0.0.9027

• Removed obsolete copyright column from the abstract table.

pmparser 0.0.0.9026

• parseMesh() now returns an additional table containing the IndexingMethod attribute.

pmparser 0.0.0.9025

• Fixed rare case of a parsing function returning a data.table with NA in columns instead of a data.table with no rows.

pmparser 0.0.0.9024

• Switched to using glue under the hood.

hugheylab/pmparser documentation built on Jan. 17, 2025, 12:22 a.m.