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Build Status

Tools for extracting and processing records from Pubmed and Pubmed Central.

This project is still very much in development... Please contact me with any questions, suggestions or bug reports.

I have built in support for searching and processing MeSH headings, making this package of particular use for biomedical researchers conducting systematic reviews and meta-analyses. Two of these functions (mesh_assoc_table and keyword_assoc_table) produce association matrices which can be fed into graph packages such as igraph to visualise the associations between different search terms.

Available functions:

  • fetch - Tools for bulk downloading of Pubmed records
    • fetch_in_chunks(ids, chunk_size = 500, delay = 0, ...)
    • pubmed_fetch(ids, file_format = "xml", as_r_object = TRUE, ...)
  • textsearch - Tools for text-mining of abstracts and metadata from downloaded records
    • get_articles_by_terms(corpus, term_list, where, case_sensitive = FALSE, ...)
    • record_counts_by_year(corpus)
  • io - saving records to disk and printing summaries of abstract lists to file or sdout
    • write_JSON_file(x, file)
    • write_record_list(articles, out_file = "", abstract_p = FALSE, markdown_p = FALSE, linestart = "* ")
  • locations - Geocoding functionality added for finding the coordinates of departments affiliated with Pubmed Articles.
    • geocode_addresses(addresses, sleeper = 0.33, depth = 3)
    • get_article_location_data(abstracts)
    • geocode_address(address, depth = 3)
  • mesh - Tools for processing and exploring associations between MeSH headings and other keywords
    • mesh_assoc_table(corpus)
    • keyword_assoc_table(corpus, keyword_list, keyword_names, ...)
    • get_mesh_headings(article)
    • mesh_heading_frequency(corpus)