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 (
keyword_assoc_table) produce association matrices which can be fed into graph packages such as
igraph to visualise the associations between different search terms.
- 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, ...)
- io - saving records to disk and printing summaries of abstract lists to file or sdout
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)
geocode_address(address, depth = 3)
- mesh - Tools for processing and exploring associations between MeSH headings and other keywords
keyword_assoc_table(corpus, keyword_list, keyword_names, ...)