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.
- 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)