rpubmed: rpubmed

Tools for extracting literature data from Pubmed.

AuthorDavid Springate
Date of publication2013-10-29 16:57:48
MaintainerDavid Springate <daspringate@gmail.com>
LicenseGPL-3
Version0.1

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Man pages

abstract_to_text: concatenates abstract list to a single string

chunker: Helper function to split a vector v into list of chunks of...

entrez_email: Set global variables

fetch_in_chunks: Downloads abstracts and Metadata from Pubmed, storing as R...

geocode: Helper function for geocode_address

geocode_address: Function to get coordinates from a supplied address If no...

geocode_addresses: Returns a data frame of geocoded addresses with longitude and...

get_article_location_data: Extracts addresses of affiliated departments from Pubmed...

get_articles_by_terms: Returns a list of articles matching the termlist items in the...

get_mesh_headings: Returns a list of MeSH headings for an article

in_abstract_p: predicate function for searching abstracts

in_mesh_abstract_p: predicate function for searching abstracts and MeSH headings

in_mesh_headings_p: predicate function for searching MeSH headings

in_record_text_p: predicate function for searching in title and abstract

keyword_assoc_table: Builds an association table for a character vector of search...

mesh_assoc_table: Builds an association matrix for all MeSH terms in an article...

mesh_heading_frequency: Returns a data frame of all MeSH headings in a corpus, with...

mesh_table: helper function for mesh_assoc_table

mesh_to_text: concatenates a list of MeSH headings to a single string

pubmed_fetch: Download data from Pubmed

read_article_json: Redundant wrapper around fromJSON

record_counts_by_year: Gives a breakdown of records per year in a corpus of Pubmed...

term_in_text_p: predicate function for presence of a term in an article text

title_to_text: concatenates a list of MeSH headings to a single string

write_JSON_file: Write a list of (e.g.) Pubmed records (e.g.) from...

write_record_list: Writes article title and citation data to file or stdout....

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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