rpubmed

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Documentation for package ‘rpubmed’ version 0.1

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abstract_to_text concatenates abstract list to a single string
chunker Helper function to split a vector v into list of chunks of chunk_size
entrez_email Set global variables
fetch_in_chunks Downloads abstracts and Metadata from Pubmed, storing as R objects
geocode Helper function for geocode_address
geocode_address Function to get coordinates from a supplied address If no match is found, it recursively calls itself on the address minus the first line of the address
geocode_addresses Returns a data frame of geocoded addresses with longitude and latitudes Uses the Google Maps geocode API
get_articles_by_terms Returns a list of articles matching the termlist items in the termlist can be strings or character vectors, concatenated to an "or" regex e.g list(c("gprd", "diabetes")) returns all articles mentioning either gprd or diabetes. different items in the list recursively filter the list e.g. list("gprd", "diabetes") returns articles mentioning gprd and diabtes
get_article_location_data Extracts addresses of affiliated departments from Pubmed metadata email addresses are cleaned out.
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 terms in a corpus. This can then e.g. be fed into igraph to generate an adjacency graph of terms Different column names can be set for the association matrix if e.g. complex regex terms are used for the keyword_list
mesh_assoc_table Builds an association matrix for all MeSH terms in an article corpus
mesh_heading_frequency Returns a data frame of all MeSH headings in a corpus, with frequencies for each
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 Records
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 rpubmed_fetch_in_chunks to json file
write_record_list Writes article title and citation data to file or stdout. Can optionally also output abstracts and output as Markdown, with customisable line starts, e.g. for unordered lists