rpubmed: rpubmed

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Tools for extracting literature data from Pubmed.

Author
David Springate
Date of publication
2013-10-29 16:57:48
Maintainer
David Springate <daspringate@gmail.com>
License
GPL-3
Version
0.1

View on R-Forge

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....

Files in this package

rpubmed/DESCRIPTION
rpubmed/NAMESPACE
rpubmed/R
rpubmed/R/global_vars.R
rpubmed/R/rpubmed_fetch.R
rpubmed/R/rpubmed_io.R
rpubmed/R/rpubmed_locations.R
rpubmed/R/rpubmed_mesh.R
rpubmed/R/rpubmed_textsearch.R
rpubmed/README.md
rpubmed/Test
rpubmed/Test/PCD_articles.json
rpubmed/Test/plasticity_abstracts.json
rpubmed/Test/plasticity_ids.json
rpubmed/man
rpubmed/man/abstract_to_text.Rd
rpubmed/man/chunker.Rd
rpubmed/man/entrez_email.Rd
rpubmed/man/fetch_in_chunks.Rd
rpubmed/man/geocode.Rd
rpubmed/man/geocode_address.Rd
rpubmed/man/geocode_addresses.Rd
rpubmed/man/get_article_location_data.Rd
rpubmed/man/get_articles_by_terms.Rd
rpubmed/man/get_mesh_headings.Rd
rpubmed/man/in_abstract_p.Rd
rpubmed/man/in_mesh_abstract_p.Rd
rpubmed/man/in_mesh_headings_p.Rd
rpubmed/man/in_record_text_p.Rd
rpubmed/man/keyword_assoc_table.Rd
rpubmed/man/mesh_assoc_table.Rd
rpubmed/man/mesh_heading_frequency.Rd
rpubmed/man/mesh_table.Rd
rpubmed/man/mesh_to_text.Rd
rpubmed/man/pubmed_fetch.Rd
rpubmed/man/read_article_json.Rd
rpubmed/man/record_counts_by_year.Rd
rpubmed/man/term_in_text_p.Rd
rpubmed/man/title_to_text.Rd
rpubmed/man/write_JSON_file.Rd
rpubmed/man/write_record_list.Rd