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easyPubMed (version 3.1.6)

Search and Retrieve Scientific Publication Records from PubMed

Description

Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.

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Version

Install

install.packages('easyPubMed')

Monthly Downloads

803

Version

3.1.6

License

GPL-3

Maintainer

Damiano Fantini

Last Published

August 25th, 2025

Functions in easyPubMed (3.1.6)

easyPubMed-class

Class easyPubMed.
print,easyPubMed-method

Print method of the easyPubMed Class.
epm_fetch

Fetch Raw Records from Pubmed.
epm_import_xml

Import PubMed Records from Local Files.
EPM_zerofill

Harmonize the Elements of a Vector by Adding Leading Zeros.
custom_grep

Retrieve Text Between XML Tags
show,easyPubMed-method

Show method of the easyPubMed Class.
epm_query

Search for PubMed Records.
epm_query_by_fulltitle

Query PubMed by Full-length Title.
fetchEPMData

Method fetchEPMData.
epm_stopwords

PubMed Query Stopwords
EPM_retrieve_data

Submit a Query and Retrieve Results from PubMed.
getEPMData

Method getEPMData.
EPM_write_to_file

Write PubMed Records to Local Files.
fetch_pubmed_data

Retrieve PubMed Data in XML or TXT Format
EPM_validate_parse_params

Validate Parameters of a PubMed Record Parsing Job.
get_epm_data

Get Processed Data from an easyPubMed Object.
get_epm_meta

Get Meta Data from an easyPubMed Object.
getEPMRaw

Method getEPMRaw.
setEPMMisc

Method setEPMMisc.
epm_query_by_pmid

Query PubMed by PMIDs.
easyPubMed-package

Retrieve and Process Scientific Publication Records from Pubmed
getEPMUilist

Method getEPMUilist.
epm_parse

Extract Information from a Raw PubMed Record.
setEPMMeta

Method setEPMMeta.
epm_parse_record

Extract Information from a Raw PubMed Record.
setEPMRaw

Method setEPMRaw.
get_epm_uilist

Get PubMed Record Identifiers from an easyPubMed Object.
get_epm_raw

Get Raw Data from an easyPubMed Object.
setEPMQuery

Method setEPMQuery.
getEPMQuery

Method getEPMQuery.
getEPMMisc

Method getEPMMisc.
get_pubmed_ids

Simple PubMed Record Search
setEPMUilist

Method setEPMUilist.
parseEPMData

Method parseEPMData.
table_articles_byAuth

Extract Publication and Affiliation Data from PubMed Records
epm_samples

Preprocessed PubMed Records and Data
getEPMJobList

Method getEPMJobList.
getEPMMeta

Method getEPMMeta.
setEPMData

Method setEPMData.
setEPMJobList

Method setEPMJobList.
EPM_date_parse

Parse and Format a Pubmed Date Field.
EPM_efetch_basic_q

Submit a Query to the NCBI EFetch Server.
EPM_auth_parse

Parse and Format Author Names and Affiliations.
EPM_detect_pmid

Detect PubMed Record Identifiers.
EPM_custom_grep

Custom XML Tag Matching.
EPM_decode_xml_meta

Decode an XML String into the Corresponding Metadata.
EPM_esearch_efetch_seq

Retrieve Results via an Esearch and Efetch sequence.
EPM_esearch_basic_q

Submit a Query to the NCBI ESearch Server.
EPM_check_guide

Check Metadata from Imported XML Files.
EPM_encode_meta_to_xml

Encode Metadata to an XML String.
EPM_prep_outfile

Map Job Batches to Filenames.
EPM_job_split

Split A PubMed Retrieval Job into Manageable Batches.
EPM_mesh_parse

Parse and Format Pubmed MeSH terms.
EPM_reference_parse

Parse and Format References.
EPM_esearch_parse

Parse Responses from the NCBI ESearch Server.
EPM_read_xml

Import PubMed Records Saved Locally in XML Format.
EPM_submit_q

Submit a Query and Read the Response from the Server.
EPM_init_unique_key

Generate a Unique Query Key.
EPM_validate_fetch_params

Validate Parameters of a PubMed Retrieval Job.