Package 'journalclub'

Retrieve information for a selection of publications

Description

Generates a data frame providing information (abstract, title, authors, journal, publication date) for a list of PMIDs.

Usage

journalclub.annotate(pmids, retmax = 100)

Value

A data frame with one row per publication.

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Retrieve new publications for a journal club

Description

Retrieve new publications for a journal club

Usage

journalclub.candidates(dir, query = NULL, recent = 30, debug = F)

Arguments

dir	Directory where the journal club history is stored.
query	PubMed query for identifying new publications (Default: NULL).
recent	Number of days to look back for publications from the current day (Default: 30).

Value

A data frame listing recent publications that have not been considered for previous journal clubs and either match the input query or cite a previously presented publication.

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Query PubMed for recent citing publications

Description

Retrieve recent publications that cite a given set of publications

Usage

journalclub.citing(pmids, days = 30, retmax = 100, verbose = T)

Arguments

pmids	PMIDs for papers to be cited.
days	Number of days to look back for publications from the current day (Default: 30).

Value

A vector of PMIDs matching the query.

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Query PubMed for recent publications

Description

Retrieve PMIDs for recent publications matching a query.

Usage

journalclub.query(query, days = 30, retmax = 1e+05)

Arguments

query	PubMed query.
days	Number of days to look back for publications from the current day (Default: 30).

Value

A vector of PMIDs matching the query.

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Update journal club history with newly presented publications

Description

Update journal club history with newly presented publications

Usage

journalclub.update(dir, presented)

Arguments

dir	Directory where the journal club history is stored.
presented	List of PMIDs for the publications that were presented.

Value

TRUE

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