Automatically Fetching References Metadata from Literature Databases

Provides functions to automatically retrieve and deduplicate reference metadata based on saved search strings. Access to Web of Science and Scopus requires personal API keys, while PubMed can be queried without one. The optional deduplication functionality requires the package 'ASySD' available from < https://github.com/camaradesuk/ASySD>.

LitFetchR

The purpose of LitFetchR is to automatically retrieve and deduplicate references based on saved search string(s). Access to Web of Science and Scopus requires personal API keys, while PubMed can be queried without one.

What it does

LitFetchR follows three steps, from the first search string to the maintenance of a living review:

Search: create_save_search() runs a candidate search string on PubMed, Scopus and Web of Science at once, returns the number of results on each platform, and saves the search strings you choose to a text file.
Fetch: manual_fetch() retrieves the references on demand, and auto_LitFetchR_setup() schedules the same retrieval at a daily, weekly or monthly frequency. Only references that were not retrieved in a previous run are returned.
Deduplicate: the references of the different platforms can be merged and deduplicated (optional, see below).

The references are written as a CSV file (default) or a RIS file (output_format = "ris"), for example for Covidence, which does not accept CSV.

Every run, manual or scheduled, is recorded in a run log (run_log.csv) with the search string, the exact query sent to each platform, the number of results, the status of each platform and any error.

Installation

Install the released version of LitFetchR from CRAN:

install.packages("LitFetchR")

Or install the development version from GitHub using devtools or remotes:

#install via devtools
install.packages("devtools")
devtools::install_github("thomasdumond/LitFetchR")

#install via remotes
install.packages("remotes")
remotes::install_github("thomasdumond/LitFetchR")

Optional packages

Deduplication (dedup = TRUE or dedup_refs()) uses the package ASySD, which is not on CRAN:

install.packages("remotes")
remotes::install_github("camaradesuk/ASySD")

Scheduling on macOS and Linux uses the package cronR:

install.packages("cronR")

On Windows, scheduling uses the Windows Task Scheduler and needs no additional package.

Tutorial

You can find all the tutorials in the Articles tab.

Requirements

This package uses APIs to access Web of Science and Scopus platforms. To enjoy the full performance of LitFetchR, request personal API keys from the platforms. For more information on API keys, you can see our tutorial Get API keys. If you are affiliated with a university we suggest contacting your local librarian to discuss the use of API keys (i.e. quota access, details of databases accessed through Web of Science).

PubMed does not require API key access, so the package can still be used to access PubMed only.

More scientific platforms and databases will be considered for inclusion in future versions of the package.

Getting help and contributing

LitFetchR is open source. Please report bugs, ask questions or suggest new features by opening an issue. Contributions to the code and the documentation are welcome by forking the repository and submitting a pull request.