rbiorxiv"

In rbiorxiv: Client for the 'bioRxiv' API

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

About bioRxiv and medRxiv

bioRxiv and medRxiv are preprint repositories for the biological and medical sciences, respectively, both hosted by the Cold Spring Harbor Laboratory (CSHL).

Metadata of preprints from both repositories can be accessed via a singular API service hosted on bioRxiv, available at https://api.biorxiv.org. This package, rbiorxiv, provides a simple interface for interacting with this API service, to allow retrieval of metadata for bioRxiv and medRxiv preprints.

Installation

Install development version from Github

install.packages("devtools")
devtools::install_github("nicholasmfraser/rbiorxiv")

Load package

library(rbiorxiv)

Usage

The main functions in rbiorxiv generally conform to the API endpoints outlined in the API documentation (see here).

Content detail

Retrieve details of either a set of preprints deposited between two dates, or lookup a single preprint by DOI:

# Get details of preprints deposited between 2018-01-01 and 2018-01-10
# By default, only the first 100 records are returned
biorxiv_content(from = "2018-01-01", to = "2018-01-10")

# Set a limit to return more than 100 records
biorxiv_content(from = "2018-01-01", to = "2018-01-10", limit = 200)

# Or set limit as "*" to return all records
biorxiv_content(from = "2018-01-01", to = "2018-01-10", limit = "*")

# Skip the first 100 records
biorxiv_content(from = "2018-01-01", to = "2018-01-10", limit = 200, skip = 100)

# By default, data is returned in a list. Use the "format" argument to specify
# that data should be returned in "json" format or as a data frame ("df").
biorxiv_content(from = "2018-01-01", to = "2018-01-10", format = "df")

# Lookup a preprint by DOI
biorxiv_content(doi = "10.1101/833400")

The bioRxiv API currently also allows querying of details of medRxiv preprints, by supplying a "server" parameter. This can be specified as follows:

# Get details of medRxiv preprints deposited between 2020-01-01 and 2020-01-02
biorxiv_content(server = "medrxiv", from = "2020-01-01", to = "2020-01-02")

The default server parameter is always "biorxiv". Note that the following functions documented below are limited to bioRxiv only (at the time of writing).

Published article detail

Retrieve details of published articles associated with bioRxiv preprints that were published between two dates:

# Get details of all articles published between 2018-01-01 and 2018-01-10
biorxiv_published(from = "2018-01-01", to = "2018-01-10", limit = "*", format = "df")

Publisher article detail

Retrieve details of articles published by a specific publisher (specified by their doi prefix) between two dates:

# Get details of all articles published by eLife (prefix = 10.7554) between 2018-01-01 and 2018-01-10
biorxiv_publisher(prefix = "10.7554", from = "2018-01-01", to = "2018-01-10", 
                   limit = "*", format = "df")

Content summary statistics

Retrieve summary statistics for bioRxiv content (e.g. number of preprints deposited):

# Get summary statistics at a montly level
biorxiv_summary(interval = "m")

# Get summary statistics at a yearly level
biorxiv_summary(interval = "y")

Usage summary statistics

Retrieve summary statistics for usage of bioRxiv content (e.g. number of pdf downloads):

# Get usage statistics at a montly level
biorxiv_usage(interval = "m")

# Get usage statistics at a yearly level
biorxiv_usage(interval = "y")

rbiorxiv documentation built on April 2, 2021, 1:07 a.m.