R Package to interface with Elsevier and Scopus APIs
The goal of rscopus is to provide an R Scopus Database ‘API’ Interface.
You can install rscopus from github with:
# install.packages("devtools")
devtools::install_github("muschellij2/rscopus")In order to use this package, you need an API key from https://dev.elsevier.com/sc_apis.html. You should login from your institution and go to Create API Key. You need to provide a website URL and a label, but the website can be your personal website, and agree to the terms of service.
- Go to https://dev.elsevier.com/user/login. Login or create a free account.
- Click “Create API Key”. Put in a label, such as
rscopus key. Add a website. http://example.com is fine if you do not have a site. - Read and agree to the TOS if you do indeed agree.
- Add
Elsevier_API = "API KEY GOES HERE"to~/.Renvironfile, or addexport Elsevier_API=API KEY GOES HEREto your~/.bash_profile.
Alternatively, you you can either set the API key using
rscopus::set_api_key or by options("elsevier_api_key" = api_key).
You can access the API key using rscopus::get_api_key.
You should be able to test out the API key using the interactive Scopus APIs.
The API Key is bound to a set of IP addresses, usually bound to your institution. Therefore, if you are using this for a Shiny application, you must host the Shiny application from your institution servers in some way. Also, you cannot access the Scopus API with this key if you are offsite and must VPN into the server or use a computing cluster with an institution IP.
See https://dev.elsevier.com/tecdoc_api_authentication.html
This is a basic example which shows you how to solve a common problem:
library(rscopus)
library(dplyr)
if (rscopus::is_elsevier_authorized()) {
res = author_df(last_name = "Muschelli", first_name = "John", verbose = FALSE, general = FALSE)
names(res)
head(res[, c("title", "journal", "description")])
unique(res$au_id)
unique(as.character(res$affilname_1))
all_dat = author_data(last_name = "Muschelli",
first_name = "John", verbose = FALSE, general = TRUE)
res2 = all_dat$df
res2 = res2 %>%
rename(journal = `prism:publicationName`,
title = `dc:title`,
description = `dc:description`)
head(res[, c("title", "journal", "description")])
}
#> Warning in entries_to_df(entries = entries, au_id = au_id, verbose = verbose): 'entries_to_df' is deprecated.
#> Use 'gen_entries_to_df' instead.
#> See help("Deprecated")
#> title
#> 1 Objectively Measured Physical Activity Using Wrist-Worn Accelerometers as a Predictor of Incident Alzheimer’s Disease in the UK Biobank
#> 2 Assessment of Renal Vein Stasis Index by Transesophageal Echocardiography During Cardiac Surgery: A Feasibility Study
#> 3 Occurrence of Low Cardiac Index During Normotensive Periods in Cardiac Surgery: A Prospective Cohort Study Using Continuous Noninvasive Cardiac Output Monitoring
#> 4 NHANES 2011-2014: Objective Physical Activity Is the Strongest Predictor of All-Cause Mortality
#> 5 Comparing Step Counting Algorithms for High-Resolution Wrist Accelerometry Data in NHANES 2011-2014
#> 6 Open Case Studies: Statistics and Data Science Education through Real-World Applications
#> journal
#> 1 Journals of Gerontology - Series A Biological Sciences and Medical Sciences
#> 2 Anesthesia and Analgesia
#> 3 Anesthesia and Analgesia
#> 4 Medicine and Science in Sports and Exercise
#> 5 Medicine and Science in Sports and Exercise
#> 6 Journal of Statistics and Data Science Education
#> description
#> 1 Article
#> 2 Letter
#> 3 Article
#> 4 Article
#> 5 Article
#> 6 ArticleAs per https://dev.elsevier.com/tecdoc_api_authentication.html: “Using
a proprietary token (an”Institutional Token”) created for you by our
integration support team”, so you need to contact Scopus to get one. If
you have one and it’s located in an object called token, you should be
able to use it as:
# token is from Scopus dev
hdr = inst_token_header(token)
res = author_df(last_name = "Muschelli", first_name = "John", verbose = FALSE, general = FALSE, headers = hdr)but I have not tried it extensively.