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Scopus Database API Interface to R

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muschellij2/rscopus

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R Package to interface with Elsevier and Scopus APIs

CRAN statusR-CMD-check

rscopus

The goal of rscopus is to provide an R Scopus Database ‘API’ Interface.

Installation

You can installrscopus from github with:

# install.packages("devtools")devtools::install_github("muschellij2/rscopus")

Steps to get API key

In order to use this package, you need an API key fromhttps://dev.elsevier.com/sc_apis.html. You should login from yourinstitution and go to Create API Key. You need to provide a website URLand a label, but the website can be your personal website, and agree tothe terms of service.

  1. Go tohttps://dev.elsevier.com/user/login. Login or create a freeaccount.
  2. Click “Create API Key”. Put in a label, such asrscopus key. Add awebsite.http://example.com is fine if you do not have a site.
  3. Read and agree to the TOS if you do indeed agree.
  4. AddElsevier_API = "API KEY GOES HERE" to~/.Renviron file, oraddexport Elsevier_API=API KEY GOES HERE to your~/.bash_profile.

Alternatively, you you can either set the API key usingrscopus::set_api_key or byoptions("elsevier_api_key" = api_key).You can access the API key usingrscopus::get_api_key.

You should be able to test out the API key using theinteractive ScopusAPIs.

A note about API keys and IP addresses

The API Key is bound to a set of IP addresses, usually bound to yourinstitution. Therefore, if you are using this for a Shiny application,you must host the Shiny application from your institution servers insome way. Also, you cannot access the Scopus API with this key if youare offsite and must VPN into the server or use a computing cluster withan institution IP.

Seehttps://dev.elsevier.com/tecdoc_api_authentication.html

Example

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$dfres2=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     Article

Using an Institution Token

As perhttps://dev.elsevier.com/tecdoc_api_authentication.html: “Usinga proprietary token (an”Institutional Token”) created for you by ourintegration support team”, so you need to contact Scopus to get one. Ifyou have one and it’s located in an object calledtoken, you should beable to use it as:

# token is from Scopus devhdr= 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.

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