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README.md

R Package to interface with Elsevier and Scopus APIs

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rscopus

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

Installation

You can install rscopus 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 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.

  1. Go to https://dev.elsevier.com/user/login. Login or create a free account.
  2. 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.
  3. Read and agree to the TOS if you do indeed agree.
  4. Add Elsevier_API = "API KEY GOES HERE" to ~/.Renviron file, or add export Elsevier_API=API KEY GOES HERE to 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.

A note about API keys and IP addresses

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.

Example

This is a basic example which shows you how to solve a common problem:

library(rscopus)
res = author_df(last_name = "Muschelli", first_name = "John", verbose = FALSE)
names(res)
#>  [1] "auth_order"            "affilname_1"          
#>  [3] "n_auth"                "affilname_2"          
#>  [5] "n_affils"              "citations"            
#>  [7] "journal"               "description"          
#>  [9] "title"                 "pii"                  
#> [11] "doi"                   "eid"                  
#> [13] "cover_date"            "cover_display_date"   
#> [15] "prism_url"             "dc_identifier"        
#> [17] "dc_creator"            "prism_issn"           
#> [19] "prism_eIssn"           "prism_pageRange"      
#> [21] "dc_description"        "prism_aggregationType"
#> [23] "subtype"               "authkeywords"         
#> [25] "source_id"             "first_name"           
#> [27] "last_name"             "au_id"
head(res[, c("title", "journal", "description")])
#>                                                                                                                                                                         title
#> 1                                    Feasibility of Coping Effectiveness Training for Caregivers of Children with Autism Spectrum Disorder: a Genetic Counseling Intervention
#> 2 Thrombolytic removal of intraventricular haemorrhage in treatment of severe stroke: results of the randomised, multicentre, multiregion, placebo-controlled CLEAR III trial
#> 3                                                                             PItcHPERFeCT: Primary Intracranial Hemorrhage Probability Estimation using Random Forests on CT
#> 4                                                                   ISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI
#> 5                                 Large-scale radiomic profiling of recurrent glioblastoma identifies an imaging predictor for stratifying anti-angiogenic treatment response
#> 6      Safety and efficacy of minimally invasive surgery plus alteplase in intracerebral haemorrhage evacuation (MISTIE): a randomised, controlled, open-label, phase 2 trial
#>                         journal      description
#> 1 Journal of Genetic Counseling Article in Press
#> 2                    The Lancet          Article
#> 3          NeuroImage: Clinical          Article
#> 4        Medical Image Analysis          Article
#> 5      Clinical Cancer Research          Article
#> 6          The Lancet Neurology          Article
unique(res$au_id)
#> [1] "40462056100"
unique(as.character(res$affilname_1))
#> [1] "Johns Hopkins Bloomberg School of Public Health"
#> [2] "Departments of Biostatistics"                   
#> [3] "Johns Hopkins Medical Institutions"             
#> [4] "Kennedy Krieger Institute"                      
#> [5] "The Johns Hopkins School of Medicine"