Update ScienceDirect in R recipe

Author: MoenMi

src/r/sdirect.md

@@ -1,40 +1,72 @@
+---
+title: "ScienceDirect API in R"
+output: 
+  html_document:
+    keep_md: true
+---
+
 # ScienceDirect API in R
 
 by Michael T. Moen
 
-These recipe examples demonstrate how to use Elsevier’s [ScienceDirect API](https://dev.elsevier.com/) to retrieve full-text articles in various formats (XML, text).
+These recipe examples demonstrate how to use Elsevier’s <a href="https://dev.elsevier.com/" target="_blank">ScienceDirect API</a> to retrieve full-text articles in various formats (XML, text).
 
 *This tutorial content is intended to help facilitate academic research. Please check your institution for their Text and Data Mining or related License Agreement with Elsevier.*
 
-- **Documentation**
-  - [ScienceDirect API](https://dev.elsevier.com/)
-  - [ScienceDirect API Documentation](https://dev.elsevier.com/sd_api_spec.html)
-
-- **Terms**
-  - [ScienceDirect API Terms of Use](https://dev.elsevier.com/api_key_settings.html)
+Please see the following resources for more information on API usage:
 
-- **Data Reuse**
-  - [Elsevier Text & Data Mining](https://dev.elsevier.com/tecdoc_text_mining.html)
+- Documentation
+    - <a href="https://dev.elsevier.com/" target="_blank">ScienceDirect API</a>
+    - <a href="https://dev.elsevier.com/sd_api_spec.html" target="_blank">ScienceDirect API Documentation</a>
+- Terms\n",
+    - <a href="https://dev.elsevier.com/api_key_settings.html" target="_blank">ScienceDirect API Terms of Use</a>
+- Data Reuse
+    - <a href="https://dev.elsevier.com/tecdoc_text_mining.html" target="_blank">Elsevier Text & Data Mining</a>
 
-> **Note:** See your institution's rate limit in the [ScienceDirect API Terms of Use](https://dev.elsevier.com/api_key_settings.html).
+_**NOTE:**_ See your institution's rate limit with <a href="https://dev.elsevier.com/api_key_settings.html" target="_blank">ScienceDirect API Terms of Use</a>.
 
+*If you have copyright or other related text and data mining questions, please contact The University of Alabama Libraries or your respective library/institution.*
 
-*These recipe examples were tested on February 7, 2025.*
+*These recipe examples were tested on October 27, 2025.*
 
 ## Setup
 
 ### Import Libraries
 
-```r
+The following packages need to be installed into your environment to run the code examples in this tutorial. These packages can be installed with `install.packages()`.
+
+- <a href="https://cran.r-project.org/web/packages/httr/index.html" target="_blank">httr: Tools for Working with URLs and HTTP</a>
+
+We load the libraries used in this tutorial below:
+
+
+``` r
 library(httr)
 ```
 
 ### Import API Key
 
-An API key is required to access the ScienceDirect API. Registration is available on the [Elsevier developer portal](https://dev.elsevier.com/). The key is imported from an environment variable below:
+An API key is required for to access the ScienceDirect API. You can sign up for one at <a href="https://dev.elsevier.com/" target="_blank">Elsevier developer portal</a>.
+
+We keep our token in a `.Renviron` file that is stored in the working directory and use `Sys.getenv()` to access it. The `.Renviron` should have an entry like the one below.
 
-```r
-myAPIKey <- Sys.getenv("sciencedirect_key")
+```text
+SCIENCE_DIRECT_API_KEY="PUT_YOUR_API_KEY_HERE"
+```
+
+Below, we can test to whether the key was successfully imported.
+
+
+``` r
+if (nzchar(Sys.getenv("SCIENCE_DIRECT_API_KEY"))) {
+  print("API key successfully loaded.")
+} else {
+  warning("API key not found or is empty.")
+}
+```
+
+```
+## [1] "API key successfully loaded."
 ```
 
 ### Identifier Note
@@ -43,41 +75,51 @@ We will use DOIs as the article identifiers. See our Crossref and Scopus API tut
 
 ## 1. Retrieve full-text XML of an article
 
-```r
+
+``` r
 # For XML download
 elsevier_url <- "https://api.elsevier.com/content/article/doi/"
 doi1 <- '10.1016/j.tetlet.2017.07.080' # Example Tetrahedron Letters article
-fulltext1 <- GET(paste0(elsevier_url, doi1, "?APIKey=", myAPIKey, "&httpAccept=text/xml"))
+fulltext1 <- GET(paste0(
+  elsevier_url, doi1,
+  "?APIKey=", Sys.getenv("SCIENCE_DIRECT_API_KEY"),
+  "&httpAccept=text/xml"))
 
 # Save to file
 writeLines(content(fulltext1, "text"), "fulltext1.xml")
 ```
 
 ## 2. Retrieve plain text of an article
 
-```r
+
+``` r
 # For simplified text download
 doi2 <- '10.1016/j.tetlet.2022.153680' # Example Tetrahedron Letters article
-fulltext2 <- GET(paste0(elsevier_url, doi2, "?APIKey=", myAPIKey, "&httpAccept=text/plain"))
+fulltext2 <- GET(paste0(
+  elsevier_url, doi2,
+  "?APIKey=", Sys.getenv("SCIENCE_DIRECT_API_KEY"),
+  "&httpAccept=text/plain"))
 
 # Save to file
 writeLines(content(fulltext2, "text"), "fulltext2.txt")
 ```
 
 ## 3. Retrieve full-text in a loop
 
-```r
+
+``` r
 # Make a list of 5 DOIs for testing
 dois <- c('10.1016/j.tetlet.2018.10.031',
           '10.1016/j.tetlet.2018.10.033',
           '10.1016/j.tetlet.2018.10.034',
           '10.1016/j.tetlet.2018.10.038',
           '10.1016/j.tetlet.2018.10.041')
-```
 
-```r
 for (doi in dois) {
-  article <- GET(paste0(elsevier_url, doi, "?APIKey=", myAPIKey, "&httpAccept=text/plain"))
+  article <- GET(paste0(
+    elsevier_url, doi,
+    "?APIKey=", Sys.getenv("SCIENCE_DIRECT_API_KEY"),
+    "&httpAccept=text/plain"))
   doi_name <- gsub("/", "_", doi)
   writeLines(content(article, "text"), paste0(doi_name, "_plain_text.txt"))
   Sys.sleep(1)