Merge pull request #176 from UA-Libraries-Research-Data-Services/add-rmd-button

Add RMarkdown button to R tutorials

Author: dachambers

rmarkdown/arxiv.Rmd

@@ -15,6 +15,15 @@ knitr::opts_chunk$set(
 
 by Adam M. Nguyen and Michael T. Moen
 
+<div class="rmd-btn-wrapper">
+  <a class="rmd-btn"
+     href="https://github.com/UA-Libraries-Research-Data-Services/UALIB_ScholarlyAPI_Cookbook/blob/main/rmarkdown/arxiv.Rmd"
+     target="_blank"
+     rel="noreferrer">
+    View RMarkdown File
+  </a>
+</div>
+
 Hosted and maintained by Cornell University, arXiv is an open-access and free distribution service containing nearly 2.5 million scholarly articles in fields including physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering and systems science and economics at the time of writing. In this tutorial we will introduce how to use the API with some examples, but for larger bulk downloads of data from arXiv, we recommend <a href="https://www.kaggle.com/datasets/Cornell-University/arxiv/data" target="_blank">Kaggle's arXiv Dataset</a>, which is updated monthly with the full arXiv data set and metadata.
 
 Please see the following resources for more information on API usage:

rmarkdown/casc.Rmd

@@ -16,6 +16,15 @@ knitr::opts_chunk$set(
 
 by Adam M. Nguyen and Michael T. Moen
 
+<div class="rmd-btn-wrapper">
+  <a class="rmd-btn"
+     href="https://github.com/UA-Libraries-Research-Data-Services/UALIB_ScholarlyAPI_Cookbook/blob/main/rmarkdown/casc.Rmd"
+     target="_blank"
+     rel="noreferrer">
+    View RMarkdown File
+  </a>
+</div>
+
 The CAS Common Chemistry API provides programmatic access to a curated subset, offering information on nearly 500,000 chemical substances.
 
 Please see the following resources for more information on API usage:

rmarkdown/chronam.Rmd

@@ -15,6 +15,15 @@ knitr::opts_chunk$set(
 
 by Michael T. Moen, Cyrus Gomes, Adam M. Nguyen, and Vincent F. Scalfani
 
+<div class="rmd-btn-wrapper">
+  <a class="rmd-btn"
+     href="https://github.com/UA-Libraries-Research-Data-Services/UALIB_ScholarlyAPI_Cookbook/blob/main/rmarkdown/chronam.Rmd"
+     target="_blank"
+     rel="noreferrer">
+    View RMarkdown File
+  </a>
+</div>
+
 The Library of Congress (loc\.gov) API provides programmatic access to Chronicling America, a vast collection of historic American newspapers, and other resources, enabling researchers and developers to search, retrieve, and analyze digitized newspaper pages and metadata.
 
 Please see the following resources for more information on API usage:

rmarkdown/college-scorecard.Rmd

@@ -15,6 +15,15 @@ knitr::opts_chunk$set(
 
 by Michael T. Moen
 
+<div class="rmd-btn-wrapper">
+  <a class="rmd-btn"
+     href="https://github.com/UA-Libraries-Research-Data-Services/UALIB_ScholarlyAPI_Cookbook/blob/main/rmarkdown/college-scorecard.Rmd"
+     target="_blank"
+     rel="noreferrer">
+    View RMarkdown File
+  </a>
+</div>
+
 The College Scorecard API is an online tool hosted by the U.S. Department of Education that contains data concerning higher education institutions.
 
 Please see the following resources for more information on API usage:

rmarkdown/crossref.Rmd

@@ -15,6 +15,15 @@ knitr::opts_chunk$set(
 
 by Michael T. Moen, Cyrus Gomes, Vincent F. Scalfani, and Adam M. Nguyen
 
+<div class="rmd-btn-wrapper">
+  <a class="rmd-btn"
+     href="https://github.com/UA-Libraries-Research-Data-Services/UALIB_ScholarlyAPI_Cookbook/blob/main/rmarkdown/crossref.Rmd"
+     target="_blank"
+     rel="noreferrer">
+    View RMarkdown File
+  </a>
+</div>
+
 The Crossref API provides metadata about publications, including articles, books, and conference proceedings. This metadata spans items such as author details, journal details, references, and DOIs (Digital Object Identifiers). Working with Crossref allows for programmatic access to bibliographic information and can streamline large-scale metadata retrieval.
 
 Please see the following resources for more information on API usage:

rmarkdown/pubchem.Rmd

@@ -15,6 +15,15 @@ knitr::opts_chunk$set(
 
 by Vishank Patel, Adam M. Nguyen, and Michael T. Moen
 
+<div class="rmd-btn-wrapper">
+  <a class="rmd-btn"
+     href="https://github.com/UA-Libraries-Research-Data-Services/UALIB_ScholarlyAPI_Cookbook/blob/main/rmarkdown/pubchem.Rmd"
+     target="_blank"
+     rel="noreferrer">
+    View RMarkdown File
+  </a>
+</div>
+
 PubChem provides programmatic access to chemical data and bioactivity information from the National Center for Biotechnology Information (NCBI), enabling efficient retrieval and analysis of chemical structures, identifiers, properties, and associated biological activities.
 
 Please see the following resources for more information on API usage:

rmarkdown/pubmed.Rmd

@@ -15,6 +15,15 @@ knitr::opts_chunk$set(
 
 by Michael T. Moen and Adam M. Nguyen
 
+<div class="rmd-btn-wrapper">
+  <a class="rmd-btn"
+     href="https://github.com/UA-Libraries-Research-Data-Services/UALIB_ScholarlyAPI_Cookbook/blob/main/rmarkdown/pubmed.Rmd"
+     target="_blank"
+     rel="noreferrer">
+    View RMarkdown File
+  </a>
+</div>
+
 The PubMed API, part of NCBI's Entrez Programming Utilities (E-utilities), provides programmatic access to biomedical literature from the PubMed database, enabling retrieval of bibliographic data.
 
 Please see the following resources for more information on API usage:

rmarkdown/sage.Rmd

@@ -15,6 +15,15 @@ knitr::opts_chunk$set(
 
 by Michael T. Moen
 
+<div class="rmd-btn-wrapper">
+  <a class="rmd-btn"
+     href="https://github.com/UA-Libraries-Research-Data-Services/UALIB_ScholarlyAPI_Cookbook/blob/main/rmarkdown/sage.Rmd"
+     target="_blank"
+     rel="noreferrer">
+    View RMarkdown File
+  </a>
+</div>
+
 Sage Journals allow downloading of articles for which you have legitimate access (e.g. open access articles and those included in your institution's subscription) for non-commercial text and data mining (see restrictions in terms below). Access to text and data mining with Sage resources requires prior approval. Contact UA Libraries or your institution to check their agreement and enable access. Please see the following resources below for more information on Sage text and data mining, API usage, and policies/terms:
 
 *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 Sage Journals.*
@@ -28,7 +37,7 @@ Sage Journals allow downloading of articles for which you have legitimate access
 - Data Reuse
     - <a href="https://www.sagepub.com/tdm-ai-policy" target="_blank">Sage Policy on Text and Data Mining (TDM) and Artificial Intelligence (AI)</a>
 
-*This recipe uses the CrossRef API to obtain the full-text URLs of the articles, as recommended in <a href="https://journals.sagepub.com/page/policies/text-and-data-mining" target="_blank">Sage's Text and Data Mining overview</a>. For more information on usage for this API, please see our <a href="https://ua-libraries-research-data-services.github.io/UALIB_ScholarlyAPI_Cookbook/src/overview/crossref.html" target="_blank">CrossRef cookbook tutorials</a> and the <a href="https://www.crossref.org/documentation/retrieve-metadata/rest-api/text-and-data-mining-for-researchers/" target="_blank">text and data mining for researchers page of CrossRef's API documentation</a>.*
+*This recipe uses the CrossRef API to obtain the full-text URLs of the articles, as recommended in <a href="https://journals.sagepub.com/page/policies/text-and-data-mining" target="_blank">Sage's Text and Data Mining overview</a>. For more information on usage for this API, please see our <a href="https://ua-libraries-research-data-services.github.io/UALIB_ScholarlyAPI_Cookbook/overview/crossref.html" target="_blank">CrossRef cookbook tutorials</a> and the <a href="https://www.crossref.org/documentation/retrieve-metadata/rest-api/text-and-data-mining-for-researchers/" target="_blank">text and data mining for researchers page of CrossRef's API documentation</a>.*
 
 **_NOTE:_** Sage Journals limits downloads to a maximum of 1 request every 6 seconds Monday to Friday from midnight to noon in the "America/Los_Angeles" timezone, and 1 request every 2 seconds outside of this time slot.
 
@@ -40,8 +49,8 @@ Sage Journals allow downloading of articles for which you have legitimate access
 
 The following external libraries need to be installed into your environment to run the code examples in this tutorial:
 
-- <a href="https://cran.r-project.org/package=httr" target="_blank">httr</a>
-- <a href="https://cran.r-project.org/package=jsonlite" target="_blank">jsonlite</a>
+- <a href="https://cran.r-project.org/web/packages/httr/index.html" target="_blank">httr: Tools for Working with URLs and HTTP</a>
+- <a href="https://cran.r-project.org/web/packages/jsonlite/index.html" target="_blank">jsonlite: A Simple and Robust JSON Parser and Generator for R</a>
 
 We load the libraries used in this tutorial below:
 

rmarkdown/sdirect.Rmd

@@ -15,6 +15,15 @@ knitr::opts_chunk$set(
 
 by Michael T. Moen
 
+<div class="rmd-btn-wrapper">
+  <a class="rmd-btn"
+     href="https://github.com/UA-Libraries-Research-Data-Services/UALIB_ScholarlyAPI_Cookbook/blob/main/rmarkdown/sdirect.Rmd"
+     target="_blank"
+     rel="noreferrer">
+    View RMarkdown File
+  </a>
+</div>
+
 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.*
@@ -34,7 +43,7 @@ _**NOTE:**_ See your institution's rate limit with <a href="https://dev.elsevier
 
 *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 March 23, 2026.*
+*These recipe examples were tested on April 7, 2026.*
 
 ## Setup
 

rmarkdown/sec-edgar.Rmd

@@ -15,6 +15,15 @@ knitr::opts_chunk$set(
 
 by Adam M. Nguyen and Michael T. Moen
 
+<div class="rmd-btn-wrapper">
+  <a class="rmd-btn"
+     href="https://github.com/UA-Libraries-Research-Data-Services/UALIB_ScholarlyAPI_Cookbook/blob/main/rmarkdown/sec-edgar.Rmd"
+     target="_blank"
+     rel="noreferrer">
+    View RMarkdown File
+  </a>
+</div>
+
 The U.S. Securities and Exchange Commission (SEC) allows free public access to documents filed by publicly traded companies in the Electronic Data Gathering, Analysis, and Retrieval (EDGAR) system.
 
 Please see the following resources for more information on API usage: