Answers.Body: <p>I don't program in R, but replace the last line of you code with the following and I suspect you will find it works,</p>
  
  <pre><code>for(i in seq(1,10000,1)){ recs &lt;- entrez_summary(db="pubmed", web_history=pubmed_search$web_history, retmax=100, retstart=i) cat(seq_start+99, "sequences downloaded\r") }
  </code></pre>
  
  <p><strong>Rationale</strong> I would guess <code>seq</code> is similar to the <code>linspace</code> function in Python, and put simply <code>10000 (total sample size) / 100 (the step size) = 100</code>, 100 being the number of downloads you observed. In the code above its <code>10000/1</code>. I would also suspect "step size = 1" is default, if this was correct then <code>seq(1,10000)</code> would give you your required output.</p>
  
  <p>As a random aside I do like the presence of curly brackets defining the loop, it reminds me of Perl.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-18T06:46:57.037Z
Answers.LastActivityDate: 2019-07-18T06:55:32.317Z
Answers.LastEditDate: 2019-07-18T06:55:32.317Z
Answers.UserDisplayName: M__
Body: <p>I'm trying to use rentrez package to retrieve NIH files, and ran the following code (I followed what was on the rentrez tutorial):</p>
  
  <pre><code>pubmed_search &lt;- entrez_search(db = "pubmed", 
                      term = "Case Reports[Filter] AND cardiovascular disease AND English[lang] AND 2009:2019[PDat])", 
                      retmax = 792711, 
                      use_history = TRUE)
  
  for(i in seq(1,10000,100)){   
      recs &lt;- entrez_summary(db="pubmed", 
                             web_history=pubmed_search$web_history,
                             retmax=100, 
                             retstart=i)   cat(    
  seq_start+99, "sequences downloaded\r") }
  </code></pre>
  
  <p>However, instead of the 10,000 texts I expected, I only downloaded 100 files. Could so</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-17T19:11:55.667Z
Comments.Text: Welcome to Bioinformatics.SE! It looks like you posted the question before you were done typing. No worries, just use the `edit` button to update it. Also, please indent code with 4 spaces or wrap it in triple backticks (`\`\`\``) so that it displays in a legible way.
Comments.UserDisplayName: Daniel Standage
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-08-19T07:10:42.750Z
Comments.Text: Also, include an API code in your Pubmed search script to increase the query limit.
Comments.UserDisplayName: arup
Tags: <r><entrez>
Title: rentrez to retrieve NIH files
ThreadText: # rentrez to retrieve NIH files
  
  (Asked by: username_0 on 2019-07-17)
  
  I'm trying to use rentrez package to retrieve NIH files, and ran the following code (I followed what was on the rentrez tutorial):
  
  ```
  pubmed_search <- entrez_search(db = "pubmed", 
                      term = "Case Reports[Filter] AND cardiovascular disease AND English[lang] AND 2009:2019[PDat])", 
                      retmax = 792711, 
                      use_history = TRUE)
  
  for(i in seq(1,10000,100)){   
      recs <- entrez_summary(db="pubmed", 
                             web_history=pubmed_search$web_history,
                             retmax=100, 
                             retstart=i)   cat(    
  seq_start+99, "sequences downloaded\r") }
  
  ```
  
  However, instead of the 10,000 texts I expected, I only downloaded 100 files. Could so
  
  **Tags:** r, entrez
  
  > **Comments:**
  > **username_1**: Welcome to Bioinformatics.SE! It looks like you posted the question before you were done typing. No worries, just use the `edit` button to update it. Also, please indent code with 4 spaces or wrap it in triple backticks (`\`\`\``) so that it displays in a legible way.  
  > **username_2**: Also, include an API code in your Pubmed search script to increase the query limit.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2019-07-18. Score: 1
  
  I don't program in R, but replace the last line of you code with the following and I suspect you will find it works,
  
  ```
  for(i in seq(1,10000,1)){ recs <- entrez_summary(db="pubmed", web_history=pubmed_search$web_history, retmax=100, retstart=i) cat(seq_start+99, "sequences downloaded\r") }
  
  ```
  
  **Rationale** I would guess `seq` is similar to the `linspace` function in Python, and put simply `10000 (total sample size) / 100 (the step size) = 100`, 100 being the number of downloads you observed. In the code above its `10000/1`. I would also suspect "step size = 1" is default, if this was correct then `seq(1,10000)` would give you your required output.
  
  As a random aside I do like the presence of curly brackets defining the loop, it reminds me of Perl.
  
  
  ---
  
  