Starting value for entrez_search

[chartgerink]

Hi,

I am using the rpubmed package (latest dev version from github) to retrieve links to articles and download the HTML subsequently. To create a more stable function, I want to retrieve the ids from entrez_search() in incremental steps (e.g., 1-1000 first, then 1001-2000, etc). However, I cannot find the argument where I can specify the starting number for the returns of the search (e.g., 1001). Is there a way to specify it?—if so, what is the argument?

It is a very tiny question, but I could not find it anywhere.

Best and thanks for the awesome package,
Chris

[sckott]

Hey @chartgerink , Will get back to you asap...S

[DASpringate]

Hi @chartgerink You can pass any of the arguments in the original api to entrez_search
www.ncbi.nlm.nih.gov/books/NBK25499/#_chapter4_ESearch_

So, a retstart argument to entrez_search to give you something like:

plasticity_ids <- entrez_search("pubmed", "phenotypic plasticity", retmax = 2600, retstart = 500)$ids
Should work for you.

[chartgerink]

Thanks! I will make sure the package is cited when we try to publish our findings. 👍

[DASpringate]

On 07/10/2013 15:57, Chris Hartgerink wrote:

Thanks! I will make sure the package is cited when we try to publish
our findings. 👍

—
Reply to this email directly or view it on GitHub
#11 (comment).

Great! Let me know when you do!