function pubmed and large requests
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@kimpel-mark-w-727
Last seen 9.7 years ago
I am having problems with R blowing up (Windows error window) when trying to retrieve large amounts of data from PubMed using the function "pubmed". I had originally thought this might be due to inadequate memory, but increasing the memory allocated to R to 4 GB did not solve the problem (thank you, however, to those whose suggestions allowed me to try this). The process works well up to about 380 pubmed id's. I reviewed the NCBI policy on such requests and have been running them at night as suggested. I am nowhere near the set limit of 5,000 requests per day per user. One possibility would be to simply break up the request into smaller chunks, but for my purposes I would like just one resultant data object. I did try breaking up my request into smaller chunks, which works, but cannot figure out if it is possible to somehow merge the resultant list-objects into one. Any help you can give this struggling biologist would be most appreciated! Thanks, Mark Mark W. Kimpel MD Indiana U. School of Medicine (
PROcess PROcess • 529 views
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