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dami82 / easyPubMed

easyPubMed package for R - dev version
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fetch_pubmed_data::retmax #13

Open dandycodingpipe opened 1 year ago

dandycodingpipe commented 1 year ago

There appears to be an issue when retrieving large amounts of PubMed data.

retmax = 2000 returns "Killing the request! Something is not working. Please, try again later"

Fortunately anything under still works (e.g retmax = 1500).

Thank you.

  #1) PMID retrieval from query
  query <- 'complement system AND (pathology OR pathologies)'
  my_query <- get_pubmed_ids(query)
  print(paste(my_query$Count, "PMIDs retrieved..."))

  #2) XML Retrieval
  sample_max <- 1000
  my_abstracts_xml <- fetch_pubmed_data(my_query, retmax = sample_max)
  all_xml <- articles_to_list(my_abstracts_xml)
  print(paste(length(all_xml), "abstracts were retrieved..."))