I'm trying to access Pubmed results via R using their API, but I consistently get fewer results than what the same query achieves when used with the web interface. By digging in the output I noticed that the problem lays in a different query translation between the two access methods.
I am using the rentrez package, but the results I get are the same also with other related rpackages, so I guess it's related to the API itself.
here's the code to reproduce the results:
install.packages('rentrez')
rentrez::entrez_search(db="pubmed", term = '((model OR models OR modeling OR network OR networks) AND (dissemination OR transmission OR spread OR diffusion) AND (nosocomial OR hospital OR "long-term-care" OR "long term care" OR "longterm care" OR "long-term care" OR "hospital acquired" OR "healtcare associated") AND (infection OR resistance OR resistant)) AND (2010[PDAT]:2020[PDAT])')$count
[1] 7157
The same query on https://pubmed.ncbi.nlm.nih.gov/ returns 9263 results.
Not sure if you still need this now. Just in case someone else has the same problem. I had the same issue as you did and I found something might be useful from a GitHub issue. It seems that the API service needs to be updated to match the new web service, but it's been a year now and still no promising announcement has been made by the official. An alternative is provided by the easyPubMed author. Hope this is what you were looking for.