This R script takes a list of Pubmed ID's and checks in batches whether they would appear in the results for another Pubmed search
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README.md

PubmedIntersectionCheck

This R script takes a list of Pubmed ID's and checks in batches whether they would appear in the results for another Pubmed search

Requirements

This R script uses the tidyverse, xml2 and httr libraries.

How to use

First, make an NCBI account (if you don't have one) and generate an API key.

Copy your API key into a file named api_key.txt in the project folder.

Then, copy a CSV with a column named pmid that contains a list of Pubmed ID's to be checked into the project folder. The R script checker.R will look for this script at pmids.csv, but you can change this on line 10 if you really feel like it.

Edit the file query.txt to contain the Pubmed search you are interested in. By default, it is a very long search string that returns animal studies from Hooijmans et al.

When you run the R script checker.R, it will write a new CSV with two columns: pmid and found in batches of a size specified by the batchsize variable on line 26. The pmid column will contain all the PMIDs from the original CSV, and found will be 0 or 1. 1 indicates that the PMID is not in the set of PMIDs returned by the Pubmed search in query.txt, 0 indicates that it is not.