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mrc-ide / epireview

https://mrc-ide.github.io/epireview/
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Lassa parameters csv file #115

Closed chloerice48 closed 1 month ago

chloerice48 commented 1 month ago

Hi! The lassa parameters csv file (epireview/inst/extdata/Lassa_parameters.csv) appears to be missing the field article_qa_score. Can you please update this file? Thank you!

chloerice48 commented 1 month ago

Also - just noticed in the lassa_articles.csv file that the article_qa_score is also not populated. Thanks for looking into this!

sangeetabhatia03 commented 1 month ago

Hi Chloe, We assign a QA score to each article, even where multiple parameters might have been extracted from an article. We have now included functionality to update QA score on the fly, like so:

lassa <- load_epidata("lassa")
articles <- assign_qa_score(lassa$articles)

articles is a 2 element list where the first element is the original data, with new columns qa_numerator, qa_denominator, and qa_score. In our analysis we sometimes found it useful to have this score also attached to the params dataset so that we could for example filter estimates based on the QA score. To achieve this, we join the updated articles data with the params data. Hope this helps! Let us know if you need more info.

chloerice48 commented 1 month ago

Ah, thanks Sangeeta! I'll make sure to do this step the next time I am loading the Lassa parameters into the GREP (WHO Collaboratory project which I believe you are very aware of!!) :) Thanks heaps!