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msberends / AMR

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.
https://msberends.github.io/AMR/
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set body site for SIR intepretation #96

Closed theanita1 closed 1 year ago

theanita1 commented 1 year ago

Hi Dr Matthijs

I updated to the 1.8.2.9103 as suggested, and am liking the new features, but having a problem with the new assumption of body sites:

image

My samples are not screening, but from bacteraemia. In this instance the R cut off is now at 1 (for screening) rather than at 2 (not screening)

I've already indicated that my isolates are not urine, but is there a way to indicate that they are all blood culture isolates?

Thanks

theanita1 commented 1 year ago

Further on in the same as.sir interpretation with the same dataset, the packaged assumed unspecified rather than screen (which is correct in this instance, but why did it assume screen for one and not for the other?) image

msberends commented 1 year ago

Hi,

Very good points you raise. We should have non-screen preferred over screen, but users should also be able to indicate this themselves. I'll think of a solution to allow this, great suggestion, many thanks!

msberends commented 1 year ago

For all your suggestions and package testing in the past months, we would also like to add you as a contributor to the package. Would you agree with this? There are no strings attached, it's just our 'acknowledgement' section 🙂

theanita1 commented 1 year ago

Thank you Dr Matthijs, that would be a huge honour - was worried you and the team would be concerned with all my bug finding!

msberends commented 1 year ago

Not at all!! It's great to have you filing all those bugs! It's much appreciated 😃

Can I have your first and last name for the contributors list? You can also send me a direct message on Twitter (@msberends) or mail me at m.s.berends [at] umcg.nl. Many thanks!

msberends commented 1 year ago

I added include_screening to as.sir(), which defaults to FALSE but can be set with a global option as well.