Custom AMR rules to expand EUCAST rules

[msberends]

Work on a new function custom_eucast_rules(), which output can be used in eucast_rules() to expand its capabilities with organisation- or analysis-specific rules.

This would also be a more durable solution to cases like #28, #19 and #25

[msberends]

Could be implemented in a similar way custom MDRO guideline can be set #23):

It basically comes down to this:

# set your own specific rules like you would in dplyr::case_when():
my_hospital_rules <- custom_mdro_guideline(CIP == "R" & age > 60 & is_isolated == TRUE ~ "Modified BRMO 1",
                                           AMX == "R" & age > 90 & is_isolated == TRUE ~ "Modified BRMO 2")

# and run them, by setting the custom rules as the `guidelines` parameter:
your_data %>%
  mutate(BRMO = mdro(guideline = my_hospital_rules))

[jukkiebah]

hai

bit confused. am I correct in assuming that now in amr 1.6 all group 2 Enterobacterales
will be set to 2GCR based on the eucast rules included in version 3.2.
And that 3GCR will be set if you use the argument in eucast_rules()
and that if you want to change the penicillins you have to use the custom MDRO settings?

[msberends]

that now in amr 1.6 all group 2 Enterobacterales
will be set to 2GCR based on the eucast rules included in version 3.2

Yes!

And that 3GCR will be set if you use the argument in eucast_rules()

Yes!

and that if you want to change the penicillins you have to use the custom MDRO settings?

Not in the current version, this is not yet implemented. Will be included in a next version! (and will not be called something like MDRO to prevent confusion)

In other words, eucast_rules() strictly follows the EUCAST rules, including rule 3/4 in EUCAST Expert Rules v3.2 to correct for ampC. Any manual change to the rules can be set in the next version.

[msberends]

This is now implemented in the master branch, so will be included in the next release! See here for the manual about how to work with it: https://msberends.github.io/AMR/reference/custom_eucast_rules.html

To test it:

# install.packages("remotes") # if you haven't already
remotes::install_github("msberends/AMR")

[msberends]

Fix released to official R repository

Just a small notice: we released a new software version, containing the fix to this issue. Please update your version using either the user interface of your software, or by running:

install.packages("AMR")