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param rules for EUCAST

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dr. M.S. (Matthijs) Berends
2018-10-18 12:10:10 +02:00
parent 693f64bdbf
commit 0ef91be3ac
7 changed files with 1431 additions and 1348 deletions
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NEWS.md
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@ -5,9 +5,10 @@
#### Changed
* Big changes to the `EUCAST_rules` function:
* It now also applies rules from the EUCAST 'Breakpoint tables for bacteria', version 8.1, 2018, http://www.eucast.org/clinical_breakpoints/ (see Source of the function)
* There's better error handling when rules cannot be applied (i.e. new values could not be inserted)
* A new `verbose` parameter can be set to `TRUE` to get very specific messages about which columns and rows were affected
* Now also applies rules from the EUCAST 'Breakpoint tables for bacteria', version 8.1, 2018, http://www.eucast.org/clinical_breakpoints/ (see Source of the function)
* New parameter `rules` to specify which rules should be applied (expert rules, breakpoints, others or all)
* New parameter `verbose` which can be set to `TRUE` to get very specific messages about which columns and rows were affected
* Better error handling when rules cannot be applied (i.e. new values could not be inserted)
* The amount of affected values will now only be measured once per row/column combination
* Data set `septic_patients` now reflects these changes
* Added parameter `combine_IR` (TRUE/FALSE) to functions `portion_df` and `count_df`, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)