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MDRO update

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dr. M.S. (Matthijs) Berends
2018-11-16 20:50:50 +01:00
parent fab64e6728
commit 4fcc2b409a
10 changed files with 207 additions and 186 deletions
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NEWS.md
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@@ -9,14 +9,16 @@
* Functions `mo_authors` and `mo_year` to get specific values about the scientific reference of a taxonomic entry
#### Changed
* Big changes to the `EUCAST_rules` function:
* Functions `MDRO`, `BRMO`, `MRGN` and `EUCAST_exceptional_phenotypes` were renamed to `mdro`, `brmo`, `mrgn` and `eucast_exceptional_phenotypes`
* `EUCAST_rules` was renamed to `eucast_rules`, the old function still exists as a deprecated function
* Big changes to the `eucast_rules` function:
* 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 number of affected values will now only be measured once per row/column combination
* Data set `septic_patients` now reflects these changes
* Added parameter `pipe` for piperacillin (J01CA12), also to the `MDRO` function
* Added parameter `pipe` for piperacillin (J01CA12), also to the `mdro` function
* Small fixes to EUCAST clinical breakpoint rules
* Added column `kingdom` to the microorganisms data set, and function `mo_kingdom` to look up values
* Tremendous speed improvement for `as.mo` (and subsequently all `mo_*` functions), as empty values wil be ignored *a priori*
@@ -41,11 +43,11 @@
* New parameter `header` to turn it off (default when `markdown = TRUE`)
* New parameter `title` to replace the automatically set title
* `first_isolate` now tries to find columns to use as input when parameters are left blank
* Improvement for MDRO algorithm
* Improvement for MDRO algorithm (function `mdro`)
* Data set `septic_patients` is now a `data.frame`, not a tibble anymore
* Removed diacritics from all authors (columns `microorganisms$ref` and `microorganisms.old$ref`) to comply with CRAN policy to only allow ASCII characters
* Fix for `mo_property` not working properly
* Fix for `EUCAST_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5
* Fix for `eucast_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5
* Support for named vectors of class `mo`, useful for `top_freq()`
* `ggplot_rsi` and `scale_y_percent` have `breaks` parameter
* AI improvements for `as.mo`: