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mdro and 1st isolate improvements

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dr. M.S. (Matthijs) Berends
2018-10-23 11:15:05 +02:00
parent 299c5bea43
commit 7997de6a6d
8 changed files with 138 additions and 95 deletions
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NEWS.md
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@@ -17,17 +17,20 @@
* Fix for `portion_*(..., as_percent = TRUE)` when minimal amount of isolates would not be met
* Added parameter `also_single_tested` for `portion_*` and `count_*` functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see `?portion`
* Using `portion_*` functions now throws a warning when total available isolate is below parameter `minimum`
* Functions `as.mo`, `as.rsi`, `as.mic` and `as.atc` will not set package name as attribute anymore
* Functions `as.mo`, `as.rsi`, `as.mic`, `as.atc` and `freq` will not set package name as attribute anymore
* Frequency tables - `freq()`:
* Check for `hms::is.hms` in frequency tables (`freq()`)
* Now prints in markdown at default in non-interactive sessions
* No longer adds the factor level column and sorts factors on count again
* Gained `na` parameter, to choose with character to print for empty values
* Support for class `difftime`
* New parameter `header` to turn it off (default when `markdown = TRUE`)
* `first_isolate` now tries to find columns to use as input when parameters are left blank
* Improvement for MDRO algorithm
* Data set `septic_patients` is now a `data.frame`, not a tibble anymore
* Check for `hms::is.hms` in frequency tables (`freq()`)
* New parameter `header` for frequency tables to turn them off (default when `markdown = TRUE`)
* Freq now prints in markdown at default in non-interactive sessions
* Freq no longer add the factor level column and sorts factors on count again
* Removed diacritics from all authors (columns `microorganisms$ref` and `microorganisms.old$ref`) to comply with CRAN policy to only allow ASCII characters
* Freq gained `na` parameter, to choose with character to print for empty values
* Fix for `mo_property` not working properly
* Fix for `EUCAST_rules` where some Streptococci would become ceftazidime R in EUCAST rule 4.5
* Support for class `difftime` in frequency tables
* 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`: