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(v0.7.1.9013) guess_mo_ab speed improvement

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dr. M.S. (Matthijs) Berends
2019-07-11 13:39:18 +02:00
parent 68230d0712
commit c652c6913f
12 changed files with 227 additions and 216 deletions
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NEWS.md
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# AMR 0.7.1.9012
# AMR 0.7.1.9013
### New
* Additional way to calculate co-resistance, i.e. when using multiple antibiotics as input for `portion_*` functions or `count_*` functions. This can be used to determine the empiric susceptibily of a combination therapy. A new parameter `only_all_tested` (**which defaults to `FALSE`**) replaces the old `also_single_tested` and can be used to select one of the two methods to count isolates and calculate portions. The difference can be seen in this example table (which is also on the `portion` and `count` help pages), where the %SI is being determined:
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* Fix for using `mo_*` functions where the coercion uncertainties and failures would not be available through `mo_uncertainties()` and `mo_failures()` anymore
* Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country
* Fix for frequency tables when creating one directly on a group (using `group_by()`)
* The name of `RIF` is now Rifampicin instead of Rifampin
* The `name` of `RIF` is now Rifampicin instead of Rifampin
* The `antibiotics` data set is now sorted by name
* Using verbose mode with `eucast_rules(..., verbose = TRUE)` returns more informative and readable output
* Speed improvement for `guess_ab_col()` which is now 30 times faster for antibiotic abbreviations
# AMR 0.7.1