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breaks param, tidyr dep change, freq markdown

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dr. M.S. (Matthijs) Berends
2018-10-22 12:32:59 +02:00
parent ec15b82fd6
commit c2a93b46db
11 changed files with 86 additions and 146 deletions
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8
NEWS.md
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@@ -17,25 +17,29 @@
* 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` and `as.mic` will not set package name as attribute anymore
* Functions `as.mo`, `as.rsi`, `as.mic` and `as.atc` will not set package name as attribute anymore
* 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
* 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
* 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`:
* `"CRS"` -> *Stenotrophomonas maltophilia*
* `"CRSM"` -> *Stenotrophomonas maltophilia*
* `"MSSA"` -> *Staphylococcus aureus*
* `"MSSE"` -> *Staphylococcus epidermidis*
* Fix for `join` functions
* In `g.test`, when `sum(x)` is below 1000, suggest Fisher's Exact Test
* In `g.test`, when `sum(x)` is below 1000 or any of the expected values is below 5, Fisher's Exact Test will be suggested
* `ab_name` will try to fall back on `as.atc` when no results are found
#### Other
* New dependency on package `crayon`, to support formatted text in the console
* Dependency `tidyr` is now mandatory (went to `Import` field) since `portion_df` and `count_df` rely on it
* Updated vignettes to comply with README