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ggplot_rsi improvements

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dr. M.S. (Matthijs) Berends
2018-08-13 16:42:37 +02:00
parent dba06c3295
commit 59ce1eb1b1
8 changed files with 140 additions and 67 deletions
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NEWS.md
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#### New
* **BREAKING**: `rsi_df` was removed in favour of new functions `portion_R`, `portion_IR`, `portion_I`, `portion_SI` and `portion_S` to selectively calculate resistance or susceptibility. These functions are 20 to 30 times faster than the old `rsi` function. The old function still works, but is deprecated.
* New function `portion_df` to get all portions of S, I and R of a data set with antibiotic columns
* New function `portion_df` to get all portions of S, I and R of a data set with antibiotic columns, with support for grouped variables
* **BREAKING**: the methodology for determining first weighted isolates was changed. The antibiotics that are compared between isolates (call *key antibiotics*) to include more first isolates (afterwards called first *weighted* isolates) are now as follows:
* Universal: amoxicillin, amoxicillin/clavlanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole
* Gram-positive: vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampicin
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* New functions `geom_rsi`, `facet_rsi`, `scale_y_percent`, `scale_rsi_colours` and `theme_rsi`
* New wrapper function `ggplot_rsi` to apply all above functions on a data set:
* `septic_patients %>% select(tobr, gent) %>% ggplot_rsi` will show portions of S, I and R immediately in a pretty plot
* Support for grouped variables, see `?ggplot_rsi`
* Determining bacterial ID:
* New functions `as.bactid` and `is.bactid` to transform/ look up microbial ID's.
* The existing function `guess_bactid` is now an alias of `as.bactid`