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select() fix for freq

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dr. M.S. (Matthijs) Berends
2019-01-17 12:08:04 +01:00
parent 1ee710c861
commit c6c3088e9f
30 changed files with 381 additions and 230 deletions
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15
NEWS.md
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@@ -7,12 +7,12 @@
* Contains the complete manual of this package and all of its functions with an explanation of their parameters
* Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis
* Support for the upcoming [`dplyr`](https://dplyr.tidyverse.org) version 0.8.0
* Function `guess_ab_col()` to find an antibiotic column in a table
* Function `mo_failures()` to review values that could not be coerced to a valid MO code, using `as.mo()`. This latter function will now only show a maximum of 25 uncoerced values.
* Function `mo_renamed()` to get a list of all returned values from `as.mo()` that have had taxonomic renaming
* Function `age()` to calculate the (patients) age in years
* Function `age_groups()` to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.
* Function `ggplot_rsi_predict()` as well as the base R `plot()` function can now be used for resistance prediction calculated with `resistance_predict()`:
* New function `guess_ab_col()` to find an antibiotic column in a table
* New function `mo_failures()` to review values that could not be coerced to a valid MO code, using `as.mo()`. This latter function will now only show a maximum of 25 uncoerced values.
* New function `mo_renamed()` to get a list of all returned values from `as.mo()` that have had taxonomic renaming
* New function `age()` to calculate the (patients) age in years
* New function `age_groups()` to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.
* New function `ggplot_rsi_predict()` as well as the base R `plot()` function can now be used for resistance prediction calculated with `resistance_predict()`:
```r
x <- resistance_predict(septic_patients, col_ab = "amox")
plot(x)
@@ -66,7 +66,8 @@
* The new `big.mark` parameter will at default be `","` when `decimal.mark = "."` and `"."` otherwise
* Fix for header text where all observations are `NA`
* New parameter `droplevels` to exclude empty factor levels when input is a factor
* Factor levels will be in header when present in input data
* Factor levels will be in header when present in input data (maximum of 5)
* Fix for using `select()` on frequency tables
* Function `scale_y_percent()` now contains the `limits` parameter
* Automatic parameter filling for `mdro()`, `key_antibiotics()` and `eucast_rules()`
* Updated examples for resistance prediction (`resistance_predict()` function)