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direct warning if failing as.mo

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dr. M.S. (Matthijs) Berends
2019-01-12 16:45:20 +01:00
parent 5aad26035c
commit 3661df7365
3 changed files with 8 additions and 8 deletions
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8
NEWS.md
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@@ -6,17 +6,17 @@
* New website: https://msberends.gitlab.io/AMR (built with the great [`pkgdown`](https://pkgdown.r-lib.org/))
* 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 [`dplyr`](https://dplyr.tidyverse.org) version 0.8.0
* Function `guess_ab_col` to find an antibiotic column in a table
* 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.
* Functions `filter_first_isolate()` and `filter_first_weighted_isolate()` to shorten and fasten filtering on data sets with antimicrobial results, e.g.:
```r
septic_patients %>% filter_first_isolate()
septic_patients %>% filter_first_isolate(...)
# or
filter_first_isolate(septic_patients)
filter_first_isolate(septic_patients, ...)
```
is equal to:
```r