P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 00:02:38 +02:00
Code Releases Activity

(v0.7.1.9036) preserve ab/mo classes in subsetting

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-12 14:48:09 +02:00
parent 1d423cca89
commit bd252a2984
23 changed files with 237 additions and 181 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19
NEWS.md
View File

@ -1,4 +1,4 @@
# AMR 0.7.1.9035
# AMR 0.7.1.9036
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
@ -46,16 +46,13 @@
* Printed info now distinguishes between added and changes values
* Using Verbose mode (i.e. `eucast_rules(..., verbose = TRUE)`) returns more informative and readable output
* Using factors as input now adds missing factors levels when the function changes antibiotic results
* Added tibble printing support for classes `rsi`, `mic`, `ab` and `mo`. When using tibbles containing antibiotic columns, values `S` will print in green, values `I` will print in yellow and values `R` will print in red:
* Added tibble printing support for classes `rsi`, `mic`, `disk`, `ab` `mo`. When using tibbles containing antibiotic columns, values `S` will print in green, values `I` will print in yellow and values `R` will print in red. Microbial IDs (class `mo`) will emphasise on the genus and species, not on the kingdom.
```r
# (run this on your own console, as this page does not support colour printing)
tibble(mo = sample(AMR::microorganisms$fullname, 10),
drug1 = as.rsi(sample(c("S", "I", "R"), 10, replace = TRUE,
prob = c(0.6, 0.1, 0.3))),
drug2 = as.rsi(sample(c("S", "I", "R"), 10, replace = TRUE,
prob = c(0.6, 0.1, 0.3))),
drug3 = as.rsi(sample(c("S", "I", "R"), 10, replace = TRUE,
prob = c(0.6, 0.1, 0.3))))
library(dplyr)
septic_patients %>%
select(mo:AMC) %>%
as_tibble()
```
* Removed class `atc` - using `as.atc()` is now deprecated in favour of `ab_atc()` and this will return a character, not the `atc` class anymore
* Removed deprecated functions `abname()`, `ab_official()`, `atc_name()`, `atc_official()`, `atc_property()`, `atc_tradenames()`, `atc_trivial_nl()`
@ -69,8 +66,10 @@
* 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
* The `name` of `RIF` is now Rifampicin instead of Rifampin
* The `antibiotics` data set is now sorted by name and all cephalosporines now have their generation between brackets
* The `antibiotics` data set is now sorted by name and all cephalosporins now have their generation between brackets
* Speed improvement for `guess_ab_col()` which is now 30 times faster for antibiotic abbreviations
* Improved `filter_ab_class()` to be more reliable and to support 5th generation cephalosporins
* Classes `ab` and `mo` will now be preserved in any subsetting
#### Other
* Added Dr Bart Meijer, Dr Dennis Souverein and Annick Lenglet as contributors