1
0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 04:42:22 +02:00

(v1.2.0.9020) ab_from_text() improvement

This commit is contained in:
2020-07-01 11:23:05 +02:00
parent 329a0eb0b6
commit cc6ce0a938
11 changed files with 55 additions and 95 deletions

24
NEWS.md
View File

@ -1,19 +1,8 @@
# AMR 1.2.0.9019
# AMR 1.2.0.9020
## <small>Last updated: 01-Jul-2020</small>
### New
* Function `ab_from_text()` to retrieve antimicrobial drugs from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally:
```r
ab_from_text(c("28/03/2020 regular amoxiciliin 500mg po tds",
"15/04/2020 started on ciprofloxi-thingy and tobra today"))
#> [[1]]
#> Class <ab>
#> [1] AMX
#>
#> [[2]]
#> Class <ab>
#> [1] CIP TOB
```
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
* [Tidyverse selections](https://tidyselect.r-lib.org/reference/language.html) for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows Tidyverse selections, like `dplyr::select()` and `tidyr::pivot_longer()`:
```r
library(dplyr)
@ -22,15 +11,6 @@
example_isolates %>%
select(carbapenems())
#> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)
tibble(J01CA01 = "S") %>%
select(penicillins())
#> Selecting beta-lactams/penicillins: `J01CA01` (ampicillin)
# select an antibiotic class manually with `ab_class()`
example_isolates %>%
select(ab_class("mycobact"))
#> Selecting antimycobacterials: `RIF` (rifampicin)
```
* Added `mo_domain()` as an alias to `mo_kingdom()`
* Added function `filter_penicillins()` to filter isolates on a specific result in any column with a name in the antimicrobial 'penicillins' class (more specific: ATC subgroup *Beta-lactam antibacterials, penicillins*)