P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 23:41:57 +02:00
Code Releases Activity

replaced bactid by mo

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-08-31 13:36:19 +02:00
parent 98ff131680
commit 5965d3c794
41 changed files with 786 additions and 411 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
NEWS.md
View File

@ -4,6 +4,11 @@
* Functions `count_R`, `count_IR`, `count_I`, `count_SI` and `count_S` to selectively count resistant or susceptible isolates
* Extra function `count_df` (which works like `portion_df`) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables
* Function `is.rsi.eligible` to check for columns that have valid antimicrobial results, but do not have the `rsi` class yet. Transform the columns of your raw data with: `data %>% mutate_if(is.rsi.eligible, as.rsi)`
* Functions `as.mo` and `is.mo` as replacements for `as.bactid` and `is.bactid`. These last two functions are deprecated and will be removed in a future release.
* Renamed all previous references to `bactid` to `mo`, like:
* Column names inputs of `EUCAST_rules`, `first_isolate` and `key_antibiotics`
* Column names of datasets `microorganisms` and `septic_patients`
* All old syntaxes will still work with this version, but will throw warnings
* Functions `as.atc` and `is.atc` to transform/look up antibiotic ATC codes as defined by the WHO. The existing function `guess_atc` is now an alias of `as.atc`.
* Aliases for existing function `mo_property`: `mo_aerobic`, `mo_family`, `mo_fullname`, `mo_genus`, `mo_gramstain`, `mo_gramstain_nl`, `mo_property`, `mo_species`, `mo_subspecies`, `mo_type`, `mo_type_nl`
* Function `ab_property` and its aliases: `ab_certe`, `ab_official`, `ab_official_nl`, `ab_property`, `ab_trivial_nl`, `ab_umcg`, `ab_tradenames`
@ -21,9 +26,9 @@
ab_atc(c("Bactroban", "Amoxil", "Zithromax", "Floxapen"))
# [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"
```
* Removed function `ratio` as it is not really the scope of this package
* Function `ratio` is now deprecated and will be removed in a future release, as it is not really the scope of this package
* Fix for `as.mic` for values ending in zeroes after a real number
* Huge speed improvement for `as.bactid`
* Huge speed improvement for `as.bactid` (now `as.mo`)
* Added parameters `minimum` and `as_percent` to `portion_df`
* Support for quasiquotation in the functions series `count_*` and `portions_*`, and `n_rsi`. This allows to check for more than 2 vectors or columns.
```r