P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 16:42:10 +02:00
Code Releases Activity

(v1.2.0.9035) as.mo() speed improvement

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-07-22 10:24:23 +02:00
parent 6ab468362d
commit 09fba38ea6
37 changed files with 174 additions and 441 deletions
Download Patch File Download Diff File Expand all files Collapse all files

11
NEWS.md
View File

@ -1,5 +1,5 @@
# AMR 1.2.0.9034
## <small>Last updated: 13-Jul-2020</small>
# AMR 1.2.0.9035
## <small>Last updated: 22 July 2020</small>
### New
* 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
@ -19,8 +19,11 @@
* Added Monuril as trade name for fosfomycin
### Changed
* Big speed improvement for using any function on microorganism codes from earlier package versions (prior to `AMR` v1.2.0), such as `as.mo()`, `mo_name()`, `first_isolate()`, `eucast_rules()`, `mdro()`, etc.
As a consequence, very old microbial codes (from `AMR` v0.5.0 and lower) **are not supported anymore**. Use `as.mo()` on your microorganism names or codes to transform them to current abbreviations used in this package.
* Improvements for `susceptibility()` and `resistance()` and all `count_*()`, `proportion_*()` functions:
* 95% speed improvement (!) by using other base R functions for calculation
* 95% speed improvement by using other base R functions for calculation
* Using unexisting columns wil now return an error instead of dropping them silently
* Using variables for column names (as well as selectors like `dplyr::all_of()`) now works again
* Improvements for `as.ab()`:
@ -33,7 +36,7 @@
* Fixed a bug for using grouped versions of `rsi_df()`, `proportion_df()` and `count_df()`, and fixed a bug where not all different antimicrobial results were added as rows
* Improved auto-determination for columns of types `<mo>` and `<Date>`
* Fixed a bug in `bug_drug_combinations()` for when only one antibiotic was in the input data
* Changed the summary for class `<mo>`, to highlight the %SI vs. %R
* Changed the summary for class `<rsi>`, to highlight the %SI vs. %R
* Improved error handling, giving more useful info when functions return an error
* Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
* Speed improvement for `mdro()` and `filter_ab_class()`