P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-09-07 11:29:39 +02:00
Code Releases Activity

new kingdom

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-11-09 13:11:54 +01:00
parent 9be5e0318b
commit 6b0f4ffbd4
17 changed files with 193 additions and 82 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
NEWS.md
View File

@@ -6,6 +6,7 @@
* Function `get_locale` to determine language for language-dependent output for some `mo_*` functions. This is now the default value for their `language` parameter, by which the system language will be used at default.
* Data sets `microorganismsDT`, `microorganisms.prevDT`, `microorganisms.unprevDT` and `microorganisms.oldDT` to improve the speed of `as.mo`. They are for reference only, since they are primarily for internal use of `as.mo`.
* Function `read_4D` to read from the 4D database of the MMB department of the UMCG
* Functions `mo_authors` and `mo_year` to get specific values about the scientific reference of a taxonomic entry
#### Changed
* Big changes to the `EUCAST_rules` function:
@@ -17,6 +18,7 @@
* Data set `septic_patients` now reflects these changes
* Added parameter `pipe` for piperacillin (J01CA12), also to the `MDRO` function
* Small fixes to EUCAST clinical breakpoint rules
* Added column `kingdom` to the microorganisms data set, and function `mo_kingdom` to look up values
* Tremendous speed improvement for `as.mo` (and subsequently all `mo_*` functions), as empty values wil be ignored *a priori*
* Fewer than 3 characters as input for `as.mo` will return NA
* Added parameter `combine_IR` (TRUE/FALSE) to functions `portion_df` and `count_df`, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)