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

speed improvement as.mo, freq title

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-10-31 12:10:49 +01:00
parent 3d4c4c678b
commit 9cd4ab928a
27 changed files with 289 additions and 224 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
NEWS.md
View File

@@ -3,6 +3,7 @@
#### New
* Repository moved to GitLab: https://gitlab.com/msberends/AMR
* Function `count_all` to get all available isolates (that like all `portion_*` and `count_*` functions also supports `summarise` and `group_by`), the old `n_rsi` is now an alias of `count_all`
* 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`.
#### Changed
* Big changes to the `EUCAST_rules` function:
@@ -10,12 +11,12 @@
* New parameter `rules` to specify which rules should be applied (expert rules, breakpoints, others or all)
* New parameter `verbose` which can be set to `TRUE` to get very specific messages about which columns and rows were affected
* Better error handling when rules cannot be applied (i.e. new values could not be inserted)
* The amount of affected values will now only be measured once per row/column combination
* The number of affected values will now only be measured once per row/column combination
* Data set `septic_patients` now reflects these changes
* Tremendous speed improvement for `as.mo` (and consequently all `mo_*` functions), as empty values wil be ignored a priori
* 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)
* Fix for `portion_*(..., as_percent = TRUE)` when minimal amount of isolates would not be met
* Fix for `portion_*(..., as_percent = TRUE)` when minimal number of isolates would not be met
* Added parameter `also_single_tested` for `portion_*` and `count_*` functions to also include cases where not all antibiotics were tested but at least one of the tested antibiotics includes the target antimicribial interpretation, see `?portion`
* Using `portion_*` functions now throws a warning when total available isolate is below parameter `minimum`
* Functions `as.mo`, `as.rsi`, `as.mic`, `as.atc` and `freq` will not set package name as attribute anymore
@@ -26,6 +27,7 @@
* Gained `na` parameter, to choose with character to print for empty values
* Support for class `difftime`
* New parameter `header` to turn it off (default when `markdown = TRUE`)
* New parameter `title` to replace the automatically set title
* `first_isolate` now tries to find columns to use as input when parameters are left blank
* Improvement for MDRO algorithm
* Data set `septic_patients` is now a `data.frame`, not a tibble anymore