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(v1.5.0.9041) SNOMED update

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dr. M.S. (Matthijs) Berends
2021-03-11 21:42:30 +01:00
parent 8d6ceb6a15
commit 4e0a9533ad
65 changed files with 86943 additions and 67626 deletions
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NEWS.md
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@@ -1,5 +1,5 @@
# AMR 1.5.0.9040
## <small>Last updated: 8 March 2021</small>
# AMR 1.5.0.9041
## <small>Last updated: 11 March 2021</small>
### New
* Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the `eucast_rules()` function and in `as.rsi()` to interpret MIC and disk diffusion values. This is now the default guideline in this package.
@@ -43,6 +43,20 @@
#> [1] "Hongos" "Levaduras"
```
* Added Pretomanid (PMD, J04AK08) to the `antibiotics` data set
* MIC values (see `as.mic()`) can now be used in any mathematical processing, such as usage inside functions `min()`, `max()`, `range()`, and with binary operators (`+`, `-`, etc.). This allows for easy distribution analysis and fast filtering on MIC values:
```r
x <- random_mic(10)
x
#> Class <mic>
#> [1] 128 0.5 2 0.125 64 0.25 >=256 8 16 4
x[x > 4]
#> Class <mic>
#> [1] 128 64 >=256 8 16
range(x)
#> [1] 0.125 256.000
range(log2(x))
#> [1] -3 8
```
### Changed
* Updated the bacterial taxonomy to 3 March 2021 (using [LSPN](https://lpsn.dsmz.de))
@@ -53,19 +67,10 @@
* All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)
* Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see `translate`)
* Plotting is now possible with base R using `plot()` and with ggplot2 using `ggplot()` on any vector of MIC and disk diffusion values
* Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the `microorganisms` data set
* `is.rsi()` and `is.rsi.eligible()` now return a vector of `TRUE`/`FALSE` when the input is a data set, by iterating over all columns
* Using functions without setting a data set (e.g., `mo_is_gram_negative()`, `mo_is_gram_positive()`, `mo_is_intrinsic_resistant()`, `first_isolate()`, `mdro()`) now work with `dplyr`s `group_by()` again
* `first_isolate()` can be used with `group_by()` (also when using a dot `.` as input for the data) and now returns the names of the groups
* MIC values (see `as.mic()`) can now be used in any mathematical processing, such as usage inside functions `min()`, `max()`, `range()`, and with binary operators (+, -, etc.). This allows easy distribution analysis and fast filtering on MIC values:
```r
x <- random_mic(10)
x
#> Class <mic>
#> [1] 0.5 64 64 128 0.125 4 0.5 0.0625 0.0625 0.125
x[x > 4]
#> Class <mic>
#> [1] 64 64 128
```
* Updated the data set `microorganisms.codes` (which contains popular LIS and WHONET codes for microorganisms) for some species of *Mycobacterium* that previously incorrectly returned *M. africanum*
* WHONET code `"PNV"` will now correctly be interpreted as `PHN`, the antibiotic code for phenoxymethylpenicillin ('peni V')
* Fix for verbose output of `mdro(..., verbose = TRUE)` for German guideline (3MGRN and 4MGRN) and Dutch guideline (BRMO, only *P. aeruginosa*)