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Code Releases Activity

(v0.7.1.9081) bug_drug fixes

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dr. M.S. (Matthijs) Berends
2019-09-23 13:53:50 +02:00
parent 66d405ff57
commit 64d9829030
26 changed files with 622 additions and 505 deletions
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NEWS.md
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# AMR 0.7.1.9080
<small>Last updated: 22-Sep-2019</small>
# AMR 0.7.1.9081
<small>Last updated: 23-Sep-2019</small>
### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
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* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)), since creating frequency tables actually does not fit the scope of this package. The `freq()` function still works, since it is re-exported from the `clean` package (which will be installed automatically upon updating this `AMR` package).
### New
* Function `bug_drug_combinations()` to quickly get a `data.frame` with the antimicrobial resistance of any bug-drug combination in a data set:
* Function `bug_drug_combinations()` to quickly get a `data.frame` with the antimicrobial resistance of any bug-drug combination in a data set. The columns with microorganism codes is guessed automatically and its input is transformed with `mo_shortname()` at default:
```r
x <- bug_drug_combinations(example_isolates)
x
# NOTE: Using column `mo` as input for `col_mo`.
#> ab mo S I R total
#> 1 AMC B_ESCHR_COLI 332 74 61 467
#> 2 AMC B_KLBSL_PNMN 49 3 6 58
#> 3 AMC B_PROTS_MRBL 28 7 1 36
#> 4 AMC B_PSDMN_AERG 0 0 30 30
#> 5 AMC B_STPHY_AURS 234 0 1 235
x[1:5, ]
#> ab mo S I R total
#> 1 AMC CoNS 178 0 132 310
#> 2 AMC E. coli 332 74 61 467
#> 3 AMC K. pneumoniae 49 3 6 58
#> 4 AMC P. aeruginosa 0 0 30 30
#> 5 AMC P. mirabilis 28 7 1 36
# change the transformation with the FUN argument to anything you like:
x <- bug_drug_combinations(example_isolates, FUN = mo_gramstain)
# NOTE: Using column `mo` as input for `col_mo`.
x[1:4, ]
#> ab mo S I R total
#> 1 AMC Gram-negative 469 89 174 732
#> 2 AMC Gram-positive 873 2 272 1147
#> 3 AMK Gram-negative 251 0 2 253
#> 4 AMK Gram-positive 0 0 100 100
```
You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R `format()` function:
```r
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* Added support for *Blastocystis*
* Added support for 5,000 new fungi
* Added support for unknown yeasts and fungi
* Changed most microorganism IDs to improve readability. **IMPORTANT:** Because of these changes, the microorganism IDs have been changed to a slightly different format. Old microorganism IDs are still supported, but support will be dropped in a future version. Use `as.mo()` on your old codes to transform them to the new format.
* Changed most microorganism IDs to improve readability. For example, the old code `B_ENTRC_FAE` could have been both *E. faecalis* and *E. faecium*. Its new code is `B_ENTRC_FCLS` and *E. faecium* has become `B_ENTRC_FACM`. Also, the Latin character æ (ae) is now preserved at the start of each genus and species abbreviation. For example, the old code for *Aerococcus urinae* was `B_ARCCC_NAE`. This is now `B_AERCC_URIN`.
**IMPORTANT:** Old microorganism IDs are still supported, but support will be dropped in a future version. Use `as.mo()` on your old codes to transform them to the new format. Using functions from the `mo_*` family (like `mo_name()` and `mo_gramstain()`) on old codes, will throw a warning.
* Renamed data set `septic_patients` to `example_isolates`
* Function `eucast_rules()`:
* Fixed a bug for *Yersinia pseudotuberculosis*