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(v0.7.1.9076) mo codes

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dr. M.S. (Matthijs) Berends
2019-09-20 12:33:05 +02:00
parent e2aa4f996b
commit 3596adb295
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19
NEWS.md
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# AMR 0.7.1.9075
<small>Last updated: 18-Sep-2019</small>
# AMR 0.7.1.9076
<small>Last updated: 20-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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x <- as.mo("E. coli")
x[1] <- "testvalue"
#> Warning message:
#> invalid microbial code, NA generated
#> invalid microorganism code, NA generated
```
This is important, because a value like `"testvalue"` could never be understood by e.g. `mo_name()`, although the class would suggest a valid microbial code.
* 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).
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```r
x <- bug_drug_combinations(example_isolates)
x
#> ab mo S I R total
#> 1 AMC B_ESCHR_COL 332 74 61 467
#> 2 AMC B_KLBSL_PNE 49 3 6 58
#> 3 AMC B_PROTS_MIR 28 7 1 36
#> 4 AMC B_PSDMN_AER 0 0 30 30
#> 5 AMC B_STPHY_AUR 234 0 1 235
# 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
```
You can format this to a printable format, ready for reporting or exporting to e.g. Excel with the base R `format()` function:
```r