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renamed year columns to ref

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dr. M.S. (Matthijs) Berends
2018-10-01 14:44:40 +02:00
parent 3119a221e5
commit ed17db0263
16 changed files with 78 additions and 66 deletions
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NEWS.md
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@@ -6,7 +6,7 @@
* Taxonomic names: `mo_phylum`, `mo_class`, `mo_order`, `mo_family`, `mo_genus`, `mo_species`, `mo_subspecies`
* Semantic names: `mo_fullname`, `mo_shortname`
* Microbial properties: `mo_type`, `mo_gramstain`
* Author information: `mo_author`, `mo_year`
* Author and year: `mo_ref`
They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:
```r
@@ -20,11 +20,11 @@
# [1] "Streptococcus grupo A"
```
Furthermore, old taxonomic names will give a note about the current taxonomic name:
Furthermore, former taxonomic names will give a note about the current taxonomic name:
```r
mo_gramstain("Escherichia blattae")
mo_gramstain("Esc blattae")
# Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)
# [1] "Gram negative
# [1] "Gram negative"
```
* Functions `count_R`, `count_IR`, `count_I`, `count_SI` and `count_S` to selectively count resistant or susceptible isolates
* Extra function `count_df` (which works like `portion_df`) to get all counts of S, I and R of a data set with antibiotic columns, with support for grouped variables