mirror of
https://github.com/msberends/AMR.git
synced 2025-07-21 01:33:25 +02:00
(v2.1.1.9269) Support 7 new languages
This commit is contained in:
48
index.md
48
index.md
@ -5,7 +5,7 @@
|
||||
|
||||
- Provides an **all-in-one solution** for antimicrobial resistance (AMR)
|
||||
data analysis in a One Health approach
|
||||
- Peer-reviewed, used in over 175 countries, available in 20 languages
|
||||
- Peer-reviewed, used in over 175 countries, available in 27 languages
|
||||
- Generates **antibiograms** - traditional, combined, syndromic, and
|
||||
even WISCA
|
||||
- Provides the **full microbiological taxonomy** of ~79 000 distinct
|
||||
@ -75,7 +75,7 @@ research at the Faculty of Medical Sciences of the [University of
|
||||
Groningen](https://www.rug.nl) and the [University Medical Center
|
||||
Groningen](https://www.umcg.nl).
|
||||
|
||||
##### Used in over 175 countries, available in 20 languages
|
||||
##### Used in over 175 countries, available in 27 languages
|
||||
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" align="right" style="max-width: 300px;" /></a>
|
||||
|
||||
@ -87,10 +87,14 @@ With the help of contributors from all corners of the world, the `AMR`
|
||||
package is available in
|
||||
<img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
English,
|
||||
<img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Czech,
|
||||
<img src="lang_ar.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Arabic,
|
||||
<img src="lang_bn.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Bengali,
|
||||
<img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Chinese,
|
||||
<img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Czech,
|
||||
<img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Danish,
|
||||
<img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
@ -103,6 +107,10 @@ French,
|
||||
German,
|
||||
<img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Greek,
|
||||
<img src="lang_hi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Hindi,
|
||||
<img src="lang_id.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Indonesian,
|
||||
<img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Italian,
|
||||
<img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
@ -119,13 +127,19 @@ Romanian,
|
||||
Russian,
|
||||
<img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Spanish,
|
||||
<img src="lang_sw.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Swahili,
|
||||
<img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Swedish,
|
||||
<img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Turkish, and
|
||||
Turkish,
|
||||
<img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Ukrainian. Antimicrobial drug (group) names and colloquial microorganism
|
||||
names are provided in these languages.
|
||||
Ukrainian,
|
||||
<img src="lang_ur.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Urdu, and
|
||||
<img src="lang_vi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;">
|
||||
Vietnamese. Antimicrobial drug (group) names and colloquial
|
||||
microorganism names are provided in these languages.
|
||||
|
||||
### Practical examples
|
||||
|
||||
@ -155,10 +169,8 @@ example_isolates %>%
|
||||
#> ℹ Using column 'mo' as input for mo_fullname()
|
||||
#> ℹ Using column 'mo' as input for mo_is_gram_negative()
|
||||
#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()
|
||||
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
|
||||
#> Phenotypes' v1.2 (2023). This note will be shown once per session.
|
||||
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023). This note will be shown once per session.
|
||||
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
#> # A tibble: 35 × 7
|
||||
#> bacteria GEN TOB AMK KAN IPM MEM
|
||||
@ -196,9 +208,9 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
|
||||
``` r
|
||||
antibiogram(example_isolates,
|
||||
antimicrobials = c(aminoglycosides(), carbapenems()))
|
||||
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
|
||||
#> ℹ 502 combinations had less than minimum = 30 results and were ignored
|
||||
```
|
||||
|
||||
| Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
|
||||
@ -221,6 +233,7 @@ yield higher empiric coverage:
|
||||
antibiogram(example_isolates,
|
||||
antimicrobials = c("TZP", "TZP+TOB", "TZP+GEN"),
|
||||
mo_transform = "gramstain")
|
||||
#> ℹ 3 combinations had less than minimum = 30 results and were ignored
|
||||
```
|
||||
|
||||
| Pathogen | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
|
||||
@ -229,7 +242,7 @@ antibiogram(example_isolates,
|
||||
| Gram-positive | 86% (82-89%,N=345) | 98% (96-98%,N=1044) | 95% (93-97%,N=550) |
|
||||
|
||||
Like many other functions in this package, `antibiogram()` comes with
|
||||
support for 20 languages that are often detected automatically based on
|
||||
support for 27 languages that are often detected automatically based on
|
||||
system language:
|
||||
|
||||
``` r
|
||||
@ -238,6 +251,7 @@ antibiogram(example_isolates,
|
||||
mo_transform = "gramstain",
|
||||
ab_transform = "name",
|
||||
language = "uk") # Ukrainian
|
||||
#> ℹ 3 combinations had less than minimum = 30 results and were ignored
|
||||
```
|
||||
|
||||
| Збудник | Гентаміцин | Тобраміцин | Ципрофлоксацин |
|
||||
@ -321,15 +335,13 @@ out <- example_isolates %>%
|
||||
# calculate AMR using resistance(), over all aminoglycosides and polymyxins:
|
||||
summarise(across(c(aminoglycosides(), polymyxins()),
|
||||
resistance))
|
||||
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
|
||||
#> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
|
||||
#> ℹ For polymyxins() using column 'COL' (colistin)
|
||||
#> Warning: There was 1 warning in `summarise()`.
|
||||
#> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
|
||||
#> ℹ In group 3: `ward = "Outpatient"`.
|
||||
#> Caused by warning:
|
||||
#> ! Introducing NA: only 23 results available for KAN in group: ward =
|
||||
#> "Outpatient" (minimum = 30).
|
||||
#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (minimum = 30).
|
||||
out
|
||||
#> # A tibble: 3 × 6
|
||||
#> ward GEN TOB AMK KAN COL
|
||||
|
||||
Reference in New Issue
Block a user