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Added function n_rsi

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dr. M.S. (Matthijs) Berends
2018-05-02 14:56:25 +02:00
parent e5ae7b98ac
commit c0fc82c794
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README.md
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@ -10,7 +10,7 @@ This R package contains functions to make **microbiological, epidemiological dat
With `AMR` you can also:
* Create frequency tables with the `freq` function
* Conduct AMR analysis with the `rsi` function, that can also be used with the `dplyr` package (e.g. in conjunction with `summarise`) to calculate the resistance percentages of different antibiotic columns of a table
* Conduct AMR analysis with the `rsi` function, that can also be used with the `dplyr` package (e.g. in conjunction with `summarise`) to calculate the resistance percentages (and even co-resistance) of different antibiotic columns of a table
* Predict antimicrobial resistance for the nextcoming years with the `rsi_predict` function
* Apply [EUCAST rules to isolates](http://www.eucast.org/expert_rules_and_intrinsic_resistance/) with the `EUCAST_rules` function
* Identify first isolates of every patient [using guidelines from the CLSI](https://clsi.org/standards/products/microbiology/documents/m39/) (Clinical and Laboratory Standards Institute) with the `first_isolate` function
@ -264,13 +264,16 @@ abname("J01CR02", from = "atc", to = "umcg") # "AMCL"
### Databases included in package
Datasets to work with antibiotics and bacteria properties.
```r
# Dataset with 2000 random blood culture isolates from anonymised septic patients between 2001 and 2017 in 5 Dutch hospitals
# Dataset with 2000 random blood culture isolates from anonymised
# septic patients between 2001 and 2017 in 5 Dutch hospitals
septic_patients # A tibble: 4,000 x 47
# Dataset with ATC antibiotics codes, official names, trade names and DDD's (oral and parenteral)
# Dataset with ATC antibiotics codes, official names, trade names
# and DDD's (oral and parenteral)
antibiotics # A tibble: 420 x 18
# Dataset with bacteria codes and properties like gram stain and aerobic/anaerobic
# Dataset with bacteria codes and properties like gram stain and
# aerobic/anaerobic
microorganisms # A tibble: 2,453 x 12
```