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support groups for portion_df, update README

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dr. M.S. (Matthijs) Berends
2018-08-12 22:34:03 +02:00
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README.md
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@@ -24,6 +24,19 @@ Erwin E.A. Hassing<sup>2</sup>,
<a href="http://www.eurhealth-1health.eu"><img src="man/figures/logo_eh1h.png" height="60px"></a>
<a href="http://www.eurhealth-1health.eu"><img src="man/figures/logo_interreg.png" height="60px"></a>
## Contents
* [Why this package?](#why-this-package)
* [How to get it?](#how-to-get-it)
* [Install from CRAN](#install-from-cran)
* [Install from GitHub](#install-from-github)
* [How to use it?](#how-to-use-it)
* [New classes](#new-classes)
* [Overwrite/force resistance based on EUCAST rules](#overwriteforce-resistance-based-on-eucast-rules)
* [Other (microbial) epidemiological functions](#other-microbial-epidemiological-functions)
* [Frequency tables](#frequency-tables)
* [Data sets included in package](#data-sets-included-in-package)
* [Copyright](#copyright)
## Why this package?
This R package was intended to make microbial epidemiology easier. Most functions contain extensive help pages to get started.
@@ -50,12 +63,12 @@ And it contains:
With the `MDRO` function (abbreviation of Multi Drug Resistant Organisms), you can check your isolates for exceptional resistance with country-specific guidelines or EUCAST rules. Currently guidelines for Germany and the Netherlands are supported. Please suggest addition of your own country here: [https://github.com/msberends/AMR/issues/new](https://github.com/msberends/AMR/issues/new?title=New%20guideline%20for%20MDRO&body=%3C--%20Please%20add%20your%20country%20code,%20guideline%20name,%20version%20and%20source%20below%20and%20remove%20this%20line--%3E).
#### Read all changes and new functions in [NEWS.md](NEWS.md).
**Read all changes and new functions in [NEWS.md](NEWS.md).**
## How to get it?
This package [is published on CRAN](http://cran.r-project.org/package=AMR), the official R network.
### Install from CRAN (recommended)
### Install from CRAN
[![CRAN_Badge](https://img.shields.io/cran/v/AMR.svg?label=CRAN&colorB=3679BC)](http://cran.r-project.org/package=AMR) [![CRAN_Downloads](https://cranlogs.r-pkg.org/badges/grand-total/AMR)](http://cran.r-project.org/package=AMR)
(Note: Downloads measured only by [cran.rstudio.com](https://cran.rstudio.com/package=AMR), this excludes e.g. the official [cran.r-project.org](https://cran.r-project.org/package=AMR))
@@ -67,7 +80,7 @@ This package [is published on CRAN](http://cran.r-project.org/package=AMR), the
- <img src="https://cran.r-project.org/favicon.ico" alt="R favicon" height="20px"> Install in R directly:
- `install.packages("AMR")`
### Install from GitHub (latest development version)
### Install from GitHub
[![Travis_Build](https://travis-ci.org/msberends/AMR.svg?branch=master)](https://travis-ci.org/msberends/AMR)
[![Since_Release](https://img.shields.io/github/commits-since/msberends/AMR/latest.svg?colorB=3679BC)](https://github.com/msberends/AMR/commits/master)
[![Last_Commit](https://img.shields.io/github/last-commit/msberends/AMR.svg)](https://github.com/msberends/AMR/commits/master)
@@ -86,6 +99,85 @@ library(AMR)
# For a list of functions:
help(package = "AMR")
```
### New classes
This package contains two new S3 classes: `mic` for MIC values (e.g. from Vitek or Phoenix) and `rsi` for antimicrobial drug interpretations (i.e. S, I and R). Both are actually ordered factors under the hood (an MIC of `2` being higher than `<=1` but lower than `>=32`, and for class `rsi` factors are ordered as `S < I < R`).
Both classes have extensions for existing generic functions like `print`, `summary` and `plot`.
These functions also try to coerce valid values.
#### RSI
The `septic_patients` data set comes with antimicrobial results of more than 40 different drugs. For example, columns `amox` and `cipr` contain results of amoxicillin and ciprofloxacin, respectively.
```r
summary(septic_patients[, c("amox", "cipr")])
# amox cipr
# Mode :rsi Mode :rsi
# <NA> :1002 <NA> :596
# Sum S :336 Sum S :1108
# Sum IR:662 Sum IR:296
# -Sum R:659 -Sum R:227
# -Sum I:3 -Sum I:69
```
You can use the `plot` function from base R:
```r
plot(septic_patients$cipr)
```
![example_1_rsi](man/figures/rsi_example1.png)
Or use the `ggplot2` and `dplyr` packages to create more appealing plots:
```r
library(dplyr)
library(ggplot2)
septic_patients %>%
select(amox, cipr) %>%
ggplot_rsi()
```
![example_2_rsi](man/figures/rsi_example2.png)
```r
septic_patients %>%
select(amox, cipr) %>%
ggplot_rsi(x = "Interpretation", facet = "Antibiotic")
```
![example_3_rsi](man/figures/rsi_example3.png)
It also supports grouping variables. Let's say we want to compare resistance of these antibiotics between hospitals A to D (variable `hospital_id`):
```r
septic_patients %>%
select(hospital_id, amox, cipr) %>%
group_by(hospital_id) %>%
ggplot_rsi() + # start adding ggplot elements here with `+`
facet_grid("hospital_id") + # splitting the plots on our grouping variable
labs(title = "AMR of Amoxicillin And Ciprofloxacine Per Hospital")
```
![example_4_rsi](man/figures/rsi_example4.png)
You could use this to group on anything in your plots: Gram stain, age (group), genus, geographic location, et cetera.
#### MIC
```r
# Transform values to new class
mic_data <- as.mic(c(">=32", "1.0", "8", "<=0.128", "8", "16", "16"))
summary(mic_data)
# Mode:mic
# <NA>:0
# Min.:<=0.128
# Max.:>=32
plot(mic_data)
```
![example_mic](man/figures/mic_example.png)
### Overwrite/force resistance based on EUCAST rules
This is also called *interpretive reading*.
```r
@@ -132,69 +224,12 @@ guess_bactid("VISA") # Vancomycin Intermediate S. aureus
guess_bactid("VRSA") # Vancomycin Resistant S. aureus
```
### New classes
This package contains two new S3 classes: `mic` for MIC values (e.g. from Vitek or Phoenix) and `rsi` for antimicrobial drug interpretations (i.e. S, I and R). Both are actually ordered factors under the hood (an MIC of `2` being higher than `<=1` but lower than `>=32`, and for class `rsi` factors are ordered as `S < I < R`).
Both classes have extensions for existing generic functions like `print`, `summary` and `plot`.
These functions also try to coerce valid values.
#### RSI
The `septic_patients` data set comes with antimicrobial results of more than 40 different drugs. For example, columns `amox` and `cipr` contain results of amoxicillin and ciprofloxacin, respectively.
```r
summary(septic_patients[, c("amox", "cipr")])
# amox cipr
# Mode :rsi Mode :rsi
# <NA> :1002 <NA> :596
# Sum S :336 Sum S :1108
# Sum IR:662 Sum IR:296
# -Sum R:659 -Sum R:227
# -Sum I:3 -Sum I:69
```
You can use the `plot` function from base R:
```r
plot(septic_patients$cipr)
```
![example_1_rsi](man/figures/rsi_example1.png)
Or use the `ggplot2` and `dplyr` packages to create more appealing plots:
```r
septic_patients %>%
select(amox, cipr) %>%
ggplot_rsi()
```
![example_2_rsi](man/figures/rsi_example2.png)
### Other (microbial) epidemiological functions
```r
septic_patients %>%
select(amox, cipr) %>%
ggplot_rsi(x = "Interpretation", facet = "Antibiotic")
```
# G-test to replace Chi squared test
g.test(...)
![example_3_rsi](man/figures/rsi_example3.png)
#### MIC
```r
# Transform values to new class
mic_data <- as.mic(c(">=32", "1.0", "8", "<=0.128", "8", "16", "16"))
summary(mic_data)
# Mode:mic
# <NA>:0
# Min.:<=0.128
# Max.:>=32
plot(mic_data)
```
![example_mic](man/figures/mic_example.png)
Other epidemiological functions:
```r
# Determine key antibiotic based on bacteria ID
key_antibiotics(...)
@@ -318,7 +353,7 @@ Learn more about this function with:
?freq
```
### Databases included in package
### Data sets included in package
Datasets to work with antibiotics and bacteria properties.
```r
# Dataset with 2000 random blood culture isolates from anonymised